Technology on Michael’s Domain

Adding "Add to calendar" buttons for multiple targets (Google, Outlook, iCal) to an email invitation

Sat, 11 Jul 2026 00:00:00 +0000

This is more work than it should be in 2026. These were the first instructions that worked for me: https://www.litmus.com/blog/how-to-create-an-add-to-calendar-link-for-your-emails/ . The instructions essentially use hand-written code (and code generated with Amit Agarwal’s Calendar Links tool ( https://www.labnol.org/apps/calendar.html ).

Installing Zotero on Linux/Ubuntu

Mon, 11 May 2026 00:00:00 +0000

The official way to install Zotero on Linux is mildly speaking a nightmare ( https://www.zotero.org/support/installation ). The fact that you need detailed instructions and command line skills to succeed in the installation speaks for itself:

Application is not responding

Fri, 27 Mar 2026 00:00:00 +0000

In Gnome, you get a warning if an application takes too long to complete a task. This can be really annoying if you know that the application is just trying to do its job with the available resources. Gdebi, Zotero and SnapGene are some of the apps that frequently cause this timeout warning on my (rather slow) laptop. To let Gnome know to stop sending this disturbing notification (or at least make them much less frequent), you can increase the timeout like this:

The find command on an old Asustor

Sat, 21 Mar 2026 00:00:00 +0000

Instead of clicking randomly through endless hierarchies of folders on the web GUI of Asustor, you can just ssh into the device and search on the command line using find. However, there are important differences between the find command on contemporary Linux systems and the find command of ADM (the OS of Asustor NAS servers). My EOL Asustor (AS-304T) uses 3.5.9.RWM1, which uses the BusyBox find v1.19.3, while my Ubuntu Linux uses GNU find 4.9.0. BusyBox find trades features for a small binary footprint and is locked to GPL-2. On the GPL-3 side on Linux, significant new features and performance enhancements have been added. Here is the find command that you need if you want to search all disks on your Asustor:

How to install the color-blind-safe Nature Color Palette in Inkscape

Wed, 28 Jan 2026 00:00:00 +0000

This one is short and easy on Linux. For instructions how to install this color palette on Windows or macOS, please visit https://github.com/atsuyaw/NatureColorPalette .

The Asustor AS-304T NAS cannot mount contemporary ext4 filesystems

Thu, 22 Jan 2026 00:00:00 +0000

The Asustore AS-303T is meanwhile quite old (from 2013), but I still wanted to keep it around to store backups from the last 15 years or so. I originally had placed four 2TB-drives into the device, but now I happened to have four old 3TB-drives lying around and I wanted to use them to maximize the storage capacity. So I temporarily copied the data from the NAS’s RAID to a few external drives before upgrading the NAS with the 3TB-drives. I did some of the copying via a direct point-to-point cable connection with my laptop , which was a bad idea, because when I later tried to copy back the data using the local USB3-port on the NAS, the NAS’ operating system did not recognize the ext4 file system, that my Ubuntu 24.04 had been using. It turns out that the Asustor NAS uses BusyBox v1.19.3, and even though it can read the ext4 filesystem, it does not know the modern ext4 features and thus failed to mount the drives (ADM version 3.5.9.RWM1, which received its latest update on August 29th, 2022). In order for the Asustor OS to recogize these drives, I needed to “downgrade” the ext4 filesystem. Below are the necessary commands to disable the newer ext4 features:

Routing network traffic through two different NICs

Sat, 03 Jan 2026 00:00:00 +0000

I am just copying a lot of files from our NAS-Backup do my laptop. Since the WiFi was too slow (1 TB takes a few hours in the real world), I connected the NAS directly to my laptop with an ethernet cable. Both machines needed to setup their IP address manually within the same network (which can be whatever; I used 192.168.8.150 for my laptop and 192.168.8.199 for the NAS, and Netmask for both 255.255.0.0). Since this “internal” network does not provide internet access, my Ubuntu 24.04 laptop fell automatically back to WiFi. To force the laptop to use the wired network, I needed to deactivate WiFi. But now I cannot get online without WiFi. So I needed to tell the computer to use the wired network only for the NAS which has the IP 192.168.8.199. The command I needed is:

My Samsung Work Phone Came Preinstalled With Spyware

Thu, 25 Dec 2025 00:00:00 +0000

Working at the University of Helsinki, you might get the impression that the IT department is serious about protecting your digital safety. For example, the IT department forces all UH employees to take a yearly “exam” to prove that we still remember the basics of computer security and privacy. They also continue – against all experts’ advice – to force users to update their passwords annually. Studies have shown that both above practices are lowering and not increasing the security posture [1,2]. Privacy is more of a theater than reality in today’s digital world [3]. Should I have been surprised that the Android phone model officially recommended by my own IT department came preinstalled with spyware?

Python rules our plants

Wed, 24 Dec 2025 00:00:00 +0000

In 2025, we updated our 12-year-old router (the Asus RT-AC66U, WiFi 5/IEEE 802.11ac) and replaced it with a WiFI 6 Flint 2 (GL-MT6000) . While the default user interface of the Flint 2 is pretty basic, its advanced setup is a powerhouse. When you click “Advanced Setup”, you can access the underlying OpenWRT user interface. OpenWRT is a Linux distribution for routers. And unsurprisingly, it is very powerful. A year ago, we started to use a LED array to help our plants survive the winter. To automatically operate the lights, we use a Shelly smart plug via a Python script that calculates the light levels and electricity prices (using the sähkönhintatänään API to get the price data) and switches the plant lights only on when both light levels and electricity prices are low. Today, we moved this Python script from my desktop computer to the Flint 2 router. There are thousands of installable packages available for OpenWRT (directly from the router UI: Applications > Plug-ins). To make my Python script work on the router, we first needed to install the openssh-server to get shell access (btw. the p/l combo is root/“same password as for the web UI”, the router correctly opens the access only to the local network). We also installed python3 and python3-pip and then pip-installed the two non-standard packages ShellyPy (to address the smart plugs) and astral (to calculate the dark/bright periods for any given day at Helsinki latitude, which is around 60°North). We just needed to add an entry to the crontab to run the script once every hour. Since you are logged in as root, you just need to execute crontab -e and add this line to the crontab 0 * * * * python3 /root/plantlight.py and restart the cron daemon (which you can do via the OpenWRT UI under “System > Startup”).

Instructions how to convert an Asustor AS7004T into an Ubuntu Server

Sat, 22 Nov 2025 00:00:00 +0000

This weekend, I upgraded our old Asustor AS7004T NAS to run an Ubuntu 24.04 server. The ADM OS had not been received any updates anymore for more than a year and it had been switched off and sitting on shelf since. This is a shame because there was absolutely nothing wrong with it. I had early on upgraded the original 2 GB memory of the device with an 8 GB module to a total of 10 GB. But you can run an Ubuntu server on 2 GB if you wanted to… What do you need for the conversion? Obviously, you need to plug in a USB-keyboard and a mouse. Apple USB keyboards do not work. The cheaper the keyboard the better. Sometimes there were problems with the mouse and then it helped to plug it into another USB port. And of course you need to connect the NAS to a monitor via an HDMI cable. I recommend to install Ubuntu Server 24.04.3. Ubuntu Desktop 24.03 also works (I tested it), but I don’t need it and the server has a much smaller footprint. Unlike with older Asustor NAS devices and distributions, fan control worked without problems. However, LED control and display info do not work: The display always shows “Starting system. Please wait…”.

Exporting from Avidemux to MP4

Sat, 20 Sep 2025 00:00:00 +0000

For some reason, Helsinki University’s Unitube crashes when trying to upload an MKV file. The same used to work last year… Only proprietary formats seem to be ok (such as MP4). This creates lots of additional work for me, since I use open source tools to edit my lecture recordings (mostly to cut out unnecessary parts).However, to create an MP4 file, I need to transcode, which is a time-consuming process that requires changing many of the default settings. Below the process using the Open source software Avidemux:

t_coffee still fails on a standard Ubuntu 24.04 LTS install

Thu, 18 Sep 2025 00:00:00 +0000

The bug in t_coffee, reported on https://github.com/cbcrg/tcoffee/issues/27#issuecomment-1355339411, is still an issue after many years. I hardly dare to recommend t_coffee to my students, even though I would like to, because it is otherwise an excellent and very powerful program. Most of them fail to install it on our university’s default Ubuntu distribution (“Cubbli”), which is atm Ubuntu 24.04. I tried it out myself just recently (Ubuntu 24.04 LTS with both the version provided by the default Ubuntu repository via the package manager and the stable and beta versions from https://tcoffee.org/Projects/tcoffee/index.html (stable COFFEE_installer_Version_13.46.0.919e8c6b_linux_x64.tar.gz and beta T-COFFEE_installer_Version_13.46.1.b8b01e06_linux_x64.tar.gz). All of them still complain with –ERROR: MAX_N_PID exceeded. It gets stuck somewhere and takes approximately one minute before it throws the error, even with a simple task that normally takes a few seconds. With a more complex alignment, it can take minutes or hours before the error is thrown. The workaround is to set the environment variable before every run, i.e., you replace t_coffee with a shell script that calls the renamed t_coffee after setting the environment parameter MAX_N_PID_4_TCOFFEE to something big (like /proc/sys/kernel/pid_max). The issue is explained in the Github link above. See also https://github.com/cbcrg/tcoffee/issues/47 . Another workaround is to recompile with a different MAX_N_PID, which is rather straightforward; see also here https://github.com/cbcrg/tcoffee :

Wireguard

Sat, 30 Aug 2025 00:00:00 +0000

My home router (a GL-iNet GL-MT6000) offers built-in WireGuard support. To add a client, you push a button and can either scan a QR code or download the configuration file. The QR code works out-of-the-box with my Wireguard for Android App (the official client for Android), and the configuration file works equally well for Ubuntu Linux 24.04 with Network Manager. To set up the VPN, you simply import the configuration file. The last command is to prevent the VPN from autostarting after a reboot, since when I work from home there is little use in routing my traffic to my own VPN server at home if I am anyway at home.

Backing up DVDs

Sat, 09 Aug 2025 00:00:00 +0000

DVD ripping is one thing (and Handbrake is the tool I have been mostly using for that). But sometimes you want to just copy the whole DVD to your hard drive. On Ubuntu Linux, my preferred software for this is dvdbackup .

Same place, 38 years later (part A)

Sat, 19 Jul 2025 00:00:00 +0000

I visited Tallinn for the first time in 1987. It was also my first and last visit to the Soviet Republic of Estonia. I took a few photographs at the time (I had one roll of 35-mm film with 36 exposures). Last week, I went back after more than 25 years of not having been there to take re-shots of some of the places. I received help from an expert, who pinpointed the exact locations, down to a few meters, where I had taken the shots in 1987. However, it was still difficult to get the perspective right, and I clearly failed in three of the four pictures. I thought I had taken my 28-100 mm Zoom objective in 1987, but after looking at the pictures, I am not so sure anymore. I also had a 70-210 mm Zoom, and I might have used that one. It’s somehow clear from the 1987 images that I must have been far away from the people I photographed, since nobody took notice. I should have used the same camera (which I still have in a drawer that I hadn’t opened for a decade or longer), but I didn’t manage to get photographic (“chemical”) film on short notice. Shot #3 was especially challenging since none of the buildings visible in the 1987 image still exist. Happy to get feedback for my next visit!

Same place, 38 years later (part B)

Sat, 19 Jul 2025 00:00:00 +0000

#Not necessary! # #

Same place, 38 years later (part C)

Sat, 19 Jul 2025 00:00:00 +0000

This was the most tricky image and I am not sure at all whether the new image captures the correct place. Again, I think the 1987 shot must have been taken with a focal length of more than 100 mm. There was no building that could have served as a clearly identifiable fixpoint.BTW: All the 2025 images were taken with the mobile phone camera of a Samsung Galaxy A35. Taking the original camera (Ricoh XR-P) with me would have approximately doubled the weight of my luggage.

Same place, 38 years later (part D)

Sat, 19 Jul 2025 00:00:00 +0000

Next time I’ll take my old SLR camera and the 70-210 zoom objective. I guess I could have used the digital zoom of my mobile phone…

Booting my Lenovo ThinkPad X390 from USB

Sat, 12 Jul 2025 00:00:00 +0000

It’s sometimes harder than you think to boot a computer from a USB stick. It takes two non-trivial skills to pull it off:

An impossible overlap-extension PCR

Sat, 21 Jun 2025 00:00:00 +0000

A PhD student of mine asked me about plasmid maps for several DNA constructs that I had created some 20 years ago. Since SnapGene did not exist at the time, I had used the now obsolete GeneConstructionKit2. I performed many clonings at the time, but I did not continue generating maps for all of them. The GCK2 format does not allow for easy annotation. You needed a separate program for comprehensively annotating the plasmids, and this data was saved in a separate file, the so-called “illustration” file: what could possibly go wrong? Yesterday, I ended up digging out my old lab notebooks and retracing about 10 old clonings in SnapGene. However, I was unable to simulate one of the assemblies because SnapGene was too conservative in disallowing “bad” PCR primers to function. I had performed overlap-extension PCR to introduce a mutation into the mouse VEGF-D cDNA. The homologous mutation had been introduced into human VEGF-D before, and I therefore had the primers for the human sequences. Mouse and human VEGF-D are very similar. The primers designed to amplify the human PCR were not perfect when using mouse cDNA as a template, but none of the differences would result in amino acid changes. So I attempted the PCR with a primer that had a mismatch in the third nucleotide from the 3’-end. The PCR was successful, but even when I lowered the hybridisation parameters to the least stringent settings, SnapGene would not anneal this primer to my template. To simulate cloning in SnapGene and generate a map, I needed to introduce a mutation into my primer and then reverse the mutation after the overlap extension PCR. I guess I need to file a bug report (or would this be a feature request?). It seems appropriate that the program should be able to allow annealing of primers that do anneal in reality…

Python Virtual Environments

Mon, 16 Jun 2025 00:00:00 +0000

There are many different ways to run Python in a virtual environment. I have used mostly conda (together with anaconda), but I frequently end up doing work on machines that do not have it installed. Hence, I have been recently starting to use the “inbuilt” virtual environment. If you are working on a Python project in a directory, these are the steps to start using it:

ProxyJump

Thu, 01 May 2025 00:00:00 +0000

Since OpenSSH 7.3, it has been much easier to connect from the outside to Linux computers inside the UH network. With older ssh versions, you needed to use a complicated “ProxyCommand”, but now it is straightforward:

Restriction Enzyme Calculator

Tue, 29 Apr 2025 00:00:00 +0000

Use our interactive tool to calculate the volume of restriction enzyme required for your digest.

Restriction Digest Calculator

Sometimes, you need to know how much restriction enzyme is required to cut a specific amount of a certain plasmid within a given time. Here is the calculation tool you have been looking for! All data that was used to write the code for this algorithm was obtained from New England Biolabs (NEB). The survival of the enzyme in the reaction was extrapolated from the experiments reported by NEB. Just plug in the numbers into the form and hit the submit button!

Barrier (a software KVM switch)

Tue, 21 Jan 2025 00:00:00 +0000

Barrier is an incredible software that lets you use the same keyboard and mouse with different computers without the need for hardware. I have two computers on my desk, and I used to have a hardware KVM (keyboard, video, and mouse) switch, which became obsolete when my computers started to output their video via HDMI. Hence, I have two keyboards on my desk, which is not very ergonomic. I knew about software solutions to this dilemma, but I never had the time to implement them, and I also did not want to pay a subscription fee for this luxury. I now started to use Barrier: https://github.com/debauchee/barrier . It’s been working excellently so far (except for the installation and documentation), but I still need to get it to work before logging in to dump my second keyboard.here are the steps that were not well documented:When installed on Ubuntu, Barrier does not automatically create certificates. So you need to do this yourself:Execute in both client and server: /home/username/.local/share/barrier/SSL:openssl req -x509 -nodes -days 365 -subj /CN=Barrier -newkey rsa:4096 -keyout Barrier.pem -out Barrier.pemYou also need to open port 24800 if you are using a firewall. After you get Barrier working, check the correct command (ps aux) from the command line. It is probably something like this:/usr/bin/barrierc -f --no-tray --debug INFO --name computer-name [87.167.231.88]:24800startUse the Startup applications in Ubuntu and paste the above command in. This means you cannot use Barrier to log in because it is loaded only after logging in. But that’s as much as I managed to figure out so far. There is probably a way to make this work pre-login via systemd, but I did not have the time to figure out how.

Reset the admin (user #1) password in Drupal 9

Wed, 01 Jan 2025 00:00:00 +0000

I have been playing around with Drupal 9 and forgot the admin password. If this happens to you, go to the base folder of the drupal installation.

Ouriginal fails more often than not to detect plagiarism

Thu, 23 May 2024 00:00:00 +0000

Ouriginal , the plagiarism detection service formerly known as Urkund, has been in use at the University of Helsinki for a very long time. Because of Ouriginal’s inability to process some of our students’ Master’s thesis, I spent a little bit of time investigating Ouriginal and its problems. Here’s what I found out. From Swedisch to European to US-AmericanIt is unclear to me which software we are really using since Ouriginal is a merger of the Swedish Urkund and the German PlagScan, and in 2021 Ouriginal was acquired by the American Turnitin . I don’t need any of such software, but our university mandates that theses must be scanned by the software. Since I read and evaluate an increasing number of theses every year, I also increasingly use Ouriginal. Ouriginal supports many document formats, but support is buggy Looking at the history of submissions, I realized that until about mid-May 2024, all submitted PDFs had been dutifully analyzed. But last week, something changed since about half of the submitted documents were not processed. The usual tricks (submitting in another format such as .docx, .odt, .ps, .rtf) did work for some, but not all of the theses. One thesis was especially stubborn, and neither our “experts” nor the Original helpdesk staff had any clue why their software could not process it (which makes me again wonder what software their backend is actually using). Ouriginal is investigating already for a month without getting back to me with answers… Our university receives funding from the Ministry of Education based on graduating students, and we lose thousands of Euros for each student who fails to graduate on time. Fee-liable students also have a strong incentive to graduate on time in order to avoid additional costs. Therefore, every delay in the graduation schedule is unacceptable. Ouriginal’s performance disappoints with a shocking detection rate Since there are dozens of ways how to turn a Word document into a PDF, I tried to isolate the problem by submitting test documents to the Ouriginal service. I used manuscripts that we had published over the last few years. I was shocked when I realized that Ouriginal failed to detect plagiarism in more than half of all cases. Paywalls are not to blame since almost all our publications are freely available. Neither the novelty of the publication nor the quality of the journal made a perceivable difference. However, it seems evident that Ouriginal has more problems with non-English documents. It is very difficult to explain why so many freely available scientific texts from reputable journals ( Scientific Reports , Angiogenesis , Annals of Anatomy ) are not indexed by Ouriginal. Failure to detect plagiarism from Helsinki University’s own thesis repository Original does not even index our own university’s freely available PhD theses ( https://ethesis.helsinki.fi ). None of the PhD thesis written in my own lab was recognized. I also checked my own PhD thesis , and it was the only one that was recognized (Ouriginal found it on docslib.org , not our own university’s official thesis repository). Does it make any sense to pay for such an imperfect service? I don’t think so. The omission of freely available texts from important journals seems inexcusable since a simple Google search does a better job. I did Google searches for sentences from the unrecognized texts, and in most cases, Google identified the original source without problems. A Python script to split texts into sentences for individual Google searches and to aggregate the results can be written by any programmer in an afternoon. Why would you maintain your own database if Google does a better job than you can? Plagiarism to the following published manuscripts/theses/proceedings was NOT detected:*

Taking an webcam image from the command line

Fri, 05 Apr 2024 00:00:00 +0000

There are probably not many use cases, but remote surveillance is an example, both in a malicious and legitimate context. Malware can take pictures of the unwitting user, and “Has anybody searched through my office after I forgot to close the door last Friday?”, respectively.

Overstretched IT support

Fri, 23 Feb 2024 00:00:00 +0000

The problem: Crash during boot

More than a year ago, a few weeks after receiving my new work computer, it failed to reboot after a system update and got stuck early in the boot process. I soon realised I could still start the computer using “safe mode”. Strangely, nothing seems to be wrong because when I manually exit safe mode at the end of the boot process, the computer works fine. Our IT department has tried to fix the problem many times without success. I even had to work without a computer for about 3 weeks while it was “under repair”. You probably know how much work you can get done without a computer: close to zero.My computer runs Cubbli 20.04.06LTS, an unofficial Ubuntu spin maintained by the University of Helsinki for internal use. Although you can do bioinformatics on a Windows or macOS computer, Linux is hands-down the first choice. Many bioinformatics developers don’t even bother to release their software for Windows. MacOS works mostly fine (since it is also UNIX-compliant OS), but I would have to pay twice the price for the same calculating power.The computer is a Lenovo P350 with an NVIDIA T1000 graphics card, which I use to address two screens. I mainly need the graphics card for 3D modelling, phylogenetics analysis and similar tasks. This graphics card may have caused the trouble. I initially did not want to buy this model, but since there was a shortage of graphic cards at the time, IT convinced me to swap out my original choice against the T1000.

Unbricking the Netgate pfsense SG-3100

Fri, 10 Nov 2023 00:00:00 +0000

The current process of restoring functionality on the Netgate pfsense SG-3100 router after an unsuccessful firmware upgrade is too difficult (although the device is magnificent otherwise). Today, I experienced the third failed upgrade within six years. Recovery worked every time without problems, but it should be MUCH easier if you want me to recommend this router to my less tech-savvy friends. To pull the recovery off, you need an 8-GB USB stick and USB cable with a high-profile micro-USB connector at one end and a regular USB-A connector at the other. These are the steps that you need to do to unbrick the device:

Withings Body Scan smart scales

Thu, 29 Jun 2023 00:00:00 +0000

In 2009, we bought our first Withings smart scales. Although I tried them out at the time, I soon stopped using them because of their limited functionality. Now, more than ten years later, I believe that smart scales technology has finally advanced to the point where it is genuinely useful. What’s more, I now fit the target demographic for this device: I’m a middle-aged, overweight man with a family history of heart disease who does some sport, but probably not enough. To sum up in advance: I intend to use the Body Scan scales every single day from now on. Aside from some more useful and some less useful features, it reminds me that, once you reach a certain age, you need to actively maintain your cardiovascular health. Withings has recently launched three smart scales at different price points: the Body Scan, Body Comp and Body Smart. We received the top-of-the-range Body Scan model for review. It arrived four days before we set off on our summer holiday, which is why I haven’t tested all its features. Some features require a certain minimum number of repeated measurements, so this article may be updated once I’ve used the scales for a longer period. What can the scales do? Apparently, they can measure your weight and the composition of different parts of your body (body fat and muscle percentage). They also claim to be able to distinguish between visceral and subcutaneous fat. Not all fat is equally bad: visceral fat is much more dangerous than subcutaneous fat, which can even be beneficial. If the scales could reliably distinguish between visceral and subcutaneous fat in the body, it would be an astonishing technical breakthrough (more on this later). ECG FEATURE The Body Scan scales can perform an ECG (electrocardiogram), meaning they can measure the heart’s electrical activity. An ECG can be used to detect a wide range of heart problems, but the number of electrodes (measurement points) on the body is crucial for this measurement. The medical standard is 12 electrodes. For practical reasons, devices intended for consumers are less sophisticated, and therefore have only limited ability to detect different types of heart problems. The Body Scan device has 6 electrodes, which is the best currently available in a device intended for consumers. However, such a 6-lead ECG is significantly inferior to the standard medical ECG and may even fail to detect an acute, recent heart attack. In fact, the only medical conditions that this ECG can reliably detect are atrial fibrillation and atrial flutter. Atrial fibrillation is a heart rhythm disorder that can be detected by feeling the pulse (e.g. the heart beats twice instead of once). Atrial flutter is a somewhat similar condition, characterised by a rapid heart rate (> 250/min), which may occur episodically (lasting from hours to days) but can also be continuous. Both conditions require medical treatment, and it therefore seems sensible that a consumer device should be able to detect them. However, clinical studies show that the results of mass screening for atrial fibrillation are not clearly beneficial. Experts are, in fact, divided on whether mass screening is a good idea: the 2020 guidelines issued by the European Society of Cardiology recommend mass screening, whilst the US Preventive Services Task Force and the UK National Screening Committee do not currently recommend them. Although atrial fibrillation is fairly common, it is usually secondary to other heart conditions, and the target group for the Withings Body Scan (health-conscious, middle-aged, middle-class) may not be the group that would benefit most from this feature. In one study investigating atrial fibrillation (the so-called LOOP STUDY), did not use a device intended for consumers but rather sensors designed for professional use, which is a more reliable method for detecting atrial fibrillation. Furthermore, the study focused on individuals with risk factors for a heart attack. Unsurprisingly, the detection (and treatment) of atrial fibrillation tripled, but despite this setup, the study found no benefit in terms of a reduction in heart attacks or arterial embolisms.Some experts believe that there are different types of atrial fibrillation and that we simply do not yet know how to distinguish the dangerous types from the benign ones.In summary, it can be said (also based on some more recent data) that the benefit of the Body Scan ECG appears to be small. The benefit is likely to be significant only in high-risk population groups who are unlikely to use a €400 smart scale (e.g. the elderly).It is not yet known (as such devices have not become widely adopted amongst consumers) what the burden on the healthcare system is due to false-positive results. It is also worth noting that there is currently no digital infrastructure in place to enable the data generated by the scales to be transferred to a doctor for review. In fact, there is not even a standardised file format. Whilst there is an open data transfer standard (DICOM) for X-rays and similar imaging data, there is no equivalent for ECG data. All of the above explains why the Body Scan is not yet available in the US. The FDA has not approved it as a medical device. The regulatory frameworks and requirements differ between the EU and the US, but according to Withings, the Body Scan will become available in the US from the third quarter of 2023, following FDA approval. In Europe, the device ‘only’ needs to obtain the CE mark for medical devices. To obtain the CE mark, the device must meet certain standards, which depend on its classification. Body Scan is classified as a Class IIA device (which, interestingly, places it alongside dental fillings, surgical clamps and tracheostomy tubes). Conformity assessment is not carried out by the European Medicines Agency (EMA) but by independent accredited organisations (known as ‘Notified Bodies’). They analyse and certify the device’s safety and performance. Approval by the EMA and the FDA is essential, as it is naturally important to have independent confirmation that the device actually detects the arrhythmias it claims to detect, and so on. Here is a YouTube video from Medlife Crisis discussing the benefits of atrial fibrillation screening. The video focuses on the Apple Watch, but in principle the same applies to any consumer device: https://www.youtube.com/watch?v=rW3DGnHO2iY&t=719s DETERMINING BODY COMPOSITIONBody composition data is extremely useful for assessing your health and fitness levels. An easier measure to use is the body mass index (BMI), which requires only your height and weight to calculate: (weight in kilograms)/(height in metres²). Although BMI correlates with health, there are many exceptions, particularly concerning very fit individuals with a high amount of muscle mass (who are often technically overweight), and lean individuals with little muscle mass (who are not technically overweight but may still have too much body fat). A much better measure of fitness is body fat percentage, which this scale determines using bioelectrical impedance analysis (BIA). The scale measures the percentages of fat and muscle mass in the torso and other body parts. Put simply, this means that the scales send electrical impulses through the body. As fat conducts electricity less efficiently than muscle, the scales can deduce the amount of fat between two measurement points. Unfortunately, BIA is not a particularly accurate method for determining segmental body composition. To truly know where the fat is located, and in particular to distinguish between visceral and subcutaneous fat, the gold standard is magnetic resonance imaging (MRI). At present, however, this method is rarely used for this purpose outside of medical research, and it is also very expensive. A less accurate method for measuring body fat percentage is dual-energy X-ray absorptiometry (DEXA/DXA), which is primarily used to determine bone mineral density, but which can also be used to measure body fat percentage. However, DEXA has difficulty distinguishing between subcutaneous fat and visceral fat (if you wish to have this type of analysis carried out, you should ask your service provider what data their device provides). To obtain segmental body composition data, you’ll need a smart scale from the Body Scan range. The Body Comp and Body Smart models do not offer this feature. The big question is: how do the scales carry out this measurement, and how reliable is it? There isn’t much information available, except that the scales use multiple frequencies to improve measurement accuracy. Thanks to the BMI calculated from the arms and legs, the segmental body composition is probably reasonably accurate. However, it is completely unclear how the scales determine the percentage of visceral fat. There are no explanations, patents or – most importantly – scientific publications that would validate the technology against the gold standard of MRI. The percentage of visceral fat is also displayed separately from body composition, which may suggest that this measurement is taken using a different method. Paradoxically, the legendary six-pack is not a good indicator of fitness: if there is fat covering the six-pack muscles, you cannot see the six-pack, even if it is there. However, the fat covering the muscles is not the most dangerous type of fat. The dangerous fat is found beneath the six-pack muscles, in the body cavity where your organs are located. You may have a visible six-pack despite the fact that dangerous fat has accumulated on and around your vital organs (liver, kidneys, intestines, etc.). The body fat percentage determined by the scales is probably reasonably accurate. However, without external validation, I suspect that the visceral fat index shown to me by the scales is nowhere near a meaningful value in reality. What does this ‘visceral fat index’ actually mean? According to the explanation, it is a value between 1 and 20. But what is it? I would understand if body fat percentage were broken down into visceral and non-visceral fat (but that figure would be between 0–100 per cent). As long as it remains shrouded in obscurity, this value is likely to be rather useless (and I’ve seen it fluctuate quite rapidly from one day to the next, which suggests it isn’t very reliable). ASSESSING THE RISK OF CARDIOVASCULAR DISEASEWhen it comes to cardiovascular disease, the three major risk factors are:

Dynamic DNS with DomainDiscount24 and pfsense

Sat, 27 May 2023 00:00:00 +0000

Many companies offer free dynamic DNS. But since I use DomainDiscount24, I also use their dynamic DNS service. To update the IP address of vpn.jeltsch.org, I need to send an https request to a specific URL, including a password and the hostname for which I want the update:https://dynamicdns.key-systems.net/update.php?hostname=vpn.jeltsch.org&password=12345678&ip=autoTo automate this, I use the crontab of my pfsense router. Editing the crontab is not enabled by default, but you can download and install the cron package. After that, you get a GUI under “Services > Cron”, where you add the timing and the command:/usr/local/bin/curl "https://dynamicdns.key-systems.net/update.php?hostname=vpn.jeltsch.org&password=12345678&ip=auto"

Review: Wenger Synergy rucksack after 5 years of daily use

Sat, 21 Jan 2023 00:00:00 +0000

I am a fan of rucksacks with many pockets. No wonder I like the Wenger Synergy , which has been on the market for over 10 years with only minor modifications. However, I had my fair share of quality issues with this model. Unlike my >40-year-old Swiss knife, this rucksack kept breaking within its warranty period or soon after. It was never a problem exchanging it when it broke within the warranty period, but I got fed up with the exchange hassle after doing it twice. The rucksack’s failing part was always the same: the seams of the shoulder straps started to open. I reported the issue directly to the producer, hoping they would change something to improve the shoulder straps. However, when also the third rucksack developed the same problem, I decided not to exchange it but to fix it. My fix is optically not very pleasing, but it has lasted long enough that I can report the second point of failure: the bottom pane. It ripped where the bottom piece contacts the backplane of the rucksack. I also repaired that one because I was interested in which part would fail next. The upside: these repairs were quick and easy, and they have already lasted for 4 months without any sign of failure due to the high-quality material. The zippers limit the ultimate lifetime of perhaps all rucksacksNow I know: the zippers are starting to have problems. I am surprised that the zippers are still sort of working. The zippers have been the Achilles heel with almost all of my other rucksacks. And unlike a shoulder strap, it takes quite an effort to fix (= exchange) a badly failing zipper. This rucksack is now five years old. I have been using it literally every single day. I cycle or run with it to work, and I do my shopping with it. I travel with it and take it to the summer cottage. Am I expecting too much of a ~100€ rucksack? Is five years’ lifetime the maximum I can get out of a rucksack these days? Sustainability is mostly just lip service, whatever the industry. I am determined to keep this rucksack for another 5 years, but exchanging the zippers will cost me at least 2 to 3 hours of work. As a quick fix, I used pliers to tighten the top and bottom wings of the metal slider (like in this youtube video ). That has been working, but according to my experience, this tightening needs to be repeated in increasingly shorter intervals, and finally, the metal will break. To avoid replacing the whole zipper, you can add buttons to create a new closure , which is perhaps less work if you are not very skillful at sewing.

Wake on LAN from pfsense commandline

Sun, 17 Apr 2022 00:00:00 +0000

Pfsense is an extremely powerful firewall/router OS. I use the SG-1100 device and you can get lots of customized functionality due to the many packages that you can additionally install on top of the base configuration. I have just learned that I can use it to remotely switch on other computers that are on the same local network. Requirements:

Risk versus hazard

Sun, 10 Apr 2022 00:00:00 +0000

Last week I failed to explain the difference between risk and hazard. Perhaps because the distinction does not exist that clearly in my mother tongue (German). Both hazard and risk are somewhat exchangeably translated to “Gefahr” or “Risiko”.Anyway, when I went to the kitchen this morning to make my morning coffee, I realized there was a hazard: somebody had left some flammable items on the hot plate. This is a hazard. It has the potential to cause harm. However, it might never cause any harm.But is leaving flammables on the hot plate also a risk? Sure! The risk is the likelihood of harm happening. If the hot plate is never used because nobody ever cooks, the risk might be low. However, if small kids are around who get a kick out of switching on and off electrical devices, the risk might be high. Risk can be quantified. Playing Russian roulette comes with a risk, which can be quantified: 1/6 for every pull of the trigger. A hazard has always a probability of 0 or 1 (it either exists or doesn’t). On top of the probability, risk also implicitly includes the severity of the mishap. Therefore Russian roulette is very risky, but jumping from the 3-m diving board is not so much, even though there is a risk that you injure yourself.

How to reset the admin password in Drupal 9

Sat, 09 Apr 2022 00:00:00 +0000

Go to the base folder of the drupal installation
Generate the hash for your password: php core/scripts/password-hash.sh ’newpasswd'
Execute in mysql: UPDATE users_field_data SET pass=‘hash_result_from_previous_command_goes_here’ WHERE uid = 1;
Clear the cache: DELETE FROM cache_entity WHERE cid = ‘values:user:1’;

University helpdesk recommends Zotero, but does not provide meaningful support

Sun, 20 Mar 2022 00:00:00 +0000

With the end of last year (31.12.2021), the University of Helsinki discontinued licensing its default bibliographic software tool RefWorks . Strangely, you cannot license RefWorks as an individual. That means when your academic affiliation ends, there is no way for you to continue using the software. Perhaps, the current owner of RefWorks (Clarivate) will kill it completely because RefWorks is a direct competitor of Endnote , which is the reference management solution that Clarivate is focussing on, given Endnote’s integration with Publons and the Web of Science (WoS), which is best known for its Impact Factor . Not coincidentally, Clavivate is owned by Thomson Reuters, which is the company that litigated against Zotero for offering its users the possibility to convert proprietary EndNote citation style sheets into the interoperable and standard CSL format . The recommended replacement for RefWorks is Zotero . I have no problem with this since I like Zotero and have been using it as my default bibliography management tool for now more than 10 years. On top of the fact that it is free, it combines two important features, which make it unique and superior to commercial solutions:

Finding the annual return on investment (ROI) for assets at OP bank

Sun, 09 Jan 2022 00:00:00 +0000

I am a customer of the Finnish OP bank . Like many other people, I had more leftover money than normally during the coronavirus pandemic. And like many others, I also invested some of that money into the stock market. I do not follow the stock market, but at the end of the year, I want to know how my investments performed: I want to know the annual return on investment (ROI) or the IRR (internal rate of return) for my whole portfolio and also for my individual stocks.

Missed a TV broadcast?

Fri, 26 Nov 2021 00:00:00 +0000

If you have missed a TV show, that is not available online, you might try this service: https://www.onlinetvrecorder.com/v2/signup/1905125 .

How to manually encrypt a second hard drive in Ubuntu 20.04

Fri, 19 Nov 2021 00:00:00 +0000

You have added a second hard drive to your encrypted Linux system. The Debian installer makes it easy to encrypt during system installation, but how do you encrypt this new drive?

Reset Wirelesstag's outdoor probe's flash memory

Sat, 09 Oct 2021 00:00:00 +0000

I really like the products from https://wirelesstag.net/ . However, the product documentation is sometimes less than complete and their staff less than professional. E.g. there is no information how to reset the outdoor probe when you need to associate it with another tag manager (and you have no access to the previous tag manager). They have information (and images) on how to do that for their wireless sensor tags, but not for the outdoor probe. Customers have already asked for this, but it doesn’t seem to be a priority for them to add this bit of information.So here’s the image which pins to short-circuit. How do I know? I found out by try and error.

Why I am running Windows 11 now

Sun, 03 Oct 2021 00:00:00 +0000

My work computer broke in early summer: the graphics card failed. I used it without a graphics card since, but a few weeks ago the hard drive started to make problems. I ordered a new machine, but since the new Lenovo models will be coming soon, IT asked whether I want to wait for a few weeks in order to get the newer model (the P350 instead of the P340). So I have to bridge this time with something. I tried the old desktop that controlled the Äkta Avant, but it was pretty unusable (boot time ~ 3 minutes), but the solution appeared to be our old HP Elitebook G3. Most people who know me know that I am a big fan of open source software. Many of the best open source programs can run on Windows OS: Firefox, VLC, Inkscape, Blender, Scribus, Zotero. However, some open source software has never been ported to Windows. And often, the Linux version of the software runs better than the Windows version. One example is Gnumeric, Gnome’s spreadsheet calculator, which has an excellent chart export function to SVG. I have often recommended to my Windows-using students to install the Linux Subsystem for Windows (WSL) in order to run Linux programs, but only now have I done so myself. In order to do this, I needed to upgrade Windows 10 to Windows 11. I followed these instructions: https://docs.microsoft.com/en-us/windows/wsl/tutorials/gui-appsStrangely when I tried to upgrade, Windows complained that my hardware is not “compatible” with Windows 11, but nevertheless started and succeeded with the upgrade.Here you can see a Win 11 running on a decomissioned HP Elitebook G3, which my university had refused to upgrade from Windows 7 to Windows 10 in 2019 (even though it was technically one day within the limits). I did a fresh install of Win 10 with the official installation media which I downloaded from Microsoft. For some strange reason, it never asked me for a license (even though the I had exchanged the SATA-SSD for an NVMe SSD). In fact the computer is actually very fast and usable, and I will definitely keep it around for a few years as my only Windows machine, because there are still rare occasions when I need a physcial Windows installation.On the downsider, the Win 10 install was a PITA because my university IT locks the BIOS, and once the machine is decomissioned, they don’t feel the responsibility to give these machines a second life. IMHO, this is totally against the sustainability goals of our university. Fortunately, one can mostly work around a locked BIOS. In the worst case, one needs to exchange it against a spare BIOS from China.

Erichsen Geld & Gold

Sun, 01 Aug 2021 00:00:00 +0000

This post was originally only available in German because I was writing about what I consider to be the best German-language podcasts on the subject of money and finance. Money and finance are country-specific topics. When it comes to things like pensions or health insurance, advice from US podcasts is pretty much useless. Who here has a 401(k) plan (1)? But even within Europe, countries differ so greatly from one another that you should think carefully before adopting well-meaning advice from another country. A simple example is the differences in the use of cash: Here in Scandinavia, EVERYTHING is paid for by card , regardless of the amount. Cash is mainly only around here because of German tourists! As I live in Finland, I should therefore listen to a Finnish podcast about money and finances. Unfortunately, I haven’t found an interesting one yet. You probably need a certain amount of choice so that you can a) find something that suits your own life situation and b) something that is of high quality in terms of both content and production. Life circumstances, age and, not least, social attitudes create for all podcasters a (more or less) limited perspective, from which it is difficult to break free. That’s probably why my clear number one among finance podcasts is Erichsen: Geld und Gold . Why do I think “Erichsen Geld & Gold” is better than all the others? Probably because, apart from our professions, my life situation and Lars Erichsen’s are strikingly similar – from our age and family circumstances right down to details in our CVs and our social outlook. If I’d stayed in Germany, I’d be a Northern Light too (2). The fact that I can draw this comparison also says something about the podcast: although it’s a finance podcast, as a regular listener you quickly get the feeling that you know Lars Erichsen well as a person. It is this quasi-personal connection that has helped podcasts achieve their breakthrough, and it’s something that television – or even the professionally produced podcasts from media conglomerates, of which there are more and more – simply cannot compete with. The Handelsblatt ? Forget it!

Ways how to keep a process running after logging out

Sat, 26 Jun 2021 00:00:00 +0000

There are many ways how to keep a process running after logging out. Each if them has its own advantages and disadvantages: nohup, disown, screen, tmux, ssh2go, etc. Screen is certainly not the most feature-rich and modern solution, but it is available by default on all Linux installations. That’s why I use it. Here’s how it works:

Installing perl modules

Tue, 22 Jun 2021 00:00:00 +0000

I have not done this for perhaps a decade or more. But apparently, things are still the same on Ubuntu 18.04:

Where to move to from RefWorks?

Thu, 10 Jun 2021 00:00:00 +0000

I never understood why our university pays for proprietary reference management software. Perhaps some old people in the administration still live in the 90s of the last millennium when EndNote was de-facto the only decent reference management software for WYSYWIG text processors. But those times are long gone. Finally, our university is at least dumping one of its proprietary reference managers:

Directory hard links in Linux

Thu, 03 Jun 2021 00:00:00 +0000

Directory hard links in Linux are forbidden because they would:

create cycles in the directory hierarchy.
break the assumption that directories form a tree.
complicate deletion and reference counting.
make filesystem traversal and maintenance much harder.

Instead, Linux allows hard links for regular files and symbolic links for both files and directories. To emulate something similar to directory hard links, you can mount any file system path into any other directory (bind mount). However, you need to be careful because you can get the same problems as with directory hard links, namely circular and thus infinite file paths…sudo mount --bind /home/user/Documents/Desktop/ /home/user/Desktop/. Such a link disappears after a reboot. If you want to make it permanent, you can add the mount to /etc/fstab:/home/user/Documents/Desktop/ /home/user/Desktop none bind. Some say this does not work with LVM, but at least, on Ubuntu 20.04 it does. Obviously, this entry should be at the bottom of the fstab!

Randomized controlled potato chip tasting trial

Sun, 16 May 2021 00:00:00 +0000

We did a blinded randomized controlled potato chip tasting trial (RCPCT) yesterday. Unfortunately, everybody wanted to participate and therefore, we could not do it in a double-blinded fashion. We went for the plain type, for which we could find in Prisma three different brands: Estrella, Taffel, and Xtra.We only evaluated taste, and the results were clear and a bit surprising: Xtra and Estrella shared the first place and Taffel took the third/last place in the opinion of all four contestants. Given the fact that both Taffel and Estrella are almost twice as expensive (8.49€ and 8.18€ per kg, respectively) as the Xtra brand (4.3€/kg), it seems to be a no-brainer to buy the Xtra brand. What about nutritional aspects? Both Estrella and Xtra have 1.4% salt, while Taffel gets away with 1.1% salt. And the fat? Xtra uses exclusively sunflower seed oil, while both Taffel and Estrella use a mix of sunflower and rapeseed/canola. Consequently, Estrella and Taffel both have a healthier fatty acid composition that Xtra, and Estrella takes the lead with the least amount of saturated fatty acids.Which one to choose is not really clear: You get good taste for the least money buying Xtra, but it’s not the most healthy choice. On the other hand, it is not really clear whether Taffel or Estrella takes the lead in the health category (if we can speak about such category when evaluating chips at all). Taffel has less salt, but more saturated fatty acids. Estrella has more salt, but less saturated fatty acids. Since the price is roughly equal, let the taste decide.PS: Both English and German do not distinguish between the two different Brassica species, that are used to produce rapeseed/canola oil (Brassica rapa and Brassica napus). However, in the Finnish language, Brassica rapa translates into rypsi, while Brassica napus translates into rapsi. The nutritional values with respect to the fatty acid composition are similar for both plants.

Multiple Python versions on Ubuntu 20.04

Fri, 30 Apr 2021 00:00:00 +0000

Adding a new python version to Ubuntu 20.04 (for my system it is the 3rd version after 2.7 and 3.8): sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.6 3

Eduroam installation on Linux

Tue, 23 Feb 2021 00:00:00 +0000

This morning it took me an hour to get Eduroam working. Eduroam is the international WLAN roaming service for university students and staff. I brought in my (non-university managed) laptop to work and tried to get connected. I finally found the instructions on the IT Helpdesk site on place place 19 (from 21 results shown on the first page when searching for “Eduroam Linux”): https://helpdesk.it.helsinki.fi/en/instructions/logging-and-connections/networks/installation-eduroam-network-on-ubuntuAs usual, the instructions are from many years back and no longer work on a “recent” system such as Ubuntu 20.04 LTS. On top of this, I had some old, dysfunctional Eduroam settings lingering around from a previous failed attempt. For the instructions below, you will need the Eduroam configuration tool, which you can download from https://cat.eduroam.org . To make it work, I had to do the following things:

Editing Zoom recordings of teaching sessions with FFmpeg

Wed, 25 Nov 2020 00:00:00 +0000

Based on student feedback, we have been organizing a new course for the TRANSMED MSc program about drug discovery and development. It is what you call in German a “Schupperkurs”. I never have found a satisfactory translation of this word in English. It means that we just want to raise the students’ interest in this course. If they like it, they can take any of the many in-depth courses that are offered e.g. at the Faculty of Pharmacy , where there will be more teaching in English in the coming years due to the planned International MSc program in Pharmacy.

Grub2

Mon, 19 Oct 2020 00:00:00 +0000

Grub2 has been the default boot loader for Ubuntu for more then 10 years now. Its configuration file is nowadays /boot/grub/grub.cfg, but you MUST NOT edit /boot/grub/grub.cfg in order to modify the Grub boot menu. Instead, you need to add your own entries to the file /etc/grub.d/40_custom. Some general preferences are also set in the the file /etc/default/grub and any file under /etc/default/grub.d/.

Listing all active internet connections on Linux

Wed, 02 Sep 2020 00:00:00 +0000

netstat -natp

However, it is not always easy to figure out what the actual program is that is responsible for the connection. E.g. my Brave browser shows up as

Apache forward proxy

Fri, 31 Jul 2020 00:00:00 +0000

Anyway: What is a forward proxy (and what is a reverse proxy for that matter)? If the proxy is a forward proxy, the server thinks the proxy is the client. If the proxy is a reverse proxy, the client thinks the proxy is the server.

Counting files (list and word count, ls & wc)

Wed, 29 Apr 2020 00:00:00 +0000

How do you count the number of files in a directory? That becomes non-trivial if you have thousands of files in a directory. Your file manager chokes on counting them, especially if they are not local. On the Linux command line, this task is fast and easy:ls | wcls lists your files one per row and wc returns three numbers: lines, words and bytes. In the file counting example, lines and words are the same and equal the number of files in the directory. To count all files recursively in the directory tree “backcheck”:find backcheck/ -type f | wc -l

Repairing our refrigerated centrifuge

Tue, 17 Mar 2020 00:00:00 +0000

Refrigerated tabletop centrifuges are quite expensive. Although discontinued, a refurbished Eppendorf 5415R (the model we use) still sells for $1-2K. The second of our two Eppendorf 5415R broke already more than a year ago and since then, we have been either centrifuging in the cold room or using the neighboring lab's cold fudge. But having two broken centrifuges of the same type, but different failure symptoms begged to assemble one functioning out of the remains.One of the centrifuge rotors was stuck (could not be turned even by hand) and the other fuge was giving sparks and smoke when starting a run. I had postponed this repair since I thought it might take much time. However, when I opened the first centrifuge, I immediately could identify the part that I needed to graft from the other fuge. The whole repair lasted less than one hour. There was a blown resistor next to the cooling fan, which was easily replaced with the part from the second fuge. You can see the broken brass-colored resistor (CGS HSA50 resistor, available from Amazon for$ 13) in the front of the picture left to the rotor.The failure of both centrifuges was apparently caused by liquid getting into the inner workings of the fuge. The rotor of the second centrifuge could not turn anymore because it was corroded from the salt and water. Also, the resistor had apparently been soaked (it is located immediately below the cooling grill on the top back of the fuge).The centrifuge works again including the cooling. I do not know for how long we will enjoy it, because it was already 2nd hand when we bought it in 2014. But even if it lasts only for another year, the repair was worth it.This type of repair might become easier in the future because if I am not mistaken, the EU is planning to mandate that manufacturers make service and repair manuals available to third party repair shops (this mandate exists already for car manufacturers to ensure that independent car repair shops can survivce).Depending on the coronavirus, I will perhaps get around repairing even more broken lab equipment. Next in the queue is the fraction collector of our old FPLC (GE Healthcare Äkta Explorer Frac-950).

Updating GE's Äkta Avant to Windows 10

Tue, 18 Feb 2020 00:00:00 +0000

The Avant is the flagship of GE Healthcare’s Äkta line of FPLC (fast protein liquid chromatography) devices. We use it on a regular basis and it is available to everybody from the University of Helsinki.Our University decided to play nice with Microsoft and to disallow all network traffic for Windows 7 computers. Because our Äkta (bought in 2015) is in use by many different researchers, we rely on Microsoft’s Active Directory to authenticate users and to track the device usage. When the University really did shut down Windows 7 traffic in late January, we finally updated the HP computer from Windows 7 to Windows 10 . Before we did that we contacted GE in order to be sure to have a working FPLC. Although the build number of Win10, that our University is using (Windows 10 Enterprise version 1809, build 17763.1039) was not supported by any of the Unicorn 7 versions that GE has released over the years (see this software compatibility chart, which I cannot find anymore from the GE website: https://drive.google.com/open?id=1cA33lEqfEr0MIaA8r9TyoQFcxiHWuZsp) , we were assured that the software would continue working. Unfortunately, this was not true.**In-place upgrade or clean install?**We performed an upgrade of Win7 to Win10 in place. I never liked these. Even on slightly superior operating systems like macOS and Linux , the in-place upgrades have not always been smooth. A fresh start has always been the safer (and also faster) bet.Connection problemsAfter the upgrade, Unicorn 7 started to lose the connection to the Äkta Avant during ongoing protein purification runs. We clearly could see during manual runs, that specific commands would trigger a disconnect. The Äkta LCD display would black out and the device would reboot. Naturally, we suspected that this was a consequence of the upgrade to Windows 10. Because Unicorn 7.0.2 had not been tested to work with our version of Windows 10, we first wanted to try to upgrade to a Unicorn 7 version that had been tested with our Win10 build. I had already asked in December for that update from GE, but my request had been ignored and I had many other things to do at the time and never bothered to come back to the issue (in hindsight a big mistake).Software updatesSomething that Chrome and Firefox do weekly silently in the background (without the user noticing) takes in the case of GE almost 2 weeks full-time engagement by the user. A simple download might work for Bio-Rad , but GE requires a complicated, obfuscated, non-transparent, user-unfriendly, constantly changing, GDPR-non-compliant syastem, which is in addition hosted on servers that feel so slow that you constantly wonder whether your browser tab has frozen. What it’s worth, GE’s web pages have always been like this despite multiple redesigns and GE’s digital transformation. The email thread between me and various GE support addresses comprises as of today 60 emails (starting with my first support request on December 2nd, 2019). On top of this, there are also quite a few phone calls (since email seems to be often regarded as “non-urgent” by default).Privacy concerns about GE’s handling of customer dataAfter placing an order for the download, receiving a quotation, confirming the order and receiving an order confirmation, I finally received the “permission” to download the newest version of Unicorn (which is 7.5). I logged into GE’s “eDeliveryPortal” only to realize that I could see the software entitlements and downloads for many other GE customers, but none of my own. After some back-and-forth the 7.5 version finally showed up under my downloads. My license is still missing as of today. But why bother? I could use any of the other licenses (after faking the MAC address of my computer as the software apparently is locked to specific computer via the computer’s network card’s MAC address). This is clearly a violation of the GDPR as there is absolutely no reason why my data (entitlement ids, MAC addresses, Names, e-mail addresses) should be available to other customers. It might be that GE considers the University of Helsinki as a single customer; that would be a violation of the GDPR by design.**Searching for the system configuration files (i.e. firmware)**However, we had not updated the system configuration files, because I had not been able to find them from the GE LifeScience website . We were running version 3, while version 3.6 was the newest one. Notably, these files do also contain the firmware for the individual Äkta components. It appears that this download is nicely hidden. I needed help from GE in order to locate it. The GE life science website has a search function and the search even finds the download. However, it is perhaps the last item in a list of nearly 1000 hits (10 hits/page). One tip to GE: Google knows search! If you just would let Google index your complete web site, customers would find everything via a Google search. Many companies are using Google for their internal web site search. However, GE seems to expose only their product pages to search engine crawlers, but not their support pages.**Where are our licensing files?**After updating the instrument configuration, the problem persisted. After sending a system report (and then sending a second “extended” system report), GE concluded that most likely our in-place upgrade from Win7 to Win10 was to blame, because they could see some irregularities in the SystemEventLog.xml file. I had no reason to doubt this explanation and therefore requested a clean Windows 10 install from our IT guys. I then installed Unicorn 7.5 only to see that the problem had not disappeared. Just as a side note: We had a self-inflicted issue with our license file (.lic). The Unicorn installer software requests the installation of a license file, which I have never seen for download anywhere in the eDelivery portal (we have received these license files as attachments to e-mails directly from GE support staff, why are they not available for download as these are prone to be lost?). We should have made a copy of our license file before we erased our computer for the clean Win 10 install, but we missed that and I had to dig out the license file from a system backup, which I had luckily made in 2016 from the machine. And I am still searching for our license files for different system components (Classic Evaluation and Column Handling), which were not yet installed when I did the system backup.Down-grading to Windows 7In order to be sure that we did not deal with a hardware failure, we decided to downgrade the system back to Windows 7 and Unicorn 7.0.2. That was more difficult than expected, because we cannot anymore install Windows 7 on university machines. Luckily we had still one old, unused Dell desktop, that was runninig Windows 7. Unicorn 7 requires two network cards (one to communicate with the outside world and one for a separate 10. network to communicate with the Äkta Avant). We swapped the network interface card from our default computer to this old Win 7 machine. However, installing and running Unicorn requires access to the internet because the software is “phoning home”. Exactly that is disallowed for Win7 machines at our university. Hence I needed to set up a private network via my phone to allow Unicorn 7 to communicate with GE headquarters. Even worse, I needed to clone the MAC address of our default computer, because our Unicorn 7 software is apparently locked to a specific computer via the computer’s MAC address. And wireless internet access was a no-go, because the original MAC address was from a wired NIC. It is not possible to clone MAC addresses between cabled NICs and USB wireless adapters, because MAC addresses from wireless cards have a fixed prefix. Hence, I had a complicated setup from my phone via a computer to a (cable) router to the Win7 Dell computer.Windows 10 is not to blame - F-Secure is the culpritTo my surprise, the Äkta Avant kept crashing when Unicorn 7 under Win7 issued commands like “pause” or “end”. But then I realized that - unlike our old Äkta Explorer - the Avant uses regular NICs for the device communication and the University of Helsinki Win10 version is by default “enhanced” by remote control and security software. I went to the Control panel and uninstalled all software add-ons that had been installed by the university. Most notably F-Secure’s Client Security Premium was among the programs, that I uninstalled. After a reboot, I was unable to make the Äkta Avant crash. To confirm the finding, I popped the NIC back into our original default computer, rebooted and got stuck at the Windows BitLocker screen. Changing the hardware configuration inevitably triggers Windows to refuse booting. This did slow me down because it required me to engage our university’s IT department, which is chronically overworked and difficult to find. I selectively disabled the firewall from F-Secure Client Security Premium and the crashes instantly ceased also on Windows 10. It is very difficult to argue why our university would need F-Secure’s products. Windows itself comes (since XP SP2) with a very capable firewall and also has its own anti-virus software ( Windows Security Essentials / Windows Defender ), which is at least as good as its best competitors in addition to the fact, that it is free and fully integrated into Windows (and it does not require to stick third-party hooks deeply into the OS).Windows 10 is too slow on our 2015 hardwareThe only thing left is to upgrade our default computer to newer hardware. Our faculty had replaced older Win7 computers in 2019 with new machines, but this computer was 1 day too new to be included in the upgrade. However, it is already 5 years old and especially after the Windows 10 upgrade, it is very slow. When your protein elutes during your purification, you do not want fraction collection to start after a few seconds, but you want it to start instantly.

Copying with rsync

Mon, 17 Feb 2020 00:00:00 +0000

Reasons why you should (not always, but often) prefer rsync over cp:

Resume Interrupted Transfers If you are copying a large file and your terminal session crashes or the power cuts out, cp will simply fail, and you have to start over. rsync can pick up right where it left off, which is a massive time-saver for large datasets.
Efficiency (Delta-Transfer Algorithm) rsync is designed to be smart. If you are copying a file that already exists at the destination (e.g., you are updating a backup), rsync only copies the parts of the file that have actually changed (the “delta”) rather than overwriting the entire file. cp, by contrast, always copies the whole file every single time.
Real-time Progress Monitoring rsync provides excellent visual feedback. By using the -P (or –progress) flag, you get a real-time progress bar showing the percentage complete, transfer speed, and estimated time remaining. cp is famously silent, leaving you guessing whether the process is still running or has hung, requiring you to check at the destination via the size of the arriving file, whether anything is progressing (ls -lh filename, or du -hs filename)
Seamless Remote Transfers rsync is natively built to work over SSH. You can use it to copy files directly to or from a remote server as easily as copying files on your local machine. cp cannot do this; to use cp for a remote server, you would first need to mount the remote filesystem locally, which is far more complex and prone to errors.

Here is a common use case, the transfer of a directory, including all of its content:

Free digital signing of documents under Linux - an impossibility?

Sun, 01 Dec 2019 00:00:00 +0000

The whole story started when I tried to sign a LibreOffice document. When you belive the internet, document signing is inbuilt into LibreOffice. I still have to find the person that managed to digitally sign a LibreOffice document. This experience shows, that despite Edward Snowden most people do not proactively care about security and privacy. Debian removed scdaemon from the gnupg2 package and as usual, one needs to be a command line ninja to fix this. The scdaemon gives smartcard support (which I do not have, but without the scdaemon the Kleopatra key manager refuses to run). I am using the default Ubuntu 18.04 installation and it was quite an odyssey to get a document signed. In fact, I still do not have a satisfactory way to do this. However one does it, something’s not right. Ubuntu 19.10 has fixed at least the invokation of the key manager from LibreOffice and I can invoke SeaHorse from the document signing dialog, but I still have no clue how to make my gpg keys visible to LibreOffice. Anybody figured this out? Until somebody shows me how to sign with LibreOffice, I use the very good, but proprietary software PDFStudio to import my GPG keys and sign my PDF files.Signing services (DocuSign, HelloSign) So what do you do if you need to sign e.g. a PDF and you have no means or do not want to subscribe to one of the document-signing certificate service like DocuSign ? Even with DocuSign’s budget plan a single digital signing costs $2. DocuSign has a 30-day free trial, but I do not know whether the certificats that you generate during the trial with continue to be valid after the end of the trial. HelloSign ( https://www.hellosign.com , now owned by DropBox ) has also a free tier (allowing to sign 3 documents/month) and when signing, it embeds an invisible signature (which was invalid for some strange reason when I tested it even though HelloSign is in Adobe’s approved trust list).Self-signing, cacert and StartSSLTechnically you can created your own signatures (self-signed certificates), but if such PDFs are viewed with Acrobat Reader, the signature will be flagged as invalid and the fact of self-signing is displayed. There used to be http://www.cacert.org/ , but to my knowledge, all browsers have removed the CAcert certificates and the same is likely true for Acrobat. StartSSL used to give out free certificates, but they do not exist anymore (they were seriously challenged with their own security).PDF Viewer supportInterestingly many PDF Viewers do anyway ignore the signing (e.g. the inbuilt PDF viewer from Firefox does not display anything). Other PDF viewers will display the signature, but NOT indicate, that it is not trusted (e.g. the Chrome Browser’s PDF viewer and Ubuntu’s default PDF viewer Evince). Since you have no idea what viewer your target will use to display your signed PDF, you are anyway in a bad situation (even if you subscribe to a document signing service). LetsencryptTo increase the trust in the signing, one can use a Letsencrypt certificate for signing. This signature certifies that the author of the document controls a specific website (in my case jeltsch.org). That is more than a self-signed certificate (and if the website is trusted, this is arguably also more than buying a subscription from DocuSign), but the re-purposed Letsencrypt certificate is not being trusted by Adobe since obviously the Letsencrypt endeavor was never meant for document signing (“Signer’s identity is unknown because it has not been included in your list oif trusted certificates and none of its parent certificates are trusted certificats”). However, the maximum lifetime of such a certificate is 3 months, after which it becomes invalid. It can still be used, but it will display that it is not valid because it has expired (or is not valid yet).How to misuse the Letsencrypt certificateFirst, you need a web server, that uses Letsencrypt certificates to verify the web site identity. This is out-of-scope for this blog post, but there are several good tutorials (e.g. from the Let’s Encrypt people themselves or from Digital Ocean ). Once you have your Let’s Encrypt certificates, this is the process to “misuse” them for signing documents:Since Letsencrypt requires certificate renewal every three months, there will be lots of fullchain.pem and privkey.pem files in the same directory and they are numbered. You obviously want to use the newest (the only valid) certificate and perhaps you want to renew the Let’s Encrypt certificate immediately before exporting it for document signing:certbot --apache --force-renewal -n -d jeltsch.org or if you want to renew all certificates: certbot --apache --force-renewal If you choose to renew all certificates, certbot will try to issue a single certificate for all domains that exist on your server (this possibility did not exist in the beginning of the Letsencrypt ecosystem, but was introduced later). If your server serves more than one domain, you need to manually specify the domain name, for which you want the certificate.For more details about how to use the certbot script, see https://certbot.eff.org/docs/using.html#certbot-commandsThis is the command, that converts the certs into a PKCS#12 file:openssl pkcs12 -export -out signing_certificat.p12 -in /etc/letsencrypt/archive/website-name/fullchain1.pem -inkey /etc/letsencrypt/archive/website-name/privkey1.pemThe PKCS#12 file stores the certificate and the private key in one encrypted file (with the file extension .p12). Therefore, the command will ask from you a keyphrase, which you absolutely need to remember to be able to use the certificate. Then you can transfer the p12 file to your desktop computer and use it to sign PDF files.Time stamping serversIf your PDF application asks for a time stamping server, you can use one of the free services, e.g. ca.signFiles.com/TSAServer.aspx or http://zeitstempel.dfn.de . However, also these time stamping services are not trusted by Adobe Acrobat.Here the commands to generate a self-signed certificate (it asks for a (temporary) passphrase, just make up something and remember it, you need it in the second step):openssl req -x509 -newkey rsa:4096 -keyout key.pem -out cert.pem -days 3650Conversion into a signing certificate (it first asks you for the temporary passphrase from above and then for the final passphrase, which you need to remember in order to use the certificate:openssl pkcs12 -export -out signing_certificat.p12 -in cert.pem -inkey key.pem

PXE-booting from Netgate Pfsense SG-3100

Fri, 15 Nov 2019 00:00:00 +0000

To install Linux without the need of a CD/DVD/USB-stick, I now use PXE-booting (“pixie”-booting) on our local home network. I could not find good instructions and had to try out things before it started working, but the process itself is fairly simple. Here are the steps:

Nautilus (Ubuntu's file manager) and bookmarks

Tue, 06 Aug 2019 00:00:00 +0000

In the very old days, the Ubuntu’s file manager’s bookmarks were stored directly as invisible file in the home folder ($HOME/.gtk-bookmarks). Since 14.04, they have been hiding two levels deep in $HOME/.config/gtk-3.0/bookmarks.And if you wonder where the Nautilus scripts are, they are nowadays at $HOME/.local/share/nautilus/scripts/.

Mounting lvm2 manually

Fri, 02 Aug 2019 00:00:00 +0000

All commands as sudo:

vgscan (--mknodes)
vgchange -ay (volumegroupname)
(lvdisplay or lvs or ls -l /dev/volumegroupname/)
mkdir -vp $PATH/{home,root} (to make a moint point)
mount /dev/volumegroupname/home $PATH/home
mount /dev/volumegroupname/root $PATH/root
(ls -al $PATH/home)

How to enable passwordless logins to a server

Wed, 24 Jul 2019 00:00:00 +0000

Enable root login with password on the server. To do so, you need to edit the file /etc/ssh/sshd_config.Modify the lines starting with “PermitRootLogin” like this:#PermitRootLogin prohibit-passwordPermitRootLogin yes
Restart the sshd server:sudo systemctl restart sshd
On the client, copy the public key files to the server with the ssh-copy-id command:ssh-copy-id root@server
On the server, disable root login with password and enable root login with public key authentication:PermitRootLogin prohibit-password#PermitRootLogin yes

Ḿanuscript reviewing by annotating PDFs

Fri, 28 Jun 2019 00:00:00 +0000

Manuscripts for scientific peer-review are delivered as PDF files. Thus it appears most natural to comment the PDF file itself instead of submitting the comments as a separate text (file). However, many submission systems do not allow to submit comments in form of an annotated PDF file.In addition, there is no easy-to-use free/Open Source PDF editor for Linux (my platform of choice). Yes, there is PDFEdit ( http://pdfedit.cz/en/index.html) , but it requires substantial learning and its last release dates back to 2012. There are free online PDF editors (e.g. https://www.pdfescape.com/) , but sometimes I need a local tool. Although not Open Source and not free, the tool of my choice has been PDF Studio Pro . It has all the features I need (actually much more than I need), it is truly cross-platform (Windows, Mac, Linux), easy to use and very affordable for what it offers ($129 single permanent license). Unfortunately, Quoppa software - the maker of PDF Studio - does not offer academic discounts.PDF Studio ViewerA while ago, the makers of PDF Studio started to offer a free version called PDF Studio Viewer . This free version has gotten more useful over time. Since last year, it also supports PDF annotation, which is very important for my work, mostly when I am peer-reviewing scientific manuscripts. For many academic users, the PDF Studio Viewer might be fully sufficient.Libre Office and InkscapeOf course Libre Office Draw and Inkscape can edit PDFs, but they are not specialized for annotating. If you need to do extensive annotations, the process becomes soon very painful. In addition, Inkscape editing can be destructive (i.e. when you modify text), but I have used it e.g. to fill out forms.Apart from the lack of dedicated annotation and reviewing tools (“markups” like “replace text”, “crossout text”, “delete text”, “insert text” or callouts), Libre Office Draw is actually a quite capable PDF editor, but fails still sometimes to correctly open very complex PDF documents (I have had problems with background images/patterns). Strangely, the only reviewing tool (comments) are not exported by default. You need to check the “Export comments” box when you export your edited PDF file as PDF (the “Save” operation creates an ODG file, which you probably don’t want).PDFsamIf you do not have the need to annotate, then you might get away with the Open Source tool PDFsam . Unlike PDFEdit, PDFsam is available from the Ubuntu repositories. PDFsam also has two non-free versions ( PDFsam Enhanced and PDFsam Visual ). PDFsam Basic (the Open Source version) is just a simple GUI on top of some command line utilities, whereas the PDF Studio Viewer offers a true visual editing experience. I canot talk about the non-free versions of PDFsam as they are not available as free trials. In fact, all of the operations of PDFsam can be achieved via the command line (see here for my blog post about how to perform common PDF editing tasks using mostly the command line tool pdftk ).Reducing file sizePDFsam Basic and PDF Studio Viewer do not offer any functionality to reduce file size. The LibreOffice Draw PDF export dialog let’s you reduce image resolution and JPEG compression, which you can use to reduce file size. But at the Open Source front, the only capable tools to reduce PDF size seem to be command line tools. I use ghostscript for this task, but the command is not easy to remember:gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/screen -dNOPAUSE -dQUIET -dBATCH -sOutputFile=output.pdf input.pdfWith PDF Studio Pro, you obviously do not need to remember the different keywords for the different output quality option (screen, ebook, printer, prepress) as you just choose from the drop down menu between the available options. If you are looking for an Open Source graphical wrapper for ghostscript, perhaps try workerPdf . Signing documents and adding signaturesPDF Studio Viewer let’s you sign documents if you have a DocuSign subscription . However, I am mostly concerned about being able to prove myself that I created a certain document (“self-signed signature”) and not that others are able to verify my authorship. For this scenario you are out of luck with PDF Studio Viewer. And apparently, PDFSam does not offer any possibility for signing (neither self-signing nor 3rd party signing). However, Libre Office Draw allows documents signing! I have been looking for an affordable solution (not self-signed, but trusted by other PDF readers) to sign PDF documents, but there seems to be no appropriate solution if you need to sign only rarely. The basic plan by DocuSign ($10/month) appears too expensive when signing only one document per month.Take-home messageIf you want to stay with free or Open Source solutions, you probably need to combine several tools in order to cover all typical PDF editing tasks without pain: PDFsam Basic, LibreOffice Draw, PDF Studio Viewer and ghostscript. But if you edit PDFs often (as I do), buying PDF Studio Pro is clearly the way to go.

Ubuntu 18.04 boot messages

Tue, 25 Jun 2019 00:00:00 +0000

After switching computers (but staying on the same version of Ubuntu), I copied my openvpn configuration (/etc/openvpn) to the new system. And when I booted next time, I received a weird request during boot to type in my username and password. There was no mentioning for what purpose, so I had to guess. Additionally, there is a bug that required me to press twice the Enter key after the username and password. It appeared to be openvpn, which tried - by default - to start up all openvpn configurations that it could find in /etc/openvpn. On my old system I had set it not to start anything automatically. And of course this setting is not in the /etc/openvpn directory, but in /etc/default/openvpn. In order to prevent automatic starting, you need to uncomment the#AUTOSTART="none" line.In order to see what process was asking for the password during boot, I needed to see all the boot messages. This is done by pressing Esc shortly after boot to see the grub boot menu (if you have only Ubuntu installed, otherwise you’ll see the boot menu by default). You just press e to get into edit mode. Here you edit the line that starts with linux and delete the two words “silent splash”. Then you press F10 to start the boot process.

Is Ubuntu 18.04 still using the SSD drive for swap?

Fri, 10 May 2019 00:00:00 +0000

In an Ubuntu 18.04 two disk setup (/ on SSD, /home on spinning drive), my Ubuntu 18.04 has still defaulted to use swap space on the SSD although there was a swap partition of the same size on the spinning drive. This was not a new install, but a system upgrade from 16.04 (where I had created a swap partition manually on the spinning drive to spare the SSD). Linux is able to determine whether a drive is spinning or not, but apparently the installation/upgrade script was not very smart.What swap partitions are available?sudo fdisk -l[…]Disk /dev/sda: 74,5 GiB, 80026361856 bytes, 156301488 sectorsUnits: sectors of 1 * 512 = 512 bytesSector size (logical/physical): 512 bytes / 512 bytesI/O size (minimum/optimal): 512 bytes / 512 bytesDisklabel type: dosDisk identifier: 0x34836041Device Boot Start End Sectors Size Id Type/dev/sda1 * 2048 148054782 148052735 70,6G 83 Linux/dev/sda2 148056062 156301311 8245250 4G 5 Extended/dev/sda5 148056064 156301311 8245248 4G 82 Linux swap / SolarisDisk /dev/sdb: 931,5 GiB, 1000204886016 bytes, 1953525168 sectorsUnits: sectors of 1 * 512 = 512 bytesSector size (logical/physical): 512 bytes / 512 bytesI/O size (minimum/optimal): 512 bytes / 512 bytesDisklabel type: dosDisk identifier: 0xf6870277Device Boot Start End Sectors Size Id Type/dev/sdb1 2048 8390655 8388608 4G 82 Linux swap / Solaris/dev/sdb2 8390656 1953525167 1945134512 927,5G 83 Linux[…]Checking which drive is the SSD:cat /sys/block/sda/queue/rotational0cat /sys/block/sdb/queue/rotational1Which swap partition is used?more /etc/fstab[…]# swap was on /dev/sda5 during installationUUID=fdb5ad84-f758-4326-a6c8-7adf91d21079 none swap sw 0 0[…]Check whether the UUID corresponds to the SSD:sudo blkid /dev/sda5/dev/sda5: UUID="fdb5ad84-f758-4326-a6c8-7adf91d21079" TYPE="swap" PARTUUID="34836041-05"

Linux copy (cp)

Wed, 17 Apr 2019 00:00:00 +0000

In order to copy all xml files from one directory to another without overwriting existing files with the same name:cp -vnpr /source/*.xml /destination

Denkbar knapper Sieg der Finnischen Sozialdemokraten über die ultrarechten Basisfinnen

Mon, 15 Apr 2019 00:00:00 +0000

Die gestrigen Parlamentswahlen in Finnland verliefen so dramatisch wie lange nicht mehr. Bis in die frühen Morgenstunden hatten viele Wähler gezittert, weil es zeitweilig so aussah, dass die Rechtaussenpartei der Basisfinnen die stärkste Fraktion im finnischen Parlament stellen würde und damit auch traditionell den Vortritt bei den Regierungsverhandlungen gehabt hätte. Der letztendliche Vorsprung der Sozialdemokraten vor den Basisfinnen fiel mit 0.2% hauchdünn aus. Obwohl die Sozialdemokraten nach 1999 erstmals wieder die stärkste Fraktion stellen werden, ist die Freude verhalten. Da keine Partei über 20% der Stimmen erreichen konnte, wird die Regierungsbildung schwierig. Alle demokratischen Parteien hatten im Vorfeld der Wahlen eine Koalition mit den Basisfinnen ausgeschlossen. Die von einigen erhoffte Schwächung der ultrarechten Basisfinnen durch eine Parteispaltung vor nicht einmal zwei Jahren ist nicht eingetreten und macht den Wahlerfolg der Basisfinnen um so verstörender. Das finnische Konzept, die Anziehungskraft der ultrarechten Parteien durch ihre explizite Einbinding in die Politik zu schwächen hat sich somit wahrscheinlich als Fehler herausgestellt. Zwei zentrale Standpunkte der Basisfinnen waren die verschärfte Einwanderungs- und Flüchtlingspolitik und die vielleicht geringste Priorität aller Parteien bezüglich des Umweltschutzes und speziell der Bekämpfung der globalen Erwärmung. In beiden Punkten unterscheiden sich die Basisfinnen grundlegend von fast allen anderen Parteien. Traditionell ist aber die finnische Politik eine Konsenspolitik und mit wenigen Ausnahmen sind Koalitionen jeder Partei mit jeder anderen Partei denkbar. Zur Zeit sieht noch so aus als ob alle demokratischen Parteien sich an ihr Wahlversprechen halten werden, nicht mit den Basisfinnen zu koalieren. Der wahrscheinliche zukünftige Ministerpräsident der Sozialdemokraten Antti Rinne hat in einem Interview nach der Wahlnacht noch einmal die Unvereinbarkeit der Standpunkte der Basisfinnen mit sozialdemokratischen Werten betont und das er eine unterschiedliche Behandlung von Menschen aufgrund ethnischer Zugehörigkeit oder Hautfarbe unmöglich akzeptieren kann.Im Prinzip ging es bei den Wahlen um eine Abrechnung mit der seit vier Jahren im Amt befindlichen Koalitionsregierung unter dem Ministerpräsidenten Juha Sipilä. Juha Sipilä hatte schon vor einem Monat den Rücktritt seiner Regierung bekanntgegeben, und war nur noch geschäftsführend im Amt, weil er zentrale Versprechen zur Erneuerung des Gesundheitssystems aufgrund mangelnder Unterstützung nicht einhalten konnte. Sipilä von der Finnischen Zentrumspartei ist (oder sollte man lieber sagen war) ein Quereinsteiger aus der Wirtschaft in die Politik. Obwohl die konservativen Sammlungspartei und die Basisfinnen (dem finnischen Pendant zur AfD) auch der bisherigen Koalitionsregierung angehörten, wurde nur die Zentrumspartei vom Wähler für die Politik der letzten Jahre mit massiven Verlusten von über 7% abgestraft, ihrem schlechtesten Ergebnis seit 100 Jahren.Ob meine eigenen Hoffnungen nach verstärkten Investitionen in Bildung und Forschung sich erfüllen, steht und fällt mit den Sozialdemokraten und deshalb haben sie auch meine Stimmen erhalten. Obwohl auch alle anderen Parteien versprochen haben die Ausgaben für R&D langfristig zu verdoppeln, ist die Ideologie der schwarzen Null auch in Finnland bei den Konservativen beliebt. Zumindest die Konservativen und die Zentrumspartei haben innerhalb der letzten 10 Jahre jede Gegegenheit verpasst zu zeigen, dass ihnen Investitionen in unsere Zukunft und in unsere Kinder am Herzen liegen. Es ist schon merkwürdig, dass es Geschäftsleuten wie Juha Sipilä ein fremder Gedanke sein sollte, dass man die Zukunft investieren muss, um wettbewerbsfähig zu bleiben.

ChemBio Finland

Thu, 28 Mar 2019 00:00:00 +0000

The biyearly ChemBio Finland event at the Helsinki Fair Center is taking place on this week’s Wednesday and Thursday. I presented our key project at the booth of the Academy of Finland ( http://www.aka.fi/fi/akatemia/media/Ajankohtaiset-uutiset/2019/tervetuloa-suomen-akatemian-osastolle-chembio-messuille/) . Many people showed up to listen to our work on how to move in-vitro antibody generation technologies into the 21st century using synthetic biology and Crispr.

Passwordless login via the GUI and ssh defaults

Mon, 25 Mar 2019 00:00:00 +0000

I use cloud services at CSC (e.g. pouta.csc.fi), and they do not allow SSH login with a traditional username/password combo. When I want to make a bookmark in my file manager (Nemo oder Nautilus/Files), pointing to this location. I need to specify an RSA key file that is used for the login. On the command line, it looks as follows:

Changing swappiness on Linux and SDD

Tue, 19 Feb 2019 00:00:00 +0000

The swappiness parameter is available from/proc/sys/vm/swappiness

“0” means “swap only to disk when you absolutely have to”
“100” means “swap immediately to disk”

If you are running you OS from an SDD, you might not want the default of 60, especially not if you have decent amounts of RAM (16 or 32 GB). In order to preserve the lifetime of your SDD drive, executesudo sysctl vm.swappiness=10.However, the setting disappears after a reboot and in order to make it permanant, you need to add the following line to /etc/sysctl.conf:vm.swappiness=10

Mounting group directories via the fstab

Mon, 11 Feb 2019 00:00:00 +0000

At the University of Helsinki, one can apply for group directories, which is simply disk space on a NAS. These are easily mounted when you use a university-managed computer via the university menu, but what about if you use your own machine? At least for Ubuntu Linux, the way to mount these directories has changed multiple times during the years and it again broke recently. The current entry in the /etc/fstab file in my (Vanilla, non-university-managed) Ubuntu 16.04 is as follows:# HY group directories//group2.ad.helsinki.fi/h204 /home/local_username/GROUP-drive cifs noauto,user,user=hy_username,nobrl,uid=1000,gid=1000,file_mode=0666,dir_mode=0777 0 0Then you can simply execute “mount /home/local_username/GROUP-drive” and you will be asked for your HY password. The number 2 and the string “h204” in the server address (group2.ad.helsinki.fi/h204) are specific for the cost center which is in this case H2042 (taking the first digit from the cost center string and first four characters from the cost center string, respectively).And here are some instruction on how to do it manually on a Macintosh:https://helpdesk.it.helsinki.fi/en/instructions/saving-and-sharing/group-storage-space/remote-access-home-and-group-directory-mac

How to change the MAC address of the Ubiquity Edge Router X

Wed, 14 Nov 2018 00:00:00 +0000

Bring up the command line tool (CLI) from the browser GUI. If you use any special characters in your password, you might need to change your password first via the GUI. Despite considerable effort, I did not manage to type special characters into the CLI using Firefox on a Mac (copy-paste does not work). Assuming that you want to change eth0:configureset interfaces ethernet eth0 mac 00:03:0D:51:B4:D2commitsave

Nicht für das Leben, sondern für die Schule lernen wir

Tue, 13 Nov 2018 00:00:00 +0000

Non vitae sed scholae discimus („Nicht für das Leben, sondern für die Schule lernen wir.“; “Thus we learn our lessons, not for life, but for the lecture-room.”) ist ein ungefähr 2000 Jahre altes Zitat Senecas aus einem Brief an einen seiner Schüler. Mein Sohn ist der gleichen Ansicht: das meiste, was er in der Schule lernen müsse, wäre nicht wichtig für das wirkliche Leben. Leider muss ich ihm (und viele andere Experten mit mir) da Recht geben. Dem Stolz und der Freunde, die den Anfang der Schullaufbahn der meisten Kinder begleiten, folgt oft innerhalb weniger Jahre die Ernüchterung. Schon wenige Wochen nach den grossen Ferien warten die Kinder nur noch auf die Herbst und dann auf die Weihnachtsferien, obwohl Lernen doch Spaß machen kann. Was läuft hier falsch? Wie schaffen es die Schulen so schnell, die natürliche Neugierde und Motivation der Kinder zu abzutöten?Ich habe anfangs zu argumentieren versucht, dass es nicht wichitg is WAS man lernt, sondern dass man das LERNEN lernt. Und das könne man ja an beliebigen Themen. Leider ist dieses Argument ein Armutszeugnis für diejenigen, die die Lehrpläne für unsere Schulen erstellen oder umsetzen. Warum lässt man dann die Schüler nicht LERNEN lernen an Themen, die interessant und relevant sind? Wo vor hundert Jahren Lesen, Schreiben und die Grundrechenarten genügten, wächst das Wissen heutzutage exponentiell. Und die einzige Antwort der Schulbürokraten ist, immer mehr neuen Stoff in die Lehrpläne zu packen, ohne Altes aus den Lehrplänen zu streichen. Dabei währen eher mehr Freiräume als früher notwendig, weil die Vermittlung vieler der heutzutage benötigten Kompetenzen Spielraum und flexible Strukturen benötigt. Mir ist klar, das die (personellen und finanziellen) Möglichkeiten der meisten Schulen begrenzt sind. Trotzdem gibt es viele Lehrer, die dem Mangel (in einem der reichsten Länder der Welt!) die Stirn bieten und mit mit viel Energie und Engagement modernen Unterricht gestalten.Viele sehen das Heil in einer verstärkten Rolle der MINT-Fächer (MINT = Mathematik, Informatik, Naturwissenschaft und Technik; auf Englisch STEM: science, technology, engineering and mathematics), aber gerade hier ist der Informationszuwachs so rasant, das Lehrpläne und vermutlich auch die meisten Lehrer nicht annährend mit der Realität mithalten könnten, auch wenn das zu vermittelnde Wissen unmittelbar relevant wäre. Deshalb sind heute Lehrer gefragt, die ihren Schüleren nicht nur Fakten beibringen, sondern Methoden. Solche Konzepte kann man gerade mit hochaktuellen und interessanten Themen vermitteln:

OpenVPN server on pfsense and client on Ubuntu 16.04

Fri, 02 Nov 2018 00:00:00 +0000

I have been setting up an OpenVPN server on my Netgate SG-3100 router . I hope this makes syncronizing backups to a physically separate location easier. There are many walkthroughs to set up an OpenVPN server on a pfsense router and that works nicely. However, I am using Ubuntu 16.04 at work and setting up the client requires a bit more than doing the same on MacOS or Windows. On Ubuntu, it is mandatory to update DNS information manually after establishing the VPN tunnel if you have opted for the setting to route all internet traffic originating from the client through the VPN server. If you do no update the DNA resolver information on the Ubuntu client, you can access the the VPN-internal network (in my case 10.0.0.0/24), but you cannot use hostnames. E.g. ping www.google.com will fail, but ping 172.217.21.164 will succeed. Similarly, your browser will not find any URLs. And browsing with IP-addresses (“http://172.217.21.164”) is not very practical.The default configuration on Ubuntu does not allow for this update of the DNS resolver to happen automatically for security reasons. There is a script included in the Ubuntu package of openvpn that updates this information (/etc/openvpn/update-resolv-conf). But in order for this to work one needs to

SSD or spinning disk?

Wed, 12 Sep 2018 00:00:00 +0000

sudo apt install smartmontoolssudo smartctl -a /dev/sdaorcat /sys/block/sda/queue/rotational

Lehrpläne aus der Vergangenheit

Mon, 10 Sep 2018 00:00:00 +0000

Non vitae sed scholae discimus („Nicht für das Leben, sondern für die Schule lernen wir“) ist ein ungefähr 2000 Jahre altes Zitat Senecas aus einem Brief an einen seiner Schüler. Meine Kinder sind der gleichen Ansicht: das meiste, was er in der Schule lernen muss, wäre nicht wichtig für das wirkliche Leben. Leider muss ich ihm (und auch viele Experten mit mir) da Recht geben. Dem Stolz und der Freunde, die den Anfang der Schullaufbahn der meisten Kinder begleiten, folgt oft innerhalb weniger Jahre die Ernüchterung. Schon wenige Wochen nach den grossen Ferien warten die Kinder nur noch auf die Herbst- und dann die Weihnachtsferien, obwohl Lernen doch Spaß machen könnte. Was läuft hier falsch? Wie schafft es die Schule so schnell, die natürliche Neugierde und Motivation der Kinder zu töten?Ich habe früher zu argumentieren versucht, dass es nicht wichitg is WAS man lernt, sondern dass man das LERNEN lernt. Und das könne man ja an beliebigen Themen. Leider ist dieses Argument ein Armutszeugnis für diejenigen, die die Lehrpläne für unsere Schulen erstellen und umsetzen. Warum lässt man dann die Schüler nicht lernen lernen an Themen, die interessant und relevant sind? Wo vor hundert Jahren Lesen, Schreiben und Rechnen genügte (und mit Rechnen meine ich die Grundrechenarten), wachsen heutzutage Wissen (leider auch Desinformation) exponentiell. Und die einzige Antwort der Schulbürokraten ist, immer mehr neuen Stoff in die Lehrpläne zu packen, ohne Altes aus den Lehrplänen zu streichen.Viele sehen das Heil in einer verstärkten Rolle der MINT-Fächer (MINT = Mathematik, Informatik, Naturwissenschaft und Technik; auf Englisch STEM: science, technology, engineering and mathematics), aber gerade hier ist der Informationszuwachs so rasant, das Lehrpläne und vermutlich auch die meisten Lehrer nicht annährend mit der Realität mithalten könnten, auch wenn das zu vermittelnde Wissen unmittelbar relevant wäre. Deshalb sind heute Lehrer gefragt, die ihren Schüleren nicht nur Fakten sondern auch die Natur von Wissen und Realität nahezubringen imstande sind. Solche Konzepte kann man gerade mit hochaktuellen und interessanten Themen vermitteln, z.B. Klimaveränderung: warum wir wissen, was wir wissen; was ist der Unterschied zwischen “Fakten” und “Meinungen”, warum gibt es in der Wissenschaft keine “Wahrheit” gibt, warum es trozdem Theorien, gibt, die mit an Sicherheit grenzender Wahrscheinlichkeit richtig sind und was eigentlich “richtig” und “falsch” in der Wissenschaft bedeutet und warum Wissenschaft eben keine Anhäufung von Fakten ist, sondern eine Methode. Und zwar die besten Methode, die wir kennen, um uns der Realität zu nähern (damit oute ich mich als Gegner der postmodernen Beliebigkeit, die auch die Wissenschaft als kulturbestimmt und ohne irgendwelche spezielle Beziehung zur Realität oder zur Wahrheit betrachtet).Die aktuellen Lehrpläne (zumindest die der Schule meiner Kinder) bereiten auf das vor, was vorgestern wichtig war. Die heutigen Kinder brauchen anstatt Stoffwissen Methoden. Und die Methoden kann man anhand eines Stoffes lernen, der interessant für jedes individuelle Kind ist. Und dabei geht es auch nicht um die Stoffmenge, sondern eher um die Tiefe. Kreativiät, Engagement und Verantwortung sind andere Dinge, die heutige Schulen lehren sollten und die für das Überleben der Menschheit unabdingbar sind; mehr zu diesem Thema gibt es zuhauf im Internet, hier nur zwei Links zur Anregung: https://www.cicero.de/kultur/wir-brauchen-eine-bildungsrevolution/51963 und http://www.spiegel.de/plus/a-00000000-0002-0001-0000-000158147643/ .

SnapGene and partial restriction digests revisited

Thu, 23 Aug 2018 00:00:00 +0000

Snapgene is a software for the wet lab molecular biologist, who does lots of cloning work (construct design and annotation). Since I last wrote about the SnapGene software ( https://www.snapgene.com/ ), many good things have happened:

Scanning my home network (nmap)

Sun, 18 Mar 2018 00:00:00 +0000

Scanning my home network for all devices that are listeningon port 80 (http):nmap -p80 192.168.0.0/24 -oG - | grep 80/openSometimes this doesn’t work (because nmap tries to be smart and only scan hosts that are available). In order to make nmap scanning without intelligence, use the e-Pn (no ping) option. This scans all ports of host 192.168.0.2:nmap -Pn -p0-65535 192.168.0.2

Literature list for Poster #XX:

Thu, 01 Mar 2018 00:00:00 +0000

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Computer time: Windows against the rest of the world

Sat, 10 Feb 2018 00:00:00 +0000

I am not sure, but Windows seems to be the only operating system, that wants the computer clock to be set to the local time zone instead of universal standard time (UTC). Maybe that is a relic of the times when Microsoft thought that the internet was not very important for the future of computing. All other operating systems apparently use UTC: MacOS, Android, Linux, BSD, … However, if you are dual-booting your computer, you can get into trouble. Not all operating systems detect automatically a dual boot install and adjust their behaviour in order to be compatible with Windows. If this is the case, the easiest is to change the behaviour of Windows. A clear write-up how to do so is available from https://liliputing.com/2016/03/fix-time-problem-dual-boot-computers-windows-linux-android.html , but here are the steps in a nutshell:

Syncthing

Wed, 24 Jan 2018 00:00:00 +0000

Syncthing is one of the best tools for keeping folders synchronized across the internet. However, for one or the other reason, it occasionally stops to work on my Ubuntu 16.04 and because I use it in a “set it and forget it” fashion, I also forget how to check that it is operational.Make it start automatically at boot time (as a system service): systemctl enable syncthing@username.serviceStart the service: systemctl start syncthing@username.serviceCheck the status: systemctl status syncthing@username.serviceThe URL of the GUI: https://127.0.0.1:8384 However, the above solution does not work well if e.g. the files to syncronize reside on an encrypted folder which is mounted only after the user has logged in (e.g. in Ubuntu 16.04, there was the possibility to encrypt the user folder, which was only unlocked during user login). Alternatively, one can run the service as a “user service” like this:cp /usr/lib/systemd/user/syncthing.service ~/.config/systemd/user/systemctl --user enable syncthing.servicesystemctl --user start syncthing.serviceSyncthing seems to regularly loose a file called “.stfolder”, which is supposed to be in the root of any shared folder (or it gets converted into a folder). For me the problem gets usually fixed by simply recreating that (empty) file (and deleting the folder with the same name if it exists).

Remote desktop sessions to your Helsinki University work computer

Mon, 15 Jan 2018 00:00:00 +0000

If you have a work laptop, you can take it home to do work. But what if you have a desktop computer and need to access it from home? The technology to make this possible exists for more than 20 years, but if you think that University IT has made this easy for you, you would be wrong. In fact, I don’t know anybody who knows how to do this (let alone how to make the process easy). Even with the setup explained below, some things do not work well (e.g. I never could figure out how to get the file sharing to work with a Mac-to-Mac connection and thus I still use Fugu with a separate tunnelled sftp connection to transfer files). You have several options:

The magic sequence to wake up Apple's SuperDrive on Linux

Sat, 09 Dec 2017 00:00:00 +0000

sudo apt-get install sg3-utils (only needed the first time)ls /dev (to check whether sr0 or sr1, usually it’s sr0 unless you had already other USB drives connected)sg_raw /dev/sr0 EA 00 00 00 00 00 01

The most effective ways to reduce your carbon footprint

Thu, 12 Oct 2017 00:00:00 +0000

According to this study from the University of Lund, the most effective ways to tackle climate change are largely not being discussed. Not surprisingly, they touch such the things dearest to our hearts: our car, our holidays, our children and our favorite foods.

Nazis in the German Parliament

Sun, 24 Sep 2017 00:00:00 +0000

Sad day for Germany: Nazis are sitting again in the German parliament. They don’t called themselves Nazis. Instead, they use the name AfD (Alternative für Deutschland = Alternative for Germany). And many people argue (in my opinion correctly) that Angela Merkel did nothing to prevent that from happening.Both big parties - conservatives and social democrates - massively lost support amoung the voters. Virtually all small parties could eithe keep or increase their representation in the German parliament, the Bundestag. Merkel needs at least two of them to stay in power and the numbers allow a coaliton of the Conservatives, Greens and Liberals (called Jamaica coalition after the colors of those three parties: colors black, green and yellow). The once revolutionary Greens will perpetuate the status quo in Germany… Many people seemingly voted against their own interest, but the social democrats could not convince enough people that they are the only viable alternative to Angela Merkel’s political agenda.

Toni Nett's rules

Sat, 16 Sep 2017 00:00:00 +0000

More than 50 years ago Toni Nett published his book Der Lauf. In the book, he presented thumb rules to calculate possible personal running records for common distances for middle and long distances. The possible personal bests are calculated based on known performances on the next shorter distance. Manfred Steffny extended Toni Nett’s rules to cover the marathon and the 100 km. He found these rules surprisingly accurate when comparing personal bests of hundreds of runners of different levels from beginner to world champion. I have been writing about these thumb rules previously here . Now I made a small php script that does the calculation for you.

Deleting files with "illegal characters"

Fri, 08 Sep 2017 00:00:00 +0000

In the cross-platform environment of our university, at least three different OS connect to the smb shared group directories. Apparently Macs are able to save files with characters that are not allowed on other platforms and which cannot be easily deleted. Recently we had several files which ended with a ‘.’ (dot) or a ’ ’ (space), and we were not able to remove them via the GUI. In Windows 7, I managed via the command line with:delete "file." ordelete "file "I have, however, not found a way to so from my Ubuntu machine and it is annoying to boot into Windows merely to delete some files. Unfortunately, this became necessary because the Cloudberry backup system (which is running on Ubuntu) chokes on such files. I am looking into a new backup system for our lab’s computers since CrashPlan decided to discontinue support for non-business customers…

Windows changes my computers clock

Mon, 28 Aug 2017 00:00:00 +0000

If I am not mistaken, Windows is the only OS, that uses local time for the system clock (instead of UTC). This means that in multiple boot configurations, every restart of the system into Windows will screw up the system time. In order to reset it (in Ubuntu 16.04), usesudo timedatectl set-timezone Etc/UTC

Amber from Stutthof

Tue, 01 Aug 2017 00:00:00 +0000

While running at the Baltic beach close to Kąty Rybackie (Poland), I picked up some amber. Some of it didn’t pass the floating test (in 20% w/v NaCl in water at room temperature), but I have not clue what the non-floating stones actually are (they are too soft for glass, maybe plastic?).I did not know when I arrived here for a one-week beach holiday, that the small village we were staying in belonged to the municipality of Stutthof , where one of the Nazi concentration camps was located. Actually, I twice made a detour from my daily morning runs at the beach to have a look at the camp, which is nowadays a museum. Interestingly, children below the age of 12 are not allowed to visit the site. This is different from those memorial sites of concentration camps in Germany that I know: the decision whether to take children for a visit is left to the parents.Another notable memory from these holidays were the road trips, which made me reconsider my firmly held opinion, that most car drivers in here in Finland are driving irresponsibly and mostly too fast. As a matter of fact, it was almost impossible to drive within speed limits in Poland as nobody seems to do so. I realized that traveling in a speed-limit-abiding car would be more dangerous than traveling in a recklessly speeding one as it would be subject to constant overtaking maneuvers on narrow country roads. Hence, I was also speeding. Not surprisingly, Poland features the highest traffic mortality rates in Europe ( https://www.economist.com/blogs/easternapproaches/2013/06/polish-driving ). The Polish government’s claimed intention is to reduce the numbers, but instead of lowering the speed limits, they increased them in 2011. According to Wikipedia the maximally allowed speed on highways changed from 130 to 140 km/h and on dual carriageways from 110 to 120 km/h. A rough estimate (based on these numbers ) shows that approximately as many people have died on Polish roads in the last 20 years as were killed by the Nazis in Stutthof in the years 1939-1945. Maybe the Polish police should start enforcing the limits?

Accessing shared folders in VirtualBox (Linux guest)

Fri, 28 Jul 2017 00:00:00 +0000

Transferring files from the host to the guest OS and vice-versa doesn’t work out-of-the-box when you install VirtualBox from the Ubuntu repositories and download an Ubuntu VirtualBox image (e.g. from http://www.osboxes.org/virtualbox-images) . After installing the guest additions, drag-and-drop didn’t seem to work for me and I needed to set up a “Shared Folder”. After setting it up via the GUI, it doesn’t automatically appear on the guest desktop. You need to mount it:sudo mount -t vboxsf name(as_specified_via_VirtualBox_GUI) ~/mount_point_in_the_guest_OS/There are obviously many other ways how to achieve this (e.g. via Samba or sftp or sshfs)…

Fertig

Sat, 04 Mar 2017 00:00:00 +0000

Nach einem Jahr von mühsamenm Teilesammelns und Bauens haben Tobias und ich heute das Lego Millennium Falcon Ultimate Collector’s Edition (Lego Set 10179, http://brickset.com/sets/10179-1/Ultimate-Collector-s-Millennium-Falcon ) fertig gebaut. Diese Version des Millennium Falcons wird nicht mehr verkauft und gebrauchte Sets werden für wahnsinnige Preise von um die €5.000 bei Ebay verkauft.Wir haben die notwendigen Legosteinie von zwei anderen Lego Star Wars Modellen genommen: aus dem Death Star (Lego Set 10188, http://brickset.com/sets/10188-1/Death-Star ) und dem Super Star Destroyer (Lego Set 10221-1, http://brickset.com/sets/10221-1/Super-Star-Destroyer).Allerdings mussten wir eine beträchtliche Menge an fehlenden Teilen dazukaufen. Viele von denen haben wir über die finnische Online-Auktions-Website Huuto ( http://huuto.net ) oder über BrickLink ( http://www.bricklink.com ), eine Art “spezialisiertes Ebay” für LEGO-Steine gekauft. Die am schwierigsten zu findenden Stücke waren die beiden hellen bläulich-grauen “Boat Mast Rigging Long 28 x 4” ( http://www.bricklink.com/search.asp?itemID=56261&colorID=86) , die im Moment für nicht weniger als €100 pro Stück verkauft werden. Wir haben diese Stücke natürlich nicht gekauft. Allerdings verkauft LEGO immer noch die schwarze Version dieses Stücks als Ersatzteil und Tobis Patenonkel hat sich die Mühe gemacht, diese zu besorgen und sie grau zu streichen. Danke Clemens!

Handbrake and protected DVDs

Thu, 02 Mar 2017 00:00:00 +0000

Ripping DVDs is a thing of the past, but occasionally I still need to do it. However, it happens so rarely that evertime I have either a new computer or a new Linux distribution and I need to install the necessary software. This time I am on Ubuntu 16.04. I usually use Handbrake and it is very comfortable, but handbrake sometimes fails to do the job. This time, I had to resort to MakeMKV . However MakeMKV only rips the video to an MKV container but it does not compress it. If you need the space reduction you should still push the file through a compressor. Here’s the whole chain of commands:I only have an Apple USB-Superdrive. Apple doesn’t want me to use it with any other computer but Macs. Therefore, in order to make it work under Linux, you needs to sens it a “Magic cookie” (see here: ):sg_raw /dev/sr0 EA 00 00 00 00 00 01If you have Handbrake installed from the default Ubuntu repository, you need to remove it (it’s crippled and you want to be able to use it also with encrypted DVDs):(sudo apt remove handbrake && sudo apt autoremove)Install this version:sudo add-apt-repository ppa:stebbins/handbrake-releasessudo apt updatesudo apt install handbrake-gtk handbrake-cliInstall software to read encrypted DVDs:sudo apt-get install libdvd-pkgHowever, you have to execute some manual commands after the install is ready, but the installer instructs you during installation.Select as source the TS_Audio folder on the DVD. If the scan never finishes or you do not see any tracks after the scan finishes, you might need something like MakeMKV. I didn’t find any PPA or deb file, so I compiled it from source, which succeeded without any problems following the isntructions from here: http://www.makemkv.com/forum2/viewtopic.php?f=3&t=224 . Here the short version:wget http://www.makemkv.com/download/makemkv-bin-1.10.4.tar.gzwget http://www.makemkv.com/download/makemkv-oss-1.10.4.tar.gztar -xvzf makemkv-bin-1.10.4.tar.gztar -xvzf makemkv-oss-1.10.4.tar.gz cd makemkv-oss-1.10.4/./configuremakesudo make installcd ../makemkv-bin-1.10.4/makesudo make installThe executable is /usr/bin/makemkv

ScanSnap iX100 support for Linux

Fri, 23 Dec 2016 00:00:00 +0000

Under Ubuntu 16.04, the ScanSnap iX100 is not supported yet by the sane package. In order to get it working, you need to install the ppa from Rolf Bensch:sudo add-apt-repository ppa:rolfbensch/sane-gitsudo updatesudo upgrade

Automated reinstall of software from package list

Sun, 20 Nov 2016 00:00:00 +0000

If I need to reinstall a Ubuntu/Debian-based Linux OS (or mirror a software selection to another machine), this is how it can be done. On the source machine:sudpkg --get-selections > ~/Package.listcp -R /etc/apt/sources.list* ~/apt-key exportall > ~/repository.keysThen just copy the files to the target machine:suapt-key add ~/repository.keyscp -R ~/sources.list* /etc/apt/apt-get updateapt-get install dselectdselect updatedpkg --set-selections < ~/Package.listapt-get dselect-upgrade -yIf some packages are not available, this will fail. This concerns in my case manually installed packages like teamviewer or snapgene / snapgene_viewer . I usually remove those packages manually from the list (there are luckily not many of them).However, the upgrade is not fully automatic, since you need to e.g. agree to various licenses (e.g. for Microsoft’s True Type fonts) and acknowledge manually other stuff (e.g. libdvd-pkg legal issues), which kind of defeats the purpose of making this automatic and painless…

Temperature Sensors

Tue, 15 Nov 2016 00:00:00 +0000

https://my.wirelesstag.net/eth/signin.html

Let's encrypt duplicated my log files

Wed, 19 Oct 2016 00:00:00 +0000

I have not been keeping log files for my web server until the beginning of 2016, when I needed to trace access to certain files (I started to use awstats , mostly because I was familiar with it since I had used it years ago when my site was still running on a Red Hat server). In March 2016 I luckily started to use Let’s Encrypt . I had used another “free” service before, which got recently into big trouble as they apparently had not control over their own security. When I looked at my Apache server’s log files (on Ubuntu 14.04), I noticed that apache did double logging (to both the individual vhost’s log file and a common log file). I realized that Let’s Encrypt specifies into every vhost’s configuration file an Import directive which sources /etc/letsencrypt/options-ssl-apache.conf. And this file in turn specifies common access.log and error.log files for all vhosts in the /var/log/apache2/ directory. I uncommented the five lines associated with this logging and the duplicate logging stopped (originally, I had thought, that this letsencrypt directive was only used for the initial Let’s Encrypt setup for the cert generation).

How to start openvpn or ssh server under Ubuntu 16.04 and 18.04

Sat, 03 Sep 2016 00:00:00 +0000

OpenVPNsudo systemctl start openvpn@clientThe “client” is derived from the configuration file name (/etc/openvpn/client.conf). If your configuration file is server.conf, the command needs to besudo systemctl start openvpn@serverWhen you want the service to start up automatically during system boot, you issue:sudo systemctl enable openvpn@serverTemplated versus non-templated servicesOpenVPN is a so-called “templated” service (it needs a configuration file when being invoked). In contrast to this, the ssh server is a non-templated service. Hence the command is simpler:sudo systemctl start sshd

Asustor AS7004T RAM upgrade

Sun, 31 Jul 2016 00:00:00 +0000

Are you about to buy the new Asustor AS7004T ? It is certainly an impressive small NAS server, but it comes only with 2GB RAM and if you want to utilize some of its cooler capabilities (like running virtual machines ) you need to add RAM. Its specs are uninformative (“2GB SO-DIMM DDR3 (Expandable. Max 16GB)”) and the memory installation guide misleading. However, it really does have two RAM slots for DDR3 SO-DIMM. The device that I bought had 2GB RAM glued into the user-serviceable RAM slot, while the virtually inaccessible factory RAM slot was empty. If you want to add RAM, it requires you to void the factory warranty as the empty RAM slot is not accessible without removing the screw that is covered by the “Void if removed” sticker. Anyway, almost complete disassembly is required for you to access the free RAM slot, which is not for the faint of heart. Especially since Asustor’s own YouTube video shows the disassembly only for the 10-bay AS7010T model, which is significantly different from the AS7004T. The biggest difference between the 7004T and the 7010T is that the 7004T has an additional cooling element screwed to the PCI back plane. This cooling element takes the heat from the mother board, but also makes removing the back plane and the mother board more tricky. You also need to remove the power supply and disconnect the power cables from the motherboard before you can take the motherboard out.

Batch renaming files on the command line

Tue, 28 Jun 2016 00:00:00 +0000

The default command line application for batch renaming files in Ubuntu 16.04 is called “rename”:rename 's/tk98i_/wt_tk98_/' *.tifIt uses Perl regular expressions with and the s/old/new/ syntax. The example above renames all files with the .tif extensions and replaces the th98i_ expression with wt_tk98_.Here are some more examples: http://tips.webdesign10.com/how-to-bulk-rename-files-in-linux-in-the-terminal

ffmpeg

Sun, 26 Jun 2016 00:00:00 +0000

Trimming an avi file: ffmpeg -i Die_Sendung_mit_der_Maus_16.06.19_09-30_ard_30_TVOON_DE.mpg.HQ.avi -vcodec copy -acodec copy -ss 00:06:04 -t 00:29:32 output.aviss is the start time and t is the duration (not the end time)webm to mp3 conversion:ffmpeg -i La_robe_de_soie.webm -vn -ab 128k -ar 44100 -y "La_robe_de_soie.mp3"Concatenate two videos:ffmpeg -f concat -safe 0 -i list.txt -c copy /tmp/output.avilist.txt:file 'video1.avi'file 'video2.avi'UPDATE:It is nice to be able to manipulate video files on the command line. However, especially for the more advanced functionality, the syntax becomes impossible to remember. Hence the need for a GUI that makes ffmpeg more accessible. The best tool that I have come acress so far is the cross-platform LosslessCut . There are also packages for Mac, Linux or Windows .

Unicorn 7-Benutzer-Einrichtung erfordert manuelle Intervention in einer Netzwerkbenutzer-Umgebung

Fri, 17 Jun 2016 00:00:00 +0000

Unicorn, Äkta Avant, Äkta Explorer, GE Healthcare, Windows, Netzwerk-Authentifizierung, Benutzer-Einrichtung, Methode, Resultat, Wissenschaft, ProteinaufreinigungSince we are operating our Äkta Avant in a multiuser environment, we need to separate the methods and results of the different users. By default, every network user is at the moment able to see every method and every result that has been generated on the machine by any other network user. This is a considerable privancy and security issue as a malicious user could delete (or even worse: modify) methods and results.Our Äkta is set up in a way that allows users to log into the Unicorn 7 computer with their university login/password via the regular Windows network authentication mechanism. However, if several people share the responsibility of a run, this setup becomes impossible as they would need to devulge their passwords to each other. Hence we have created a local account which can be used by users who wish to share the operation of the Äkta.After logging into Winodws, users still have to log into the Unicorn 7 software, which users do with their university login and password (“Windows authentication”). Using this setup, every user is able to see all methods and results, which is not acceptable.When setting up a new user with Unicorn version Access>Folders") and exactly which folders were accessible by that user and the user would see only his/her own methods and results. Since the folder structure under Unicorn 5 was a folder structure of the Windows file system, users could always copy methods and results from one folder to another and thereby make them available despite the limitations set by the Unicorn 5 program.When I first read that Unicorn 7 supports Windows network authentication, I had hoped that we would be able to avoid the painful user setup which we had to go thru for each user on the Äkta Explorer. However, the pain continues as setting up the user privileges once for a group doesn’t give us user isolation.Firstly, one cannot restrict access of individual users in Unicorn 7, but only access of groups. We had to create one Access Group for each network user, add the network user to this group, create a separate home folder for the group and then restrict the folder access to this home folder. Hundreds of clicks were required for a handful of users since the default is no access to anything and every single privilege check box needs to be enabled except for the admin privileges.In that respect, Windows (and every other OS) is way smarter than Unicorn. If a university employee logs into a machine that he or she has never been logging into before, it creates all the necessary default local folder structure automatically and mounts that users private home folder without granting access to everything other employees have been doing on that specific machine. I think that should be an option on Unicorn as well. Maybe it is and I just can’t figure it out?Another big drawback of the above described method of separating each user into an own access group is that login into the Unicorn program becomes a major ordeal: In addition to writing user name and password the user has to select the correct access group for the login to be successful. And even worse: In our setup we cannot avoid that every university employee belongs to two access groups: A manually created access group for each user for user separation and the “default” which works via the Windows network authentication - maybe Kerberos?). Hence, if users do choose the default access group (which is called “Users” in our case), they are able to log in, but they don’t see their methods and results.There are two reasons we cannot delete the “Users” access group: One is the mandate of the faculty and secondly (and we have tried), we cannot delete it anymore as many people have already created methods and generated results being in the access group “Users”. Thus UNICORN prevents us from deleting this account. I am working on this problem: I should be able to access directly the underlying MS-SQL database in order to change the ownership of the methods and results. However, GE was not exactly forthcoming when I was asking about access right handling. The answer was:The DB access credentials in a standalone UNICORN solution are encrypted and are not public. If you had an enterprise solution (hosting your own (SQL server) DB) you would have control of the credentials and in theory you could extract the wanted information (the format is something that you have to figure out by yourself and is not supported by us). You can upgrade your solution to an enterprise if you want.This sounds worse than it is, because we have physical access to the MS-SQL server and pulling out the access credentials seems not very difficult. But it takes my time to find the exploit to “break into our own system” and that is what annoys me. However, according to Lisa Bromark from GE, the 7.0.2 update seems to correct this issue:UNICORN can be configured to use a new database password. It is possible to generate an encrypted password or to enter an already encrypted password. This is done by running the UNICORN Service Tool after UNICORN installation.However, it is unbelievably difficult to get the update (at least it seems to take weeks). Distribution is apparently still via optical media and snail mail. I think the last time I got myself software via a CD/DVD was more than 10 years ago. However, GE told me that they are just moving UNICORN software updates to “electronic distribution”. Welcome to the 21 century!

Echtes Biohacking

Mon, 13 Jun 2016 00:00:00 +0000

Steven Novella hat einen interessanten Blog-Artikel ūber Biohacking geschrieben. Ich schliesse mich seiner Meinung grösstenteils an, dass die meisten diesen Begriff zu Unrecht fūr sich in Anspruch nehmen, weil sie eben nichts konzeptionell Neues machen, was diesen neuen Begriff rechtfertigte. Allerdings haben sich für die Anwendung dieses Begriffes und seine Abgrenzung zur DIY-Biologie und diversen Körper-Modifikationsbewegungen noch keine einheitlichen Maßstäbe etabliert.Die Definition von Biohacking als die “Freiheit, seine Biologie tiefgrūndig zu erforschen” ist weitgehend nichtssagend. Das Wort Hacking hat im allgemeinen Sprachgebrauch meist den Beigeschmack des Illegalen oder zumindest des Halblegalen. Diesem Sprachgebrauch folgend könnte man Doping im Sport als Biohacking bezeichnen, Kaffeetrinken aber eher nicht (einmal davon abgesehen, dass Kaffeetrinken zumindest für einige Leute den Tatbestand des Doping erfüllt). Ein anderes Beispiel, das ich als “echtes” Biohacking bezeichnen würde wäre der Gebrauch von Crispr/Cas um seine eigene DNS zu editieren. Oder die Herstellung von Medikamenten in der eigenen Garage.Die Frage ist: Macht irgendeiner sowas? Gentechnologische Verfahren und die Herstellung von Pharmazeutika sind im universitären und kommerziellen Bereich streng reglementiert, weil solche Verfahren einige Risiken mit sich bringen. Es ist daher nicht verwunderlich, dass die regulierenden Behörden sich nicht darüber freuen, noch eine weitere Szene auf Anzeichen von Bioterrorismus überwachen zu müssen.Tatsächlich wird es immer leichter, die diesbezüglich notwendigen Werkzeuge herzustellen und zu benutzen. Biotechnologie in der Garage ist Wirklichkeit, zumindest hat die Zeitschrift Nature diesem Thema ein News Feature gewidmet. Schon vor geraumer Zeit habe ich einen Vortrag gehört von Thomas Landrain, einem der Köpfe hinter dem La Paillasse-Labor (Thomas: du hattest versprochen, die Internet-Seiten von La Paillasse ins Englische zu übersetzen!), einem Biotechnologie-Laboratorium, dass ohne Startkapital in einer Pariser Vorstadt-Garage gegründet wurde und dass wirklich interessante Projekte durchführt (hier ein Artikel von Thomas Landrain über DIY-Biologie ). Und auch Konferenzen wurden schon zum Thema DIY-Biologie veranstaltet: https://www.synenergene.eu/news-item/paris-conference-what-can-do-it-yourself-biology-do . Aber wo ist die Grenze zwischen DIY-Biologie und Biohacking? E. coli-Bakterien zu modifizieren, damit sie Erythropoietin herstellen, dann das Protein aufreinigen und in sich selbst injizieren, um seine sportliche Leistung zu verbessern würde wahrscheinlich jeder als Biohacking durchgehen lassen. Meiner Meinung nach ist dieses Beispiel gar nicht so abwegig, sondern wäre durchaus mit den Mitteln der heutigen DIY-Biologie realisierbar.

BSD and Linux

Fri, 10 Jun 2016 00:00:00 +0000

I am used to the fact that a Linux installer honours a pre-existing install of Windows and offers to setup the computer with a dual-boot option during installation. Vice-versa no Windows installer honours any other pre-exisiting OS. Therefore I was surprised that when I tried to install Ubuntu 16.04 on my PFSense box (FreeBSD), the Ubuntu installer did not even see that a BSD install exists on the drive. I chose the “erase all” option, but when I rebooted after the installer has finished, the system went straight into PFSense without giving me any option to select Ubuntu. I guess the boot loader had not been touched by the Ubuntu installer. I booted from a live Ubuntu USB stick, reformatted the drive with fdisk and wrote zeros to the boot loader:dd if=/dev/zero of=/dev/sda bs=512 count=1Then I repeated the install and everything was fine. However, my PFSense installation was lost…

Netstat

Fri, 10 Jun 2016 00:00:00 +0000

To list all ports that a server is listening to:sudo netstat -plnt

Real biohacking

Mon, 23 May 2016 00:00:00 +0000

I have read an interesting blog post by Steven Novella about biohacking . I completely agree that most people that push biohacking are not doing anything, that would justify the use of the term. A new term should be used if you are doing something conceptually new. However, the use of the term biohacking and its relationship to DIY biology and diverse body modification movements has not settled yet.The definition of biohacking as the “freedom to explore biology deeply” makes the term rather meaningless. Hacking as a term has always carried the notion (rightly or not) of doing something illegal or at least borderline legal. To follow this analogy, doping in sports could be considered biohacking (but not drinking coffee - notwithstanding the fact that coffee does fulfil the criteria of doping for some people). Other examples that I would call “true” biohacking would be the use of Crispr/Cas to modify your own DNA. Or developing medical drugs to treat diseases in your own garage.The question is: does anybody do such things? The development of such techniques is highly regulated in both academic research and commercial enterprises and real genetic engineering carries real risks. Not surprisingly, law-enforcement officials are not very happy about still another subculture to watch for signs of bioterrorism . However, the tools are getting easier and easier to use and garage biotech is a real thing (at least Nature thought it is worth a News Feature ). Already a while ago, I did listen to a talk by Thomas Landrain, one of the brains behind the La Paillasse lab (Thomas: you promised that the La Paillasse web pages would be translated into English!), which is a biotech lab that was started with zero money in a garage in a Paris suburb. They are doing quite interesting research (see e.g. this article about his take on DIY biology). There are also conferences about DIY biology: https://www.synenergene.eu/news-item/paris-conference-what-can-do-it-yourself-biology-do . But when does DIY biology become biohacking? Modifying E. coli bacteria to produce erythropoietin and then purifying and injecting it into yourself to increase your sports performance would certainly qualify as biohacking. Imho that example would actually be feasible considering the state of the DIY biology technology…

Python für Kinder

Thu, 05 May 2016 00:00:00 +0000

Mein Sohn lernt gerade Programmieren. Und es macht Spass. Zuerst haben wir zusammen ein bischen in html und php programmeirt, da er ein Online-Quiz auf seiner Website machen wollte. Danach haben wir angefangen, das (deutsche) Buch “Python für Kids” ( http://python4kids.net ) durchzuarbeiten. Ich habe Python gewählt, weil es eine moderne, leicht zu lesende Sprache ist. Sie ist heute wahrscheinlich die erste Wahl für angehende Programmierer. Python ist Open Source, einfach auf allen Betriebssystemen zu installieren und leistungsfähige Programme können schon nach einer kurzen Lernphase geschrieben werden. “Python für Kinds” verwendet das Turtle-Modul , das eine grafikorientierte Einführung ins Programmieren ermöglicht. Die Grafik oben ist z.B. eines der Ergebnisse.Python ist auch eine sehr gute Wahl für Biologen und Bioinformatiker. Da Python eine Mehrzweck-Sprache ist, ist man nicht auf bestimmte Aufgaben beschränkt (wie z.B mit R). Es gibt mit Biopython ein sehr gutes Modul für den Umgang mit DNA und Proteinsequenzen (und sogar 3D-Strukturen).

Clearing the BIOS password in a HP Compaq Elite 8000

Mon, 18 Apr 2016 00:00:00 +0000

Power the computer down, remove power cable (and other cables that can carry electricity) and let residual charge drain. Open lid and remove the green jumper. Reboot and you’re done. Maybe you want to put the green jumper back not to loose them (you can also apparently leave it attached to pin 1 or pin 2, but not connect both pins).

BackupPC and Macs

Wed, 13 Apr 2016 00:00:00 +0000

I myself have been using the backup software BackupPC for almost a decade, and I started to backup our lab computers to a central backup server about two years ago. BackupPC supports deduplication and therefore much data can be stored on a couple of 2 TB drives.BackupPC supports many protocols (smb, ftp, tar/rsync via ssh), but we mostly use rsync via ssh. The data is not encrypted before the backup. Strangely not even the upcoming version 4 will support pre-egression encryption. However, we store the backup on an encrypted volume. That way it is at least protected if the backup server is stolen. And during transit, the data is protected by ssh. However, the system is not TNO (“trust no-one”), since I (as the backupc administrator) can access the files. When using Linux, one feasible method would be to encrypt the user’s home directory using eCryptFS (which is an inbuilt option when creating users on Ubuntu ) and then backup the /home/.ecryptfs directory instead of the users home directory. However, recovery would be much more of a problem. You would be able to browse the diectory structure and files of the backup, but the filenames would be meaningless since they are also encrypted in the process.There is one peculiarity in backing up Mac OSX machines: BackupPC normally connects as root via ssh into the client computer and executes the rsync backup command. In order to make this possible on university-managed Mac OSX computers, we had to create a dedicated user (“backuppc”) on the client machines and allow for this user the execution of rsync with root privileges, which is done by adding this line in the /etc/sudoers file:backuppc ALL=NOPASSWD: /usr/bin/rsync. Then we have to change the ssh/rsync command for the Mac client on the backuppc server changing “root” into “backuppc”.

dd a broken DVD

Thu, 07 Apr 2016 00:00:00 +0000

dd if=/dev/sr0 of=image.iso bs=2048 conv=noerror,notrunc iflag=nonblock

Test iframes

Mon, 04 Apr 2016 00:00:00 +0000

Essential git

Tue, 01 Mar 2016 00:00:00 +0000

git pull origin mastergit push origin mastergit commit -m "comment" -a https://www.linux.com/learn/tutorials/824358-how-to-run-your-own-git-server

Taj Mahal

Mon, 08 Feb 2016 00:00:00 +0000

One and a half years after our last big LEGO project (the big Millenium Falcon ), we finished now the Taj Mahal , which is with 5922 parts the largest LEGO set ever released for retail. Again, we used our existing LEGO parts and only bought the missing ones via Bricklink from four different online shops.

SnapGene - Simply the best DNA manipulation software

Fri, 01 Jan 2016 00:00:00 +0000

Our lab has been using different software packages to plan, document and visualize DNA constructs. Among those that we liked a lot for a long time were Textco’s GeneConstructionKit (GCK) and Clone Manager (Professional) . The latter runs unfortunately only under Windows. However, since several of our computers run Ubuntu Linux , we did run GCK versions 2.5 and 3 using WINE (a compatibility layer that allows us to run native Windows programs under Linux). However, with the upgrade to version 4, GCK became unusably slow under WINE and we were looking for a replacement. We contacted the developers of GCK, but they apparently were either not willing or able to help us. I suppose that the codebase of GCK is probably more than 20 years old and for that reason nobody dares to touch it. Just around that time, SnapGene was released and it fulfilled almost all of our requirements:

Managing OpenVPN with Network Manger

Thu, 05 Nov 2015 00:00:00 +0000

I just switched back from MacOSX to Ubuntu for work. Mostly for financial reasons. We need more computers at work and a really good PC laptop is just half as expensive as a MacbookPro or iMac. Today I wanted to connect from home to the University’s VPN network and I had a look at the instructions provided by the university.As usually, documentation was virtually absent and what was available was wrong. And exclusively in Finnish ( http://www.helsinki.fi/helpdesk/ohjeet/tietoliikenne_ja_etakaytto/yhteydet_yliopiston_ulkopuolelta/vpn_ubuntu-asennus.html) . From the image (Hardy Heron) it is clear that this page has not been updated for about at least 6 years (Hardy Heron was realased in the beginning of 2008).So what do you do if you downloaded and extracted the hy-vpn-config.tar.gz file from https://ohjelmistojakelu.helsinki.fi?First you need to install a plugin for the Network Manager: sudo apt-get install network-manager-openvpn network-manager-openvon-gnome. Then you go to the Network Manager via the icon in the menu bar on the top right of your Desktop. Below all the available wireless networks, there is an entry “VPN Connections”. Follow “VPN Connections” -> “Configure VPN” -> “Add” -> “Import a saved VPN configuration” -> “Create”. Then select the “openvpn.conf” from the downloaded and extracted files. After that, fill in the rest of the dialog box: User name, Password. For the CA Certificate, select the “HY-vpn-CA.pem” file from the downloaded files (you should have put it first somewhere safe, e.g. to “/etc/openvpn”).One problem that people are complaining about is the fact that the import does not honor the “redirect-gateway def1” directive and as a consequence you won’t be able to connect anywhere (I guess this is due to the Network Manager using dnsmasq and dnsmasq is apparently not smart enough to realize that it should send the queries somewhere else now). That’s why people are complaining that Network Manager doesn’t work to route all traffic via the VPN network. The box that you need to uncheck for this to work is well hidden: It’s in the connection editor dialog under the IPv4 Settings tab -> Routes (at the bottom right) -> “Use this connection only for resources on its network”. Why on earth do they have to call it in a way that nobody understands its meaning? Why not to call it “Do not route all traffic through this VPN connection”? I also had to check the box that said “Ignore automatically obtained routes”, although I don’t know why…As usual, setting up the OpenVPN sucks and the important tunneling back of VPN traffic needed to be added manually on the OpenVPN server:iptables -t nat -A POSTROUTING -s 10.8.0.0/24 -o eth0 -j MASQUERADEI did it by making an additional file called openvpn2 in the /etc/network/if-up.d/ directory with the following content:#!/bin/shiptables -t nat -A POSTROUTING -s 10.8.0.0/24 -o eth0 -j MASQUERADEOf course you can still start and stop the VPN via the command line. However, since systemd, the password entry is not straightforward. When you execute sudo systemctl start openvpn.service you need to execute (e.g. in another terminal) sudo systemd-tty-ask-password-agent and enter your password there. That’s clearly a kludge until they get a decent password agent…

Neon electroporation device chickens out

Tue, 04 Aug 2015 00:00:00 +0000

UPDATE: We are not the only ones that try to economize on our running costs. This lab published its experiments in with the Neon system in Analytic Biochemistry . Thanks to Joachim Goedhart ( @joachimgoedhart ) for bringing this to our attention! The Neon transfection device from Life Technologies (oops, Thermo Fischer nowadays and former Invitrogen ) was introduced about five years ago to the market. It is designed for easy electroporation of mammalian cells. We have had the device available since 2011, but it was not much in use. I don’t know whether the low adoption rate is due to the user-unfriendliness (I still don’t know how to put the electrode tip to the pipettor despite having done this hundreds of times, it’s just really finicky mechanics), expensive running costs (for its desposible gold-plated electrodes and the proprietary transfection buffer) or something else I cannot figure out.However, there are a few things that I wanted to share because real useful information about the Neon device is scarce on the web.The first thing that we had constant problems with were air bubbles in the electrode tip, which result in desastrously low electroporation efficiencies. The only way to really prevent this is to prepare at least 25% more cell suspension than actually needed. When you prepare only 10% more, the last electroporation will certainly arc due to unaviodable air bubbles (the cell suspension additionally sticks easily to the outside of the pipette tip which contributes to the need to prepare more than actually needed). As a consequence of this, we ran out of electroporation buffer R long before we ran out of pipette tips. Additionally one cannot purchase buffer R separately. The Life Technologies representative with whom I corresponded promised to send us a small batch of pipette tips/buffer in good will (that was in January), but we are still waiting for that to arrive…Unforatunately, recently our old Gene Pulser II electroporation device broke. Bio-Rad doesn’t repair it anymore and also doesn’t provide spare parts. It was mostly used for E. coli electroporation. I knew that the Neon device was not designed to electroporate E. coli. Why not and why can’t it be used for that purpose? It turns out that the electric field strength is by far not enough for E.coli (in the BioRad Gene Pulser II, a typical bacterial electroporation achieves an electrical field of 12.5kV/cm, whereas the Neon barely achieves around 850V/cm. However (I thought), the neon can do much longer pulses than the Gene Pulser II (Neon is advertised to be able to give pulses up to 100 ms, whereas the typical pulse length of the Gene Pulser II is about 5 ms). In addition to this, the Neon can deliver automatically multiple pulses. So I wanted to test whether a long and/or repeated pulse with lower field strength can transform E. coli. However, it appeared that when you use water (or 10% glycerol) as the E. coli transfection buffer (which you usually do), the machine complains the tip electrode doesn’t make contact. This is due to the fact that the machine tests whether you have inserted the tip correctly by sending a small current through the system and that current doesn’t flow if you have resuspended your E. coli in water. In order for the machine to “accept” an inserted pipette tip electrode, you need somewhere between 10 and 20 mM NaCl. So I used 15 mM sodium chloride as E. coli electroporation buffer and set the electroporation parameters to 2500V and 100 ms. Surprise: The machine refuses to give such pulse because it is “Over power limit!”. The maximum pulse length it can deliver with 2500V is 19 ms. Unfortunately even that pulse cannot be given automatically multiple times (again: “Over power limit!”). Therefore I manually executed this pulse between 1 and 20 times, but not a single bacterium received any DNA and all bacterial plates remained blank.The manual states:"The Neon TM device is designed to only input certain values and limits for each value are listed below. If your input value exceeds the maximum value, an error is displayed.Input Voltage range: 500–2,500 VInput Pulse Width range: 1–100 msInput Pulse Number range: 1–10Unfortunately, this can be very easily misunderstood. It was not clear to me that one cannot combine the three parameters within these ranges freely. One should think that Life Technology has better technical writers (but maybe they don’t use the device…)Bottom line: The device is utterly useless for anything but mammalian cells. Also some other interesting applications (e.g. electroporation of nematodes or other small critters) are difficult or impossible. While the machine might be a good choice for many mammalian cells, it’s much more limited than the old-fashioned BioRad Gene Pulser II.P.S.: I used the buffer E to fill the pipette station (for use with 10 µl tips). However, I also tested instead of buffer E a mixture of 90% 150 mM sodium chloride and 10% glycerol (which gives me the same conductivity as buffer E has). However, I still really would like to know the composition of buffer R. Why? Because I think that the tip electrodes can be recycled more often than only twice (other manufacturers of pipette tip electrodes advertise that their electrodes can be recycled many more times (e.g. the BactoZapper , although they don’t give precise numbers either). The Neon manual states that “Oxide formation at the piston surface area can be generated if the tips are used more than 2 times, which decreases electrode function of the piston.” The electode is gold plated and gold should be more resistant to oxide formation than the stainless steel electrodes of the BactoZapper…

Strawberry fields forever

Sun, 02 Aug 2015 00:00:00 +0000

Seldom does one find wild strawberries in amounts that allow you to pick liters, but this summer we did. I hope that genetic engineering will sooner or later bring back this amazing taste into the cultivated varieties, which have lost most of it over the centuries of breeding for size and appearance. When that happens, I suspect that GMO opponents will continue eating the conventional, GMO- and taste-free, but pestidicide-surcharged breeds (read more about GMO plants).For now, we have to make do with the cultivated varieties. Cultivated strawberries are sold at the grocery store by weight, whereas on the market they are sold by the liter. Being frugal by nature, I never liked this as it makes comparing prices difficult. Assuming that strawberries can be approximated by equally sized spheres, the maximum theoretical packing density could be 0.74 kg per liter (using regular packing) and 0.63 kg per liter (using random packing). Assuming that strawberries can be squeezed a bit, these number could be slightly higher. However, this is again offset by the measuring jar’s small size, which leaves lots of slack space between the walls and the strawberries.I bought a few times 1 liter of strawberries and measured their weight, which averaged at 0.517 kg. Now my thumb rule is that if the liter price it equal or less than half of the kilogram price, you should buy by the liter.UPDATE: I measured now also blueberries and they (due to their smaller size) fill better the 1-liter jar used by the market vendors. I liter is approximately equal to 0.575 kg. Another take home message is that market vendors do usually give you a bit more. If you buy a liter you often get 1.05 or even 1.1 liters. Are they are generous or do they only respond to being watched by the customer during the process of weighing?

Helkama Jääkäri - everything but the frame broke within the first 3 years

Thu, 07 May 2015 00:00:00 +0000

For one last time, I have to write about the Finnish bicycle company Helkama . I own the Helkama Jääkäri , which is a military style bicycle and marketed as extremely tough. The frame has 25 years warranty. However, pretty much everything else has been braking within the first 3 years, which ridicules the whole concept. During this year’s spring overhaul, I had to replace three parts: The stand, the saddle and the bell. And I see already signs of future trouble… In none of my previous bikes, saddle or stand have been breaking that fast. And that includes cheap bikes for half the price that I paid for the Jääkäri. Apparently, Helkama does not vet its component suppliers sufficiently. My Jääkäri’s rear wheel had to be replaced already after the first winter and the carrier meanwhile two times. When it broke the third time, I did not even bother to get it replaced again, instead I repaired and reinforced it myself . I really hope that Helkama’s advertisement is just a lie and that the Finnish Army does not use this bicycle.

Thank you, Lufthansa!

Thu, 30 Apr 2015 00:00:00 +0000

In the morning of September 25th, 2014, I was waiting at Helsinki Airport to board Lufthansa flight LH 855 to Frankfurt where I was to change planes on my way to Genoa, Italy. I had been invited to give a talk at 2:45 pm at the 40th Congress of the European Society of Lymphology. I had only 1 hour 10 minutes stopover time in Frankfurt. 1 hour 10 minutes after the scheduled departure time, me and a few other passengers had not yet managed to board (they had boot problem with their computer system and people were checked in manually). I explained the desk attendant the situation and he said that it would be absolutely no problem to get a refund in this situation when I would decide not to board as I had no chance to catch my connecting flight. They apparently had overbooked the machine and the guy next in line was very happy when I gave up my seat. However, the desk attendant was not right, when he told me that getting the refund would be easy. Actually I have not received it by the time of this writing. However, I got assured by a phone call from Lufthansa, that it would happen within the next two to three weeks.In the frenzy to be competitive, Lufthansa has been streamlining its services to such a point that they apparently are dysfunctional. My first attempt to claim refund was via the regular route: online. When nothing had happened for 3 months, I phoned. Multiple times. Mostly to be cut of after having been in the waiting queue for 15 minutes or more. Then I wrote a physical letter to a UK address that Lufthansa had posted online for customer complaints. That letter came back after about 2 months: “address unknown”. Then I wrote another letter to the new address (they finally managed to update their web pages) and after another couple of weeks, I received that phone call from Lufthansa. Very apologetic. This should never have happened. They sent me two bottles of champagne, which arrived by courier, while I am still waiting for my money. I am flying next month to Switzerland to the 41st Congress of the European Society of Lymphology. I am flying Finnair.

Creating a video from webcam still images with crontab and ffmpeg

Wed, 29 Apr 2015 00:00:00 +0000

I have a webcam that is taking images when there is movement in its view field. It uploads them to a ftp server. I wanted some automated method to generate a video file from the images of the previous day. Finally I came up with the following shell script which is living under /etc/cron.daily:#!/bin/sh## cron script to make a movie out of webcam stills## The webcam puts the images of the whole day into a folder with the date. This generates the target folder.foldername=/home/ftpuser/labcam/$(date -d "-1 days" +%Y%m%d)echo $foldername# This renames the iamges into 1.jpg, 2.jpg, etc. This is necessary for ffmpeg to recognize them. counter=1for i in $foldername/*.jpg; do new=$foldername/$counter.jpg echo $new cmd='mv $i $new' eval $cmd counter=$((counter+1))done# This does the actual conversionffmpeg -f image2 -framerate 25 -i $foldername/%d.jpg -c:v libx264 $foldername/out25.mp4# And this removes the jpg files from the target folder (in order to save space)cmd2='rm '$foldername'/*.jpg'eval $cmd2

Helkama quality woes

Sun, 25 Jan 2015 00:00:00 +0000

This post is a follow-up of my post from 2 years ago about my new bicycle, a Helkama Jääkäri . It had its fair share of problems, and even though the customer service was very responsive, the repetitive problems with its luggage carrier were too much for me. Last December, the third carrier broke. I had received also the this one as a free-of-charge replacement, but it is a nuisance when it breaks, even though replacing takes only about 10 minutes. It is not in very heavy use: the stuff I transport on it weighs about 2-3 kg, but apparently the welded/soldered connections are prone to fatigue breakage. Helkama knows that it has a quality problem with its carriers. When I asked for the second replacement carrier, the customer service told me, that they are trying to identify a suitable replacement for the subcontractor who makes these carriers. This time I thought to repair the carrier instead of asking for another replacement, which took less time and will probably last longer. I don’t know whether they have changed their component supplier. If my own repair breaks, I still have two old broken carriers I can repair, but most likely, my next bicycle is not going to be a Helkama .

The car is in the garage

Tue, 30 Dec 2014 00:00:00 +0000

Finally Claudia’s car is in our heated garage. After moving two thirds of our cellar’s content and half of our apartment’s content to our garage, it appeared questionable whether a car would still fit. I installed many additional shelves and relocated my and Marzena’s bicycles to the condo’s common bicycle storage. The other 7 bicycles and the bicycle trailer were hanged to hooks along the garage walls. Then we lifted Tobias’ 3.5 meter long cardboard rocket tightly under the garage ceiling. Finally I was able to drive it in. I drove in sort of blindly because the car had been snowed in so badly that me and Tobias could not really make any difference by scratching its windscreens half an hour (we had to stop because our fingers were too cold to continue). The snow and the cold had arrived here in Helsinki quite exactly together with the winter solstice.

Vor 25 (oder noch mehr) Jahren

Fri, 14 Nov 2014 00:00:00 +0000

Vermutlich haben alle, die sich dafür interessieren, schon die Fotos angeschaut. Trotzdem hier nochmal der Link zu den gescannten Diapositiven von unserem Segeltörn im IJsselmeer und dem Literaturkurs bei Frau Herzig: http://gallery.jeltsch.org/index.php/1989 . Einige Schwarzweiss-Portraits und andere interessante Negative warten noch darauf, wiederentdeckt zu werden…

Download SnapGene

Fri, 31 Oct 2014 00:00:00 +0000

You can get a registration code (which is valid until the end of 2014) from the course organizer.

Ubuntu is slowly getting unusable

Mon, 01 Sep 2014 00:00:00 +0000

The default Document Viewer in Ubuntu 14.04 is Evince. Recently it started to have problems with many PDF files that are opened by other PDF viewers (Okular, Acroread) without problems. Actually Evince opens them, but the window remains invisible. I tried to change the PDF viewer, but Ubuntu has apparently removed all means to do so in version 14.04 short of going into the command line and editing configuration files by hand: what a progress! In previous versions of the File Manager, it was possible to right-click a file and after selecting “Open with” > “Other Application” to choose “Set as default”. Now the only way to do so is to edit ~/.local/share/applications/mimeapps.list, replacing [Default Applications]application/pdf=evince.desktop with[Default Applications]application/pdf=kde4-okularApplication_pdf.desktop; I guess it is time to switch back to OpenSuSE…

It is finished

Sat, 30 Aug 2014 00:00:00 +0000

After one year of gathering pieces and building, Tobias and me finished today the Millennium Falcon Ultimate Collector’s Edition (LEGO set 10179, http://brickset.com/sets/10179-1/Ultimate-Collector-s-Millennium-Falcon) . This version of the Millennium Falcon is not sold anymore and used sets sell for insane prices on Ebay.We took the necessary bricks from two other Star Wars models: the Death Star (LEGO set 10188, http://brickset.com/sets/10188-1/Death-Star ) and the Super Star Destroyer (LEGO set 10221-1, http://brickset.com/sets/10221-1/Super-Star-Destroyer).However , we had to gather a substantial amount of missing parts, many of which we bought 2nd hand via the local Finnish online action site http://huuto.net or via BrickLink ( http://www.bricklink.com ), a sort of “specialised EBay” for LEGO pieces. The most difficult to find pieces were the two Light Bluish Gray Boat Mast Rigging Long 28 x 4 ( http://www.bricklink.com/search.asp?itemID=56261&colorID=86) , which sell at the moment for not less than 100€ per piece on BrickLink. We obviously did not get these pieces. However, LEGO still sells the black version of this piece as a spare part and Tobias’ mentor took the trouble to get these and paint them grey; thank you Clemens!

Fiddling around with CSL

Wed, 06 Aug 2014 00:00:00 +0000

When writing manuscripts and grant applications, you always and again have to update the bibliography. This is what reference management systems are for. There are many of them (see http://en.wikipedia.org/wiki/Comparison_of_reference_management_software) . I have been using mostly EndNote, Bibus or Zotero ( http://www.zotero.org ), which I am using also at the moment. It has the advantages to be truly cross-platform, open-source and compatible with both LibreOffice and Microsoft Office. In the past, I have also been using for a short while Papers (by Mekentosj, who claimed they NEVER would do a Windows version), Bookends, Mendeley, and RefWorks (which is licenced by my university). None of them is perfect and even the most commercialized of them (Endnote, now owned by Thomson Reuters) destroyed one of my (MS Word) manuscripts totally when it crashed. Some of these programs store the formatting instructions for inline citations and the bibliography in the so-called CSL (Citation Style Language, an XML-type language, http://en.wikipedia.org/wiki/Citation_Style_Language).However , I could not find an easy editor for CSL: the in-built one from Zotero is not great, neither is the online CSL editor ( http://editor.citationstyles.org/visualEditor).However , I needed a way to quickly export my own published papers to create a “List of Publications” for grant applications. Hence I created a group in Zotero and added all my own publications into this group. I now mark them all, right click and select “Create Bibliography from items”. In the pop-up dialog, I choose the style and mark the radio-buttons “Bibliography” and “Copy to Clipboard”). Back in my word processor I just have to paste the clipboard and I most of the work is done. However, I could not find any good style for this, so I created one myself (which is based on Vancouver). Feel free to use it…

Where did the Nautilus scripts folder go in Ubuntu 14.04?

Thu, 26 Jun 2014 00:00:00 +0000

After upgrading from Ubuntu 12.04 to 14.04, my Nautilus scripts stopped working. The reason: they are polled from a different location in 14.04. In 12.04, they used to be in ~/.gnome2/nautilus-scripts, but now they are in ~/.local/share/nautilus/scripts. I think the link above still has not been updated to reflect the new location.

Stuff the Maverick upgrade broke

Tue, 24 Jun 2014 00:00:00 +0000

My 1.5 year old MacbookPro was starting to behave badly including failure to complete booting and other niceties. The computer support guy suggested to upgrade from Mountain Lion to Maverick to see whether it would fix things.Initially that seemed to work; however, many programs refuse to run under Maverick. This includes: Gnumeric and (importantly) nfs. It appears that mounting nfs via the finder is not anymore possible. However, I still am able to do it via the command line (using the resvport option, which should not be necessary, but which nevertheless does the trick):sudo mount -o resvport -t nfs mcblserver:/var/www /Users/mjeltsch/nfs And talking about Gnumeric: I guess I need to compile it newly for Maverick myself…

Poster printing without an A0 printer

Thu, 15 May 2014 00:00:00 +0000

I failed to prepare my poster for the GRC conference on Molecular Mechanisms in Lymphatic Function & Disease in time. The A0 printer from UNIGRAFIA is not available on weekends. Hence the best I could do is to print it out on A3 and stitch it together. A definite advantage is that I do not have to run around with these ridiculously large poster tubes, that identify you as a Science nerd from half a mile distance.Unfortunately, the only application that can decently split a DIN A0 PDF into separate pages on the fly while printing is the full version of Acrobat. I tried out other options: pdfposter did a fairly good job, but it did not manage with the background: pdfposter -mA3 -pA0 input.pdf output.pdf Pdfposter also doesn’t create overlaps. A solution, that always should work is to convert the PDF into an image (convert -density 150 input.pdf output.png) and then use PosteRazor to create individual PDF files from that image. However, conversion of a A0 pdf into a high res image can last hours. Use a .png file! PosteRazor refused to work on a 60 MB TIF file. The background gradient conversion results in visible colour steps. In order to avoid that, you would have to define the background gradient as an image rather than a vector element. Otherwise PosteRazor worked well; unlike in pdfposter you can define overlaps for the assembly.I have been using Inkscape to prepare my poster and usually I export it from there as a PDF file. This did not work this time because the program consistently crashed during the export. Hence I tried to save it as an encapsulated postscript file and to distil it into a PDF. When exporting from Inkscape (actually it is “Save as”), I selected the following options:Postscript level 3Rasterize filter effects: yesResolution for rasterisation: something between 150 to 300Export area is page: yesAfter distilling it, I printed it from Acrobat Pro with the following options: Page setup: DIN A3, portrait orientationPage scaling: Tile large pagesAt a tile scale of 95% and an overlap of 10mm I got 9 pages (3x3), which is still OK for assembly.

Getting Ubuntu Trusty Tahr onto the CuBox Pro

Wed, 14 May 2014 00:00:00 +0000

eUPDATE: The Cubox guys have moved the documentation about how to install to the Cubox Pro. If you need Trusty Tahr for your Cubox Pro, you can download a 4GB image: https://drive.google.com/open?id=1CgbSfy17-UrWZwBjZtZpHYTkPgw0MXFq . You just need to write it to an SD card (using dd) in order to get your system going. If you have a larger SD card, never mind: just dd the image to the SD card and then use gparted or something similar to expand the second partiton (the root partition) to fill the entire SD card. Password/login: cuboxpro/cuboxpro. SSH is enabled, so you should be able to login remotely. It’s the desktop version, so you can also connect an HDMI cable and login via the GUI. There is still a youtube video ( https://www.youtube.com/watch?v=XfLJAchNu2c ) on how to use the original cubox installer ( http://download.solid-run.com/pub/solidrun/cubox/installer/) , but the latest version of Ubuntu that you can install with that method seems to be 13.10 at the moment of this writing. I have been buying a CuBox : perhaps the world’s smallest desktop computer. Both at work and at home I need to replace an old, loud LAMP server with something modern. I don’t even need a GUI, I am happy to run the server headless. Neither do I need much much speed.The CuBox seems like a great idea: No noise, little power consumption, no space requirements and a decent performance. However, getting it to work was far from trivial. It is definitely not an end user toy, but aimed at the tinckerer. The first difficulty was buying the box. The producer didn’t sell it directly at the time (now they do) and the only company that sold it to Finland was UK-based NewIT . Because on the producers homepage they only present their newest models (the “CuBox-i” models), I wasn’t even aware of how many different models they had released. I actually bought the CuBox Pro (but I didn’t know about it, because there is also the “CuBox-i4Pro”, which is the one I rather should have bought. Israel-based SolidRun could do definitely a better job with their web pages. They seem to have a rapid product cycle and drop quickly all links to their “older” products from their main page. This is irresponsible especially since these products are still sold.I bought the device shortly before Ubuntu 14.04 LTS (Trusty Tahr) was released with the intention to install the server version on this device. I bought it with the 4GB SD card with the preinstalled ancient Ubuntu 10.04 (Oneiric Ozelot). I connected it via HDMI to our (not full HD) TV screen and at least the first boot succeeded and the desktop appeared usable, although not snappy. But what the heck, I want to use it as a sever.So the first thing I tried to do was to upgrade to 14.04. I was sure that this would work because the community is stepping in where CuBox fails. Namely by providing ready-to-go disk images to flash to the SD card. I tried Arch Linux, Debian and an early Ubuntu 14.04 release. However, when I inserted the SD card after flashing, the CuBox did not want to boot.Because the Oneiric image (which came on the 4GB card with the device) worked, I flashed it back from a backup (which I had made using dd). Again, Oneric booted up fine. I started to upgrade the distribution to 12.04, which worked somehow, but I lost the graphics display (which I didn’t care about). But then the upgrade from 12.04 to 14.04 failed completely. And I definitely want the 14.04, because I want to set it up and forget about it for the next 5 years.However, none of the images provided (by CuBox or the community) wanted to boot (I don’t even want a GUI, I am fine with a command line access as I want to use it as a server). I have tried flashing them from Windows and Linux, but it didn’t make a difference. What could the reason have been? The partitions on the card are mounted automatically without error when I insert the card to my Ubuntu 14.04 laptop. I finally googled the Model number “CBP-300-P” which is printed on a sticker on the bottom of the cube. I had started to suspect that it is not me, but some incompatibility or broken hardware. I came across this irc conversation and I realised that I had been pulling the OS images from the CuBox-i wiki pages, whereas my model was a CuBox Pro.The relevant forum is here and the instructions do work. The instructions are not for the faint of heart, but also not overly difficult. You need a HDMI connection to a full HD screen (1920x1080). If you have less than that, you need to connect to the serial console using a mini-USB cable from another computer and use a terminal emulator as they explain here . The suggested Putty did refuse to make a connection to ttyS0 (from Ubuntu 14.04), but I managed with minicom. However, there was no color coding, but it worked also without.Because you are running the whole OS from the SD card, you might want to limit memory swapping and do a few other changes to prolong the life of the memory card, essentially the same as is done for SSD drives .

Mounting individual partitions from disk dumps

Thu, 26 Dec 2013 00:00:00 +0000

You can make disk dumps from individual partitions or from a hard drive that contains more than one partition. The ladder has the advantage that you can restore the computer by dumping back the image onto the same or another hard drive. But if you want to access an individual partition from a hard drive image, you need to know where the partition boundaries are. You can note them down from the output of fdisk. However, fdisk -l gives the partition boundaries, but the unit is sectors. You need to multiply this number by the logical sector size to get the partition boundaries in bytes.Alternatively you can use parted (after invoking parted, execute commands unit, B, print in that order) to display the partition boundaries in byte. parted can be also used on a disk dump, e.g. parted /home/backups/diskdump.img to determine the partition boundaries.jeltsch@Michael:~$ sudo parted /home/backup/diskdump.img GNU Parted 2.3Using /home/backup/diskdump.imgWelcome to GNU Parted! Type 'help' to view a list of commands.(parted) unit Unit? [compact]? B (parted) print Model: (file)Disk /home/backup/diskdump.img: 160041885696BSector size (logical/physical): 512B/512BPartition Table: msdosNumber Start End Size Type File system Flags 1 1048576B 524287999B 523239424B primary ntfs boot 2 524288000B 80282124287B 79757836288B primary ntfs 3 80283171840B 160041009151B 79757837312B extended 5 80283172864B 122626684415B 42343511552B logical ext4 7 122626768896B 157924769279B 35298000384B logical ext4 6 157932322816B 160041009151B 2108686336B logical linux-swap(v1)(parted)Then you just mount the image as a loop device with the additional parameter offset using the start boundary of the partition you want to mount:sudo mount -o loop,ro,offset=524288000 /home/backup/diskdump.img /mnt

Prisma Viikki and customer's rights revisited

Wed, 03 Jul 2013 00:00:00 +0000

I bought a lamp from Prisma for 24,95€. Because it was named “plafondi”, I assumed it is a ceiling lamp: “plafond” is French for ceiling. But I was wrong. It was not for attachment to the ceiling, but for wall-mounting (strangely on Prisma’s website it is called “Plafondi-seinävalaisin” which is an oxymoron). I realised that when I saw that the plug was of the regular type and not for a ceiling socket. So I exchanged the plug and attached it to the ceiling. When I screwed in the bulb and turned the light switch, it remained dark. I had bought the bulb (Megaman Liliput 11W E14 thread) together with the lamp from Prisma. I was even more perplexed when another E14 bulb worked perfectly in that lamp.

The old LEGO motors are still going strong

Mon, 24 Jun 2013 00:00:00 +0000

While the LEGO motors of my childhood are still going strong, the motor from the set 8287 broke barely three years after I bought it. Actually the motor is OK, but the battery box or the switch has a slack joint somewhere inside. And what is worse: I cannot get a spare part! I hope LEGO is not following the trend producing throw-away toys. The motors from my childhood (which you can see in the background) are nearly 40 years old. This proves that one can build durable toy motors.

Cyclical PhD production

Tue, 11 Jun 2013 00:00:00 +0000

I was wondering why recently nobody graduated with a PhD from our lab. My first (and wrong) conclusion was, that our lab is not as productive anymore as it used to be. When I looked at the data carefully I discovered an interesting phenomenon: The PhD production rate in our lab follows a 5-6 year cycle. And lo and behold: The cycle is about to peak again in 2013/2014, which is exactly what I expect to happen as many of our PhD students are about to finnish this or next year. I wonder whether this is specific for Kari Alitalo’s lab or whether this a general phenomenon. In any case I am looking forward to all those parties (“karonkka”) that lie ahead.The figure above shows the number of PhDs received any given year that were supervised by Kari Alitalo averaged over a window of one or three years. Shared supervision was counted as 0.5.

Screw cap of Elmex mouth wash always breaks

Sun, 09 Jun 2013 00:00:00 +0000

This is my third bottle of Elmex mouth wash. The screw cap of every single bottle broke, there must be a design flaw!

A view to the Baltic sea

Sun, 05 May 2013 00:00:00 +0000

Just to prove that one can see the Baltic sea from our living room’s window.

Reset MacOSX user passwords

Sun, 28 Apr 2013 00:00:00 +0000

Boot up with command key and S key pressed (Single user mode)
fsck -fy
mount -uw /
password username

Waffel recipe

Fri, 19 Apr 2013 00:00:00 +0000

After some awful experience with an OBH Nordica electric waffle maker (one waffle took about 12 minutes and still was not entirely done), I have bought a cast-iron waffel maker from Skeppshult. After burning it in and several unsuccesfull attempts, I actually manged to make some waffles. However, I have not yet tried to use it over an open fire, but that was actually the idea when I bought it. I used it on our electric oven and one waffle takes about 4 minutes (on position 7-8 out of 9). It has 25 years of warranty and weighs about 4-5 kg. I used the following recipe:

Updating drupal

Tue, 19 Feb 2013 00:00:00 +0000

Here’s what I need to to to update drupal (minor updates, e.g. from 7.18 to 7.19) on my Ubuntu server. I have installed drupal from the drupal source itself and not from the Ubuntu repository (because the Ubuntu repository is usually quite old and not updated as frequently). Actually the update is quite painless; I am sure somebody automated that already somewhere…cd /var/wwwsuwget http://ftp.drupal.org/files/projects/drupal-7.19.tar.gztar -xvzf drupal-7.19.tar.gz chown -R jeltsch:www-data drupal-7.19rm drupal-7.19.tar.gz cp -a drupal-7.18/sites/ drupal-7.19/The above cp command makes a copy of the complete site, which can take a long time and use lots of disk space. Instead, you can delete the “sites” subdirectory in the new drupal folder and make a link to the old “sites” subdirectory:cd drupal-7.19rm -rf sitesln -s ../drupal-sites/ sitesHere you should log into your site and put it into maintenance mode! mysqldump -u root -p --databases drupal7_jeltsch_org drupal7_claudia_jeltsch_org drupal7_lammertlab_org > drupal7_all.sqlrm drupal7ln -s drupal-7.19/ drupal7Here you should click the link to the update script. After the updates were successfully performed you can put your site online again.** ****Drupal 9**Updating Drupal 9 is most easily done using composer:composer update "drupal/core-*" --with-all-dependenciesAlso the modules can be updated. However, in my case the update was not always targeting the module that was actually in use but a module that was lower in the priority list in some other directory. For minor version updates:composer update drupal/modulename --with-dependenciesFor major version updates:composer require drupal/modulename:^2.0After this, don’t forget to visit https://yoursite.com/update.php !

x11vnc as a nxserver replacement

Thu, 29 Nov 2012 00:00:00 +0000

Now that nomachine ’s great nxclient is defunct on MacOS X and its new nxplayer is still in beta (and completely nonfunctional on my setup), I needed another solution to connect to my work desktop from home. I tried many things, but then settled for x11vnc . My work desktop is running Ubuntu Precise Pangolin (12.04) and I connect from a MacOS X 10.8 (Mountain Lion). I only had to install x11vnc and openssh-server on my work desktop and add an x11vnc.conf file to /etc/init with the following content:x11vnc -forever -rfbauth /etc/x11vnc.pass -bg -o /var/log/x11vnc.log -scale 1280x800 -display :0 -auth /var/run/lightdm/root/:0I have to create the password file:x11vnc -storepasswd password /etc/x11vnc.passThen I just have to get into my work desktop by some means or another. At the moment I jump there via the UNIX computers of the university, because direct ssh access is not possible because of a firewall. So I ssh into the UNIX mainframe and from there I ssh into my work computer. Once I am in, I establish a reverse ssh tunnel to my Macbook Pro at home:ssh -R 19999:localhost:5900 IP_address_of_homecomputerOn my Macbook at home I had to enable Sharing - Remote login first. Then I just use the inbuilt Screen sharing of the OS “Connect to server” and then I type “vnc://localhost:19999” and voila I can see my work desktop’s login screen.Alternatively I could use my openvpn server that I have installed on my Macbook and use an openvpn client on my work desktop to establish a connection to my Macbook. Then I could directly log in and avoid the hops via the university UNIX machines to set up the reverse ssh tunnel.Another, although very slow method to access the GUI of my work desktop is X11 forwarding via ssh. All I need is a working ssh connection to the server, X11 forwarding enabled in the ssh server configuration file and an X11 server on the local machine (e.g. XQuarz on MacOSX):ssh -X username@remote-server.comxclock &

Upgrading mysql on Ubuntu Lucid Lynx (10.04) hangs

Wed, 28 Nov 2012 00:00:00 +0000

Already the third time this happens to me: An update is available for the mysql server and I just “apt-get upgrade”. The upgrade process gets totally stuck at the following task:Preparing to replace mysql-server-5.1 5.1.66-0ubuntu0.10.04.1 (using …/mysql-server-5.1_5.1.66-0ubuntu0.10.04.2_i386.deb) …mysql stop/waitingThe process that got again stuck in some eternal loop (or whatever) is an egrep replacement of some textfile:egrep -qi -r ^[^#]*ndb.connectstring|^[:space:]*\[[:space:]*ndb_mgmd /etc/mysql/I just killed that process and the upgrade resumes as nothing would have happened.

Washing off the dirt from the dirty dozen

Sun, 09 Sep 2012 00:00:00 +0000

There has been much talk about the dirty dozen , a list of the 12 fruits and vegetables most contaminated with pesticides, that was assembled by the Environmental Working Group . Although I sympathize with many goals of the EWG, the EWG is nevertheless an organization with an agenda.Apples were leading the list of the dirty dozen and because apples are probably the number one fruit I eat, I decided to look closer at the methodology of the EWG’s study. The EWG states on their site: “Nearly all the studies on which the guide is based tested produce after it had been washed or peeled.” The data the recommendations are based on was not generated by the EWG themselves, but by the US Department of Agriculture (USDA) . The USDA has Standard Operating Procedures (SOP) for Laboratory Operations and looking at the relevant SOP ( PDP-LABOP Sample Processing and Analysis, Rev. 4, 07/01/12 ), I found the following: 5.3.3ApplesWash each apple under cold running tap water for approximately 15-20 seconds to assure that allsurfaces of the apple have been rinsed. Allow to drain for at least 2 minutes on paper towels on aflat surface. Do not peel. Remove the stem, if present. With a commercially available applecorer remove core or, using a clean, dry knife, cut each apple in half or quarters and remove thecore portion. Mechanically chop just until a visually homogeneous mixture is attained. Unitcounting is required. Refrigeration may not exceed 120 hours from the arrival time until thesample is homogenized.Now, from this it appears as if the apples were analyzed with the peel. Maybe apples are the exception that the EWG means when they write “nearly all”. Could it be that conventionally grown apples contain much of their pesticides on their peel? Yes, that is a possibility, since “… peeling the apples significantly reduced all pesticide residues” ( Rasmusssen et al. 2003: Distribution of multiple pesticide residues in apple segments after home processing ). Actually, lots of research has been done to address the question of whether pesticide residues can be removed from fruits and vegetabled by washing. The results point all into the same direction: with few exceptions (systemic pesticides) a majority of the pesticide residues is located in or on the peel. Water temperature is important: the hotter, the better the pesticide residues are removed. Detergents and rubbing improve the result just as is the case for washing your hands ( Holland et al. 1994: Effects Of Storage And Processing On Pesticide Residues In Plant Products , Chavarri et al. 2005: The decrease in pesticides in fruit and vegetables during commercial processing , Keikotlhaile et al. 2010: Effects of food processing on pesticide residues in fruits and vegetables: A meta-analysis approach ).I guess that’s why many people routinely remove the peel and still others wash and rub apples under hot water. And if you like to eat the peel, just buy organic. At the very least, you feel better.Image based on Red Apple by Abhijit Tembhekar.

My new Helkama Jääkäri bicycle

Thu, 26 Apr 2012 00:00:00 +0000

My Trek bicycle lasted 10 years and approximately 50000 kilometers before I had to retire it. I don’t do any preventive maintenance and fix things only when they are broken. In 2006 I bought a 450€ bicyle from Biltema . It lasted not even 5 years before it needed a major repair (including replacing the expensive bits like wheels, brakes, derailleurs, freewheel and many less expensive ones). Last June I decided to get a [Helkama Jääkäri]([img_assist|nid=581|title=Helkama Jääkäri|desc=|link=url,http://www.helkamavelox.fi/en/models/men/jaakari_3_gear-hmj3nhr_arv_k|align=left|width=240|height=160]) for about 700€. It’s an old style army bicycle and I hoped that it would last longer than the Biltema quality.This winter I cycled with my new Helkama bicycle several hundreds of kilometers on bumpy snow tracks and in February my rear wheel allmost fell of. The screws had not been tightened sufficiently and the thread was already badly damaged. To continue my way I had to remove the washer to expose some undamaged thread and tighted the screw. I contacted Helkama, because the bicycle was not even a year old. They responded quickly and I received a replacement rear wheel by post within a week. That’s good customer service and a reason to stick with the brand: When I bought a new bike for my son last month, I choose the Helkama Yoker , even though it was certainly not the cheapest choice.

The flu shot works

Fri, 20 Apr 2012 00:00:00 +0000

Last week my son was down with the flu. He got diagnosed with influenza A. He was terribly sick having more than 39°C fever for more than 4 days and was staying at home for 10 days before he was able to go to preschool again.My daughter didn’t get sick. Neither did my wife nor did I. Guess why? Because we got the seasonal flu shot. Here in Finland, the seasonal flu vaccine is free of charge for infants between 6 and 35 months, senior citizens 65 years or older, pregnant women and those with chronic diseases or medication that put them at higher risk for a severe disease or complications . Additonally, many employers offer free flu shots for their employees.Because my son doesn’t belong to any of those that gets the shot for free and because he strongly opposed to the shot and because the risk of infection for unvaccinated individuals for any given year is maybe only 5%, we let him go unvaccinated. Bad decision. There is a very good article about flu vaccinations on the Science-based Medicine blog and a very good podcast by pediacast.org about the topic. Unfortunately the flu mist (the vaccination that is inhaled as opposed to be injected) was not yet available on the Finnish market for the 2011/2012 flu season. Flu mist is produced by MedImmune , a subsidiary of AstraZeneca . According to my health care provider Mehiläinen the intranasal vaccine will be very likely available in Finland for the next flu season. The vaccine’s name will be Fluenz , under which it has been approved for by the European Medicins Agency in 2011 for the whole European Union.My son just opposed the injection, not the flu vaccine per se. Flu mist is as effective as the flu shot and it might even confer better protection compared to the shot. That makes sense, because the antigen enters via a natural route. And since it is a life vaccine, the immune response might be better and more sustained. Maybe my employer’s health care provider Mehiläinen should offer also free seasonal flu shots for the children of employees, because despite being vaccinated, I missed several days of work because I had to take care of my son.

rtmpdump - Die Sendung mit der Maus

Wed, 14 Mar 2012 00:00:00 +0000

In my post from 5 March 2010 , I wrote about Die Sendung mit der Maus. At last, you can now watch Die Sendung mit der Maus in its entirety as a Flash video online! For 7 days, until the next episode of Die Sendung mit der Maus. The resolution isn’t HD (512x288 at 25fps, H264), but at least you can save it to your hard drive – if you know how. The programme that makes this possible is, of course, open source: rtmpdump . The command line is:

Meine Podcast-Favoriten

Fri, 20 Jan 2012 00:00:00 +0000

Meine Podcast-Favoriten. Fast jede Episode ist fantastisch:

ComputerNachrichten und Informationen über Computer-Sicherheit und wie das Internet und Computer funktionieren: Security Now!
Alles über Linux: The Linux Action Show!
Jede Woche wird in FLOSS Weekly ein neues Open Source Projekt vorgestellt.

Wissenschaft und Skeptizismus

Rekombinante Proteine

Fri, 20 Jan 2012 00:00:00 +0000

Früher war hier eine dynamisch verlinkte Liste meiner Proteine. Leider musste ich die direkte Verlinkung zu unserem Labor-Datenbank-Server aus Sicherheitsgründen aufgeben. Irgendwann finde ich vielleicht die Zeit, mit einer sicheren Methode den Inhalt userer Labor-Gefrierschränke hier auf meiner Homepage zu publizieren. Bis dahin gibt es bloss eine Liste der Proteine, die ich produziert habe. Wer Fragen hat oder die Proteine für Forschungszwecke braucht, darf sich gerne an mich oder meinen Chef wenden:

My favorite podcasts

Thu, 05 Jan 2012 00:00:00 +0000

My favorite podcasts. I enjoy almost every single episode:

Computer-related stuffSecurity news and education about security and how computers and the internet work: Security Now!
Everything Linux: The Linux Action Show!
Every week one Open Source project is the topic: FLOSS Weekly

Science and Skepticism

Tobi's LEGO bricksets

Mon, 02 Jan 2012 00:00:00 +0000

SetNumberSetNameThemeSubthemeYear625-1Tractor DiggerTownClassic1978626-1Red Cross HelicopterTownClassic1978645-1Police HelicopterTownClassic1979661-1Spirit of St. LouisLEGOLAND 1976885-1Space ScooterSpaceClassic1979886-1Space BuggySpaceClassic1979889-1Radar TruckSpaceClassic1979894-1Mobile Ground Tracking StationSpaceClassic1979897-1Mobile rocket launcherSpaceClassic1979924-1Space TransporterSpaceClassic1979928-1Space Cruiser And MoonbaseSpaceClassic19791575-1Finnjet FerryFerries 19772114-1ChopovNinjagoSpinners20112116-1KraziNinjagoSpinners20113179-1Repair TruckCityTraffic20103179-1Repair TruckCityTraffic20103843-1Ramses Pyramid Games 20094915-1Mini ConstructionCreator 20075933-1Airport Building SetBricks and More 20115981-1Raid VPRSpaceSpace Police 320106191-1Fire Fighter Building SetBricks and More 20096801-1Moon BuggySpaceClassic19816821-1Shovel BuggySpaceClassic19806822-1Space DiggerSpaceClassic19816841-1Mineral DetectorSpaceClassic19806927-1All-Terrain VehicleSpaceClassic19816929-1Star Fleet VoyagerSpaceClassic19817138-1RahkshiBionicleStars20107241-1Fire CarCityFire20057245-1Prisoner TransportCityPolice20057245-1Prisoner TransportCityPolice20057566-1FarmerCityFarm20107610-1SpeedboatCreator 20067631-1Dump TruckCityConstruction20097732-1Air MailCityCargo20087741-1Police HelicopterCityPolice20087797-1Bi-PlaneCreator 20087930-1Bounty Hunter Assault GunshipStar WarsThe Clone Wars20117950-1Knight’s ShowdownCastleKingdoms20107953-1Court JesterCastleKingdoms20107977-1Seabed StriderAtlantis 20117978-1Angler AttackAtlantis 20117984-1Deep Sea RaiderAtlantis 20118015-1Assassin Droids Battle PackStar WarsThe Clone Wars20098056-1Monster Crab ClashAtlantis 20108072-1Sea JetAtlantis 20108073-1Manta WarriorAtlantis 20108083-1Rebel Trooper Battle PackStar WarsEpisode IV-VI20108086-1Droid Tri-FighterStar WarsThe Clone Wars20108088-1ARC-170 StarfighterStar WarsThe Clone Wars20108089-1Hoth Wampa CaveStar WarsEpisode IV-VI20108093-1Plo Koon’s Jedi StarfighterStar WarsThe Clone Wars20108095-1General Grievous’ StarfighterStar WarsThe Clone Wars20108096-1Emperor Palpatine’s ShuttleStar WarsEpisode III20108130-1Terrain CrusherRacersTiny Turbos20078137-1Booster BeastRacersPower Racers20078193-1Blue BulletRacersTiny Turbos20108221-1Storming EnforcerRacers 20118400-1Space SpeederSpaceSpace Police 320098665-1Highway EnforcerRacersTiny Turbos20068860-1Car ChassisTechnic 198010188-1Death StarStar WarsUltimate Collector Series2008

Tobi's LEGO bricksets

Wed, 09 Nov 2011 00:00:00 +0000

Some useful PDF editing (and search) commands

Thu, 28 Jul 2011 00:00:00 +0000

Insert pages with interleave: pdftk A=input_odd_pages.pdf B=input_even_pages.pdf shuffle A B output collated.pdf(from the pdftk package)
Split an A2-sized PDF into two A3 pages for printing (no overlap): pdfposter -m A3 -p A2 Periodic-Table_A2.pdf Periodic-Table_2xA3.pdf
Split an arbitrary-sized PDF into A3 pages for printing at 100% size (= 1), no overlap: pdfposter -m A3 -s1 Poster.pdf Poster_split_to_A3.pdf
Reverse page order: pdftk input.pdf cat end-1 output reversed.pdf(from the pdftk package)
Reduce PDF filesize: gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/screen -dNOPAUSE -dQUIET -dBATCH -sOutputFile=output.pdf input.pdf Allowed PDFSETTINGS are /screen, /ebook, /printer, /prepress, /default. (from the ghostscript package)
Convert a color PDF into grayscale: gs -sOutputFile=output.pdf -sDEVICE=pdfwrite -sColorConversionStrategy=Gray -dProcessColorModel=/DeviceGray -dAutoRotatePages=/None -dCompatibilityLevel=1.4 -dNOPAUSE -dBATCH input.pdf (from the ghostscript package)
Export bitmap images: pdfimages -j original.pdf extracted (from the xpdf package)
Convert into a bitmap image: convert original.pdf converted.png (from the imagemagick package)
Split into individual 1-page PDF files: pdftk original.pdf burst (from the pdftk package)
Merge two or more PDF files: pdftk original1.pdf original2.pdf cat output merged.pdf (from the pdftk package)
Delete page 13 from a PDF file: pdftk original.pdf cat 1-12 14-end output page13deleted.pdf (from the pdftk package>
Rotate page 5 of the PDF file 90 degrees counterclockwise: pdftk Figures_LRES.pdf cat 1-4 5L 6-end output Figures_LRES2.pdf (from the pdftk package>
Assemble a new PDF where each 4 pages from the source files are merged into one landscape page: pdfjam *.pdf –landscape –nup 2x2 For portrait orientation use the “–no-landscape” option (from the pdfjam package).
Underlay a PDF with another (background) PDF: pdftk foreground.pdf background background.pdf output overlay.pdf (from the pdftk package).
GUI PDF editors: I tried out PDFEdit , but it is too difficult for me. The Master PDF Editor" is not free, but it seems to be much more usable without extensive initialization of the user.
**Encrypt a PDF with both a owner password (to change the file) and a user password (to open the file): **pdftk input.pdf output encrypted.pdf owner_pw PROMPT user_pw PROMPT (from the pdftk package).
**If you need to do a text search through many PDF files in the current directory and all of its subdirectories, you can use pdfgrep : **pdfgrep -r searchterm * (from the pdfgrep package).
**Convert & merge all jpg files in the current directory into one PDF file:**convert *.jpg pictures.pdfIn the recent Ubuntu editions, this batch operation is not allowed due to security risks and you can disable this policy by renaming the configuration file:/etc/ImageMagick-6$ sudo mv policy.xml policy.xmlout

Rescue from the vacuum cleaner

Tue, 05 Jul 2011 00:00:00 +0000

I have identified the top reason of LEGO pieces disappearing in our household: the vacuum cleaner. On suspicion I reluctantly decided to explore the bag’s content (Miele HyClean N/G) after it was full and here is what I extracted: Three LEGO pieces, three puzzle pieces, a screw driver head, a pinwall pin, a Mastermind pin and some yet to identify metal item.

LEGO

Sat, 05 Feb 2011 00:00:00 +0000

Tobi wants Lego. To make sure that you don’t buy him sets he already owns, he has made a list at brickset.com of all his sets. And so that you don’t have to register at brickset.com, there is a mirror of this list here: Tobi’s Lego bricksets .

Statistiken über Finnland

Thu, 09 Dec 2010 00:00:00 +0000

Finnland macht oft Schlagzeilen mit seinem guten Abschneiden in internationalen Vergleichen. Zu solchen gehört etwas die 2006 OECD PISA-Studie , der jährliche Korruptionswahrnehmungsindex und Newsweeks Bestes Land zum Leben-Studie . Wenn Finnland nicht so gut im internationalen Vergleich abschneidet, wird nicht viel berichtet. Hier einige Statistiken, die ich in der öffentlichen Wahrnehmung vermisse:

Kid's series on German TV

Fri, 05 Mar 2010 00:00:00 +0000

The online offering from Germany’s public service broadcasters (i.e. ARD) for children ( kinder.ard.de ) is rather limited (although they do produce good children’s television). You can find plenty online, but rarely the actual programmes themselves – instead, there’s a lot of Flash rubbish . Selected ‘Sachgeschichten’ and clips from Die Sendung mit der Maus are the only things that interest my son. I want the whole Sendung mit der Maus! And Sesame Street isn’t available online at all, neither in full nor in part. That’s exactly what I’d like: I don’t just want to decide for myself WHAT my children watch, but also WHEN they watch. If I lived in Germany, I could record the broadcasts onto a hard drive. Fortunately, German law not only permits digital recording for personal use (“ private copy ”), but also the sharing of the recordings with friends. That’s how I get Sesame Street , The Show with the Mouse , Was ist was TV and the Bibliothek der Sachgeschichten .

Disk dumps (dd) and copying over the network (netcat)

Tue, 16 Feb 2010 00:00:00 +0000

On the receiving machine (disk sda MUST be unmounted, e.g. by booting from a live CD or USB stick):netcat -l -p 4778 | dd of=/dev/sdaOn the sending machine (disk sdb MUST be unmounted, e.g. by booting from a live CD or USB stick):dd if=/dev/sdb | netcat 192.168.0.4 4778(-l listen; -p port)To copy a directory over the network, enter the directory and execute on the sending machine:tar -cz . | nc -q 10 -l -p 45454On the receiving machine, create the directory, enter it and execute:nc -w 10 192.168.0.11 45454 | tar -xzBTW: If you want to see the progress of a disk dump (how much was already copied in what time at what average speed), you can use (in newer versions of dd) the status option. I guess this might not work for network copying, but I have not tried… dd if=/dev/sdb of=/target status=progress

A permanent static route in Ubuntu Karmic Koala (9.10), Precise Pangolin (12.04) & Trusty Tahr (14.04)

Sat, 26 Dec 2009 00:00:00 +0000

Karmic KoalaTo add a permanent static route to a Karmic Koala system with one NIC, you need to edit the/etc/network/interfaces file. The following section needs to be replaced:# The primary network interfaceauto eth0#iface eth0 inet dhcpModify as follows:# The primary network interfaceauto eth0iface eth0 inet dhcpup route add -net 10.8.0.0 netmask 255.255.255.0 gw 192.168.0.3down route del -net 10.8.0.0 netmask 255.255.255.0 gw 192.168.0.3**Precise Pangolin (12.04)**With the Precise Pangolin, I did it by adding a script called add_route to /etc/network/if-up.d:#!/bin/sh#if [ "$IFACE" = "eth0" ]; then route add -net 10.8.0.0/24 gw 192.168.0.18#fiI never added a corresponding script (del_route) to /etc/if-down.d, but that seems to be OK.**Trusty Tahr (14.04)**With Trusty Tahr, I was adding the route command as a line to the /etc/rc.local script:…route add -net 192.168.1.0/24 gw 192.168.0.3exit 0The route command needs to be before the “exit 0” line!**MacOS X 10.8 (Mountain Lion)**And here is how it is done on MacOS X 10.8: http://nellen.it/blog/2012/01/permanent-static-routes-for-mac-os-x . They details of how to to it in MacOS X have changed over time; here is the way how it was done on MacOS X 10.4.7 .

How to use jhead or exiftool to add a time stamp to a jpg image

Mon, 24 Aug 2009 00:00:00 +0000

If the jpg image doesn’t have exif header you need to create it first:jhead -mkexifThen enter the time stamp data:jhead -ts2009:08:15-10:30:00Apart from jhead ( http://www.sentex.net/~mwandel/jhead/) , there is another frequently used tool to edit exif data: exiftool ( https://www.sno.phy.queensu.ca/~phil/exiftool/ ). When you execute exiftool to display the exif data, you get a list like this:user@laptop:~$ exiftool IMG_001.jpgExifTool Version Number : 10.80File Name : IMG_001.jpg[…]Date/Time Original : 2018:09:02 13:20:13Create Date : 2018:09:02 13:20:13[…]However, in order to modify a value you need to address the individual tag and the tag name that the command line expects is NOT the same that is given in the list (the tag for “Create Date” is e.g. “CreateDate”):exiftool -CreateDate='2009:11:32 09:11:24.991000' IMG_001.jpgExiftool is probably the most capable tool, but for the same reason, it is not the most easy to use.IN order to remove all exif data, try:exiftool -all=IMG_001.jpg

Finally some good self-made chocolate ice cream

Fri, 07 Aug 2009 00:00:00 +0000

Last summer I bought this ice cream maker. Some of the ice cream I made was quite OK, but only now did I succeed in making ice cream that compares favorably to Mövenpick or similar. The secret is: EGGS and lots of FAT and SUGAR. Here is the recipe:

How to determine and convert text file encoding (file, enca, iconv)

Wed, 22 Apr 2009 00:00:00 +0000

To determine the file type of the file “sample.txt” you just type:file sample.txtUsually it’ll tell you only that it is a text file. To get to know more about the encoding type:enca -L none sample.textThe -L switch tells the program what language is used in the file. If you don’t know, just use none.To convert the encoding from ISO-8859-1 (latin1) to UTF-8:iconv --from-code=ISO-8859-1 --to-code=UTF-8 sample_iso8859-1.txt > sample_utf-8.txt

File permissions on html server (recursive chmod) differentiating between files and directories

Sun, 12 Apr 2009 00:00:00 +0000

I recursively screwed up the file permissions in my html servers root directory. To fix it I needed to deploy some “advanced” chmod settings. Obviously I want to treat directories and files differently. I didn’t come up with a better solution than the following:chmod -R u=rw-x,g=rw-x,o=r-wx *chmod -R a+X *

Old Macs and USB support

Tue, 17 Mar 2009 00:00:00 +0000

We have a few legacy Macintosh computers at work which are still running different flavours of MacOS 9 . Although these machines have USB ports, they are mostly non-functional. I think MacOS 9.0 was the first version that supported USB mass storage devices, but apparently support has been shaky until and including version 9.2.2. Apparently the various updates to MacOS 9 mainly addressed the problems with USB (and firewire) support. At least for one of these machines (running MAcOS 9.2.2) I managed to fix the USB support. I removed all non-Apple USB- and firewire-related extensions from the system folder (e.g. some from Lacie). Then I downloaded the MacOS 9.1 upgrade from Apple and extracted all USB-related extensions using TomeViewer and replaced the existing (9.2.2) extensions by these (9.1) counterparts. After a reboot my (PC-formatted) USB stick was recognized immediately. Here is the list of extensions that I replaced:

youtube to iPod and how to check video files

Mon, 23 Feb 2009 00:00:00 +0000

I was trying to extract the audio file from some youtube videos in order to play it back from my iPod shuffle. I tried various methods (including the otherwise quite versatile VLC Player , but finally settled on the following two step procedure:1. Download the flash video (file ending .flv) file to your local disk. You can use any method to accomplish this task, but as usual Firefox has the perfect plug-in for this task: Download helper .2. Extract and convert the audio file with ffmpeg using the following command: ffmpeg -i video-infile.flv audio-outfile.mp3 It is also possible to convert the flv file into a mpeg file. You need to do this e.g. if you want to import the video into iTunes . For some strange reason Quicktime can play Flash Videos, but iTunes doesn’t allow their playback. The command is almost the same: ffmpeg -i video-infile.flv audio-outfile.mpegAnother nifty usage of ffmpeg is to check video files for corruption and other problems:ffmpeg -v 5 -i file.avi -f null - 2>error.log

My rare use of LaTeX

Mon, 02 Feb 2009 00:00:00 +0000

Compiling I sometimes use LaTeX . I would like to use it more often, but I guess I belong to the Wysiwyg generation. In fact I use it so rarely that I even forget how to compile a document. The following is therefore just a reminder for myself; the filename is doc.tex:

Changing the MAC (Media Access Control) address of NICs (Network Interface Cards)

Sun, 25 Jan 2009 00:00:00 +0000

In some networks, computers have to be registered to get connected. Upon registration, the computer will receive a name and an IP address. Every time it connects to the network, the DHCP server assigns it the same name and IP address. The DHCP server identifies computers based on the MAC address, which is unique to every NIC. However, if you know the MAC address of a registered computer, you can use it to connect to the network, faking the MAC address:

cryptsetup

Sun, 25 Jan 2009 00:00:00 +0000

I switched already quite a while ago from the old cryptoloop technology to the newer cryptsetup technology. However, I still forget how to manually create and mount encrypted volumes, because I do this rarely. Here are the commands:cryptsetup create cryptovolume /dev/mapper/logical_volumemount /dev/mapper/cryptovolume /mountpointIn this case I mapped a logical volume, but of course you can map physical volumes, too:cryptsetup create cryptovolume /dev/sdb1mount /dev/mapper/cryptovolume /mountpoint

How to access encrypted volumes from live CDs

Sun, 25 Jan 2009 00:00:00 +0000

Once you have decided to encrypt your hard drive, you might find yourself in the situation where you need to pull off data from it when the regular decryption mechanisms you use are not in place. E.g. when the OS is not booting or the drive has some physical problems. In that case you need to boot from a CD/DVD that supports the encryption technology that you used. In my case I need a live Ubuntu CD/DVD, preferably the same version that was used to encrypt the disk! Otherwise there might be incompatibilities:sudo apt-get install lvm2 cryptsetupsudo modprobe dm-cryptsudo cryptsetup luksOpen /dev/sda2 crypt1 (result: key slot0 unlocked, command successful)sudo vgscan --mknodes (result: Found volume group "default")sudo vgchange -ay (logical volumes become active)sudo mkdir /volume1, etc.sudo mount /dev/default/root1 /volume1

How to erase hard drives (shred, dd)

Sun, 25 Jan 2009 00:00:00 +0000

You could write zeros to the whole hard drivedd if=/dev/zero of=/dev/hdaFor newer versions of dd, you can monitor the progress:dd if=/dev/zero of=/dev/hda status=progressHowever, it has been recommended to write a few passes of random noise (n = 3 is the default). If the writing process entirely got rid of the magnetic history and your source of randomness was perfect, a single pass would ALWAYS be enough. In reality, you only need n>1 if you are dealing with the state secrets since recovering anything after an n=1 erase requires special equipment which you cannot buy in any store. shred -vfz -n3 /dev/hda

How much toothpaste is safe to swallow for a 3 year old?

Mon, 22 Dec 2008 00:00:00 +0000

My son doesn’t like to brush teeth and he is probably no exception. In order to protect his teeth, we started to use a fluoride-containing tooth paste when he was about 2 years old. However, we were always careful and didn’t let him swallow the toothpaste in order to avoid overdosing. There are likely still quite a few cases of acute fluoride poisoning in small children every year (Shulman & Wells, 1997) and not surprisingly they are mostly caused by ingestion of large amounts of fluoride containing toothpaste. Just now I made the calculation and my son was probably never in danger of overdosing due to the fact that the water we get here in Helsinki from our local utility supplier Helsingin Vesi is very low in fluoride (0.1 mg/l or 0.1 ppm). He brushes his teeth twice a day and uses each time a pea-sized amount of tooth paste (equaling about 0.15 g). The toothpaste he uses (OralB Stages) contains 0.11% sodium fluoride (equaling 0.05% fluoride). This means that if he swallowed all of his toothpaste he would ingest 0.15 mg of fluoride per day. This is 30% of the daily amount of fluoride supplementation recommended by the American Dental Association for children between 3 and 6 years of age and still less than the daily amount recommended for children of ages between 6 months and 3 years (0.25 mg). I have not encouraged him to swallow the tooth paste although there seems nothing to argue against doing so apart from my parental inconsistency. Daddy probably doesn’t know as he changes his mind all the time… But I guess since he is chewing very avidly his xylitol chewing gum , he should be fine even without much fluoride.

WINE regression testing

Sun, 30 Nov 2008 00:00:00 +0000

I am using Textco ’s Gene Construction Kit (version 2.5) do draw my DNA vector maps. Unfortunately this company doesn’t care about Linux users. Therefore I have to use WINE to run the Windows version of the program. Admittedly, I could run VMware, VirtualBox or Parallels, but all that just to run a small program? Unfortunately either the Gene Construction Kit (GCK) is not coded according to standards or WINE is still not able to deliver full compatibility but now and then a WINE upgrade renders the program unable to run. Therfore I had to resort to regression testing to find the version that can still do the trick for GCK. Here is the command listing and what I did:cdmkdir winecvs -z 3 -d :pserver:cvs@cvs.winehq.org:/home/wine checkout wine (password 'cvs')cvs update -PAd -D"2007-06-01 CDT"./configuremake dependmakesudo make installThe source from the date above it the latest that appears to work.

The E-numbers of ADHD-like behaviour inducing food colors and additives

Fri, 28 Nov 2008 00:00:00 +0000

There has been a publication about artificial colors and other food additives influencing children’s behaviour ( McCann, 2007 ), making it more ADHD-like. This is perhaps due to the chemicals’ influence on brain chemistry. This claim is not new, just the methodology (double-blind, randomized). I just checked out this paper and figured out the corresponding E numbers. Unfortunately the research used “cocktails” of these additives and therefore some of these might be harmless. But nevertheless, here is the list:

Chocolate and onion-syrup against cough

Thu, 27 Nov 2008 00:00:00 +0000

Cough serves a useful purpose if it is productive, i.e. if it removes excessive mucus from the airways. However, unproductive cough can be problematic, especially since there seems to be no safe cough medication for children; many of the over-the-counter drugs for treating cough in children have been banned due to their serious side effects. On the search for safe alternatives, I came across commonly used food items which effectively suppress cough and dilate the airways (chocolate) and which (presumably) help against respiratory tract infections (honey and onion).ChocolateTheobromine is used as an effective anti-tussative agent and as a brochodilator ( Usmani 2005 , Simons 1985 ). Therefore it should be possible to achieve the same cough-suppressing effect by consuming cocoa or chocolate. A typical dose of theobromine is 500-1000 mg (i.e. about 10 mg/kg). The theobromine content of cocoa varies between 0.5% and 2.7%. In order to get into the therapeutic range, my son (16 kg) would have to eat about 200 mg of theobromine. The maximal cocoa content he tolerates in chocolate is 85% (which is quite surprising, but since I hardly eat anything below 70% cocoa content he got used to it early on). So he needs to eat about 10-20 grams of very dark chocolate. Children metabolize theobromine quite fast, so the effect is not very long-lasting. My son has agreed to test this and it seems to work.Honey-onion syrupThe other remedy against cough is onion syrup. I take an onion. I prefer red ones as they are not as hot as the white ones. I cut it into very small pieces (cubes of 1-2 mm length) and then I mix them with about the same amount of crystalline, good-quality honey. After a a few hours the mixture becomes liquid as the sugar pulls out the water from the plant cells (osmosis). Then I squeeze out the juice from the mix. One onion per day is the approximate dosage for respiratory tract infections. Honey and onion contain both anti-bacterial compounds, but I haven’t found any good studies showing that this mix really helps. However, unlike the chocolate, this is an old, traditional recipe against cough.

Reinstallation of packages from a list

Fri, 26 Sep 2008 00:00:00 +0000

If I install a new computer for myself (or if I do a fresh reinstall on an old machine), I want the computer have the software I am used to. To automatize this process, there a different approaches. If you use Ubuntu, you can use Ubuntu One to syncronize your software selection across many different machines (starting from Ubuntu 11.10 Oneiric Ocelot). If you use something else, it is getting tricky. You can use the following commands to generate a list of installed packages and load the list later for installation:dpkg --get-selections > installed-packages.lstdpkg --set-selections < installed-packages.lstdselectHowever, this creates big problems, because the list contains ALL packages including those that are hardware-specific. Actually you are only interested in the user-installed software. For reloading the software onto the same (or an identical) machine, this command works fine, but what if you want to use KDE instead of Gnome on the new computer? You still want to use the same programs, but the commands above will wreak havoc and may even break your desktop experience. Unfortunately I have not found anything better, but to open the text file generated with dpkg and to manually erase all lines that do not contain user-installed software (which is most of them).

tar copying via ssh

Fri, 26 Sep 2008 00:00:00 +0000

tar czv sourcepath | ssh -l username 192.168.0.5 tar xz -C targetpath

mysql server restart

Thu, 11 Sep 2008 00:00:00 +0000

My mysqld runs on Ubuntu Hardy and after replacing the complete mysql data with a dump from another server the “/etc/init.d/mysql stop” command fails, because the system administration account doesn’t work anymore. So I had to recreate it again:GRANT ALL PRIVILEGES ON *.* TO 'debian-sys-maint'@'localhost' IDENTIFIED BY 'password' WITH GRANT OPTION;The password can be obtained from /etc/mysql/debian.cnf.

Sheep

Sat, 27 Oct 2007 00:00:00 +0000

*And always remember: That everyone is doing it is a good enough explanation!

Finding files with find

Mon, 24 Sep 2007 00:00:00 +0000

Finding files with the find command is actually more difficult than it should be. This finds and lists the largest files (more than 200 MB) on the whole file system:find / -type f -size +200000k -exec ls -lh {} \; | awk '{ print $9 ": " $5 }'The same, but simpler syntax:find / -size +200M -lsThis finds the most recently changed files under the current directory:find . -type f -printf '%TY-%Tm-%Td %TT %p\n' | sortAnd this command pipes the results of the find command into another command. First find looks for Quicktime movies (based on the file extension .mov) and then ffmpeg converts them into avi files.find . -name '*.mov' -exec sh -c 'ffmpeg -i "$0" -sameq "${0%%.mov}.avi"' {} \;This commands finds and lists all filenames that contain the string ‘bitcoin’:find . -name '*bitcoin*' -lsAnd this command finds Quicktime movies and deletes them:find . -name '*.mov' -exec sh -c 'rm "$0"' {} \;And this finds files that have been modified (created or updated) during the last 2 minutes:find . -cmin 2This finds crap which you copied over from a Macintosh and which you don’t need under Linux:find . -name '*.DS_Store' -type f -deleteSimilar story here:find . -name '._*' -type f -deleteWhen being in the root directory, this should find all files with the name ‘syncthing’:find . -name 'syncthing' -lsAnd this finds all files larger than 200MB in the /home directory:find /home -size +200M -lsFind recursively all files that end in .gz and count them:find . -name '*.gz' | wc -lFind recursively all files that do NOT end in .gz and count them:find . -not -name '*.gz' | wc -lWhen you want to search recursively through the content of text files, you need to use the grep command:grep -rnw '/path/to/target-directory' -e 'pattern'When you search for PDF files modified in October 2024:sudo find / -type f -name "*.pdf" -newermt "2024-10-01" ! -newermt "2024-11-01" 2>/dev/null

Encrypted backup using BackupPC, LVM and cryptsetup

Sat, 22 Sep 2007 00:00:00 +0000

I do offsite backups using BackupPC. The amount of data increases constantly so I need to add occasionally hard disks. Additionally I want the data to be encrypted, at least after powering off the system that is running the BackupPC application. So I decided to use logical volume management (LVM) and block device encryption (cryptsetup). The following steps were needed (on Ubuntu Feisty):

cryptsetup on lvm on Ubuntu Feisty

Thu, 20 Sep 2007 00:00:00 +0000

I wanted to encrypt my Documents. My home folder is on a logical volume. So I made some space by removing another logical volume and creating a new one, which gets encrypted by cryptsetup. Here are the commands:

E-mail: migrating from kmail to Evolution

Tue, 17 Jul 2007 00:00:00 +0000

I recently switched from kde to gnome and at the same time from kmail to Evolution. There is no easy way to transfer you mail if you have organized it in several mailboxes in kmail. You need to select all messages in a folder and then right-click and save them in mbox format. This step you need to repeat for every folder. Then you can use the import function of Evolution (import from single file). If you can accept that all files end up in the same folder, you can concatenate your .mbox files to save you the trouble of importing multiple files:cat *.mbox > allmail.mbox

Installing awstats on Ubuntu Feisty

Wed, 27 Jun 2007 00:00:00 +0000

I started to use awstats for creating the site statistics on our server. After installing the ubuntu package, there are still a few things that I had to do:

Why some scripts in the cron.hourly directory do not become executed

Sat, 09 Jun 2007 00:00:00 +0000

Because I have a very basic mp3 player that cannot play back anything but ISO-standard mp3s, I often need to re-encode podcasts which my podcast-catcher downloads (I use Amarok). I created bash scripts to re-encode all downloaded mp3s and to generate a new RSS feed based on the directory content where the re-encoded mp3s get stored. However, the scripts did not get executed every hour and the reason was their naming (“podacst_downsampling.sh”). There are quite strict rules how the names have to look like (which I don’t remember), but if you use only a-z characters you should be always fine. After renaming to “podcastdownsampling” everything worked fine.

(Re)installing GRUB bootloader

Sat, 26 May 2007 00:00:00 +0000

We had the following problem on the computer:2 hard drives (hda and hdb).hda contains the MBR (master boot record) and a Windows 2000 install on the first partition. hdb contains Linux (and its first partition is a boot partition that contains a GRUB installation as done by the RedHat 9 installer).In the BIOS you can only specify one hard drive into the boot priority sequence and that was hda (probably defined by it being the master on the first IDE chain). Therefore we had to start Linux from a boot floppy (because the floppy drive had boot priority over the hard drive). To get a functioning GRUB, we did the following:$/sbin/grub (starting grub shell)grub> root (hd1,0) (telling which one is the boot partition where grub got installed)Filesystem type is ext2fs, partition type 0x83 (tells us that it found the partition)grub> find (hd1,0)/grub/stage1(fd0)(hd0,0)(hd1,0)(hd1,1)(hd1,2)(hd1,5)(hd1,6) (this command is maybe not necessary, it apparently list all possible partitions on which the grub bootloader could be installedgrub> setup (hd0)Checking if "/boot/grub/stage1" exists… noChecking if "/grub/stage1" exists… yesChecking if "/grub/stage2" exists… yesChecking if "/grub/e2fs_stage1_5" exists… yesRunning "embed /grub/e2fs_stage1_5 (hd0)"… 16 sectors are embedded.succeededRunning "install /grub/stage1 d (hd0) (hd0)1+16 p (hd1,0)/grub/stage2 /grub/grub.conf"… succeededDone. (this installs the bootloader onto the first hard drive, apparently not into the first partition, maybe into the MBR?)grub> quit (exit the grub shell)emacs /boot/grub/grub.confNow you just have to edit the grub configuration file. Ours looks like this:grub.conf generated by anacondaNote that you do not have to rerun grub after making changes to this fileNOTICE: You have a /boot partition. This means that all kernel and initrd paths are relative to /boot/, eg.root (hd1,0)kernel /vmlinuz-version ro root=/dev/hdb3initrd /initrd-version.imgroot=/dev/hdb1 default=0 timeout=10 splashimage=(hd1,0)/grub/splash.xpm.gztitle Red Hat Linux (2.4.20-19.9)root (hd1,0)kernel /vmlinuz-2.4.20-19.9 ro root=LABEL=/ hdd=ide-scsiinitrd /initrd-2.4.20-19.9.imgtitle Red Hat Linux (2.4.20-18.9)root (hd1,0)kernel /vmlinuz-2.4.20-18.9 ro root=LABEL=/ hdd=ide-scsiinitrd /initrd-2.4.20-18.9.imgtitle Red Hat Linux (2.4.20-13.9)root (hd1,0)kernel /vmlinuz-2.4.20-13.9 ro root=LABEL=/ hdd=ide-scsiinitrd /initrd-2.4.20-13.9.imgtitle Red Hat Linux (2.4.20-9)root (hd1,0)kernel /vmlinuz-2.4.20-9 ro root=LABEL=/ hdd=ide-scsiinitrd /initrd-2.4.20-9.imgtitle Red Hat Linux (2.4.20-8)root (hd1,0)kernel /vmlinuz-2.4.20-8 ro root=LABEL=/ hdd=ide-scsiinitrd /initrd-2.4.20-8.imgtitle Windows 2000rootnoverify (hd0,0)chainloader +1title Floppyrootnoverify (fd0)chainloader +1title Rebootreboottitle Halthalt

Acrobat Reader 5.07 for Linux

Sat, 26 May 2007 00:00:00 +0000

There is an rpm for Acrobat Reader 5.07 for Linux from Gurulabs . It anyway didn’t work on my machine, so I had to stick to the old reader (version 4.05 that is). But today I found a fix on the web:OK, this is the error message:$ /usr/local/Acrobat5/bin/acroread$ Warning: charset "UTF-8" not supported, using "ISO8859-1".$ AbortedBut editing the acroread file (/usr/local/Acrobat5/bin/acroread) really works. After the line:install_dir=/usr/local/Acrobat5/Readerjust insert these two lines:LANG=Cexport LANGBTW you need to have root accession rights to be able to modify the acroread file.

Audio CDs to the Rio 500 mp3 player using Linux

Sat, 26 May 2007 00:00:00 +0000

OK, it is easier on a Mac. iTunes is free and does it all for you (and does it well). To replace iTunes I need at least three applications on Linux :-(

Binhexed attachments and Mozilla (hexbin, macutils)

Sat, 26 May 2007 00:00:00 +0000

OK, today I tried to open the final version of the manuscript for Cell & Tissue Research. My boss sent it to me as an e-mail attachment some 2 weeks ago. I use Mozilla Mail and saved the attachment. Open Office didn’t manage to open it. Obviously my boss uses still Macintosh binhex encoding to attach files to his e-mail instead of MIME to make himself as incompatible to the rest of the world as possible. There is luckily the command line utility hexbin in Linux, which converts the binhexed file into some readable stuff:hexbin -3 Lymphangio_review_CTR.docThat is the theory. The conversion didn’t succeed with the error message “unexpected EOF”. I suspected that Mozilla was involved and thus I used pine to extract the attachment and voila hexbin managed to convert the macintosh-gibberish into three files.For these three different files the only useful part (the Word Document data) appeared as Lymphangio_review_CTR.doc.data. From this I still had to delete the .data ending and Open Office had no problems anymore to open it. Whow. It took me only 2 hours to figure out all that stuff (including to set up pine locally to access the e-mail server via SSL-secured connection). I still have to figure out why Mozilla Mail handles binhexed attachments wrongly…The hexbin utility is e.g. included in the macutils package (available for Suse and RedHat).

BitTorrent

Sat, 26 May 2007 00:00:00 +0000

Today I installed the latest in file sharing: BitTorrent. Was a bit cumbersome as I first had to install wxPython. And to install wxPython, I needed wxGTK. There is apparently a RedHat9 RPM around, but the download site was down all day long, so I got the source wxPythonSrc-2.4.1.2.tar.gz from sourceforge. After that I tried to download the RedHat9 CDs as I need a clean Linux install to test Adobe Acrobat 5.0.7 and Crossover Office (Acrobat 5 crashes immediately after start on my RedHat9 system and the Crossocer Office seems also to be somehow compromised by excess fiddeling). BitTorrent is said to be very fast. So far the download rate is 23 kB/s.

Changing the Runlevel (inittab, telinit)

Sat, 26 May 2007 00:00:00 +0000

Usually you change the default runlevel by editing /etc/inittab. However, sometimes you boot into runlevel 3 (e.g. by selecting safe mode from the grub menu) and then want to change to runlevel 5. This you accomplish on the fly with the command: telinit 5In RedHat 9, just change in the /etc/inittab file the runlevel from 5 to 3 and you will have only the command line left by default upon booting. No X11 graphical login etc. In newer Ubuntu releases, this apparently doesn’t work anymore, although telinit + number should still change the runlevel, but at least in the Precise Pangolin (12.04), telinit 2-5 appears not to do anything. Telinit 1 tries to shutdown the machine, but the shutdown got stuck halfway when I tested it. To achive something similar to changing to runlevel 3, you will have to shutdown the GUI (meaning to kill the gdm or lightdm process). The runlevel concept seems to be dead.

Comparing two directories (diff)

Sat, 26 May 2007 00:00:00 +0000

diff -r path1 path2

Creating a shared directory under Linux

Sat, 26 May 2007 00:00:00 +0000

When two users on Linux need to share files, accession rights can be quite a problem. By default only the one who creates the file can read and modify it, even if it is saved in a directory that is accessible by the other. It appears to me still impossible to solve this problem completely as Linux cannot “inherit” privileges to newly creates/saved files based on their parent directories privileges (BTW: how has Mac OS X solved this problem?)The following instructions create a shared directory, but require additional tweaks.As root

Floppies and Linux

Sat, 26 May 2007 00:00:00 +0000

Since I started to use html and CSS to create my presentations (instead of OpenOffice instead of Microsoft Office), even quite large presentations fit on regular 1.4MB floppies. Thus I popped an empty floppy into the drive and formatted it as ext2. Funnily the GUI floppy mounter is not able to recognise the file system when it is set to autodetect. Thus I formatted as MS-DOS and the autodetect file system works. Strange…

Hot-swapping different user GUIs under Linux

Sat, 26 May 2007 00:00:00 +0000

I read that Windows XP has a “new” feature that lets users hot-swap their desktops. Instead of logging out, a user can put his session into the background and another user can log in. This is of course very useful if you are downloading large files or running services and you don’t want to interrupt the process. If figured out that Linux is able to do the same already for years:When I have a process with a GUI running in GNOME (or KDE; let’s say lmule) and another user wants to access his account using GNOME and I don’t want to terminate my own GUI session, I switch to another (virtual) terminal via Ctrl-Alt-F2 and the other user logs in and starts an x session (“startx – :1”). Using RedHat 9, the new x session started from F2 is initially accessible via both consoles (F2 and F8).When the other user has finished his work, I can without problems go back to my GNOME with Ctrl-Alt-F7 and resume whatever I have been doing under GNOME.However, when the other user wants to access again his x session, it can only be accessed via Ctrl-Alt-F8. When switching to the F2 console one might get the impression that X has crashed (which is not the case).If the Ctrl-Alt-Fx combination doesn’t work, you have selected a wrong keyboard layout (one that is not meant for x windows sessions, but for a command line terminal). You can switch to correct terminal via the GNOME keyboard layout switcher. The GNOME keyboard layout switcher is an applet that you can add to your panel (click the panel in an empty area, add to panel, utility, keyboard layout switcher). To choose a correct keyboard layout right-click the keyboard layout switcher icon in the panel, Preferences, Add. When you click the triangle in front of the different languages and then the triangle in front of the country, you sometimes see two different options (in my case: Finnish keymap and Finnish xkb keymap). You should choose the xkb keymap, otherwise Ctrl-Alt-Fx won’t work.

How do I run the Gene Construction Kit under Linux?

Sat, 26 May 2007 00:00:00 +0000

There are only a few Mac or Windows programs that don’t have a good equivalent on Linux. One of these few is the Gene Construction Kit (GCK) from Textco . GCK is available for both Windows and Mac. So it should be possible to run it on an i86-Linux machine using wine (a sort of emulator). I tried that and failed (I didn’t try really hard). However, probably any Windows program can be run under Linux using VMware . Unfortunately VMware is commerical and expensive (but there is a fully functional time-limited demo). GCK does run under VMware 4.0/W2K/RedHat9 without problems. The only disappointment in VMware is the “Shared Folders” option. It is much better to share your Linux home directory via Samba and then have it automounted when you log into your emulated Windows OS. I even managed to hide Linux-specific files in my home directory that start with a dot (like .mozilla) by inserting “hide dot files = yes” into the samba configuration file /etc/samba/smb.conf. Although I am using VMware at the moment, I plan to switch to Wine in order to avoid any Microsoft code.

lmule and xmule trouble

Sat, 26 May 2007 00:00:00 +0000

Suddenly lmule stopped working (or xmule). Somehow files is the ~/.lmule/ can get easily corrupted. Just remove all the files (or even delete the whole directory) and the program works again. Don’t forget to save the files from the Temp and Incoming directories! You can copy them later back into the newly created ~/.lmule/Temp and ~/.lmule/Incoming directories.

Mac-Linux Connectivity (netatalk, atalk, Appletalk)

Sat, 26 May 2007 00:00:00 +0000

Connecting from a Macintosh to LinuxI did this already a while ago, but just for documentation purposes: You need to install a Appletalk server on your Linux machine. The package you need is called netatalk. Things worked OK, I just had a problem concerning Appletalk zones. Despite setting the default zone in the atalkd.conf file as “Biomedicum cancerbio” (the zone I want to be in), netatalk overrides this upon service restart. Thus my linux machine ends up always in the default zone (which is called in Finnish “Kadotus”).The atalkd obviously has to negotiate the zone somehow with the router, but how? Macs obviously manage to stay in the zone that they specifcy in their Preferences. They only end up in “Kadotus” when they do not specify a zone, consequently it should be possible to do so as well under Linux. By try and error I figured out that changing the zone in /etc/atalk/atalkd.conf doesn’t do the trick. One has to delete the default entry in /etc/atalk/afpd.conf and replace it by another entry (in Suse 9 the location is /etc/netatalk instead of /etc/atalk):"Michael's Linux Box@Biomedicum cancerbio" -transall -uamlist uams_clrtxt.so,uams_dhx.so -nosavepasswordand then the definition of the shares (in the AppleVolumes.default):"Public" -uamlist uams_guest.so -loginmesg "Welcome guest!"However, netatalk is actually only needed in order to connect from older Macs to Linux. Mac OS X can run SAMBA and to my experience file sharing using SAMBA is more reliable than netatalk. Long file names (I think >31 characters) got netatalk to choke in several cases, while SAMBA did the trick without any problems. Both Mac OS X and Linux support filenames >31 characters, but apparently netatalk doesn’t.Connecting from Linux to MacintoshNow this depends on whether you want to connect to a Mac running OS 9.2 or below or Mac OS X. To be able to connect to a Mac running OS 9.2 or below, you need the afpfs module. This module is not maintained and the last compilation has been done for the 2.1 kernel. Meaning: you are most probably out of luck unless you are a real geek (or you use the still the 2.1 kernel). In order to connect from Linux to Mac OS X, you just should use SAMBA. In GNOME you just need to type smb:// into the Location field of the Nautilus browser window and you will see the domains/workgroups/computers that are visible on the network. I admit network discovery is quite slow. So if you know the workgroup or domain name (e.g. mcbl as in my case), just type smb://mcbl

Mount Samba shares (why doesn't Nautilus work?) and making smb mounts permanent

Sat, 26 May 2007 00:00:00 +0000

Mount Samba sharesApparently it is very easy to connectfrom within Nautilus to Windows computers (or rather to computers running smb services). The only thing you have to do is to type smb:/// into the URL bar and the network is browsed for available domains, workgroups and services. However when one tries to open some files (e.g. some image) there often appears the error message that those files cannot be accessed via samba.What to do? I figured that when you mount smb shares, that this works correctly. In order to mount my user directory on another computer this is the command:sudo mount -t smbfs -o username=michael,password=here_goes_my_password //paula/michael /mnt/smbpaula is the netbios name of the other computer and michael is the name of the share.You can also set the owner of all the files of the mounted file system with the -o uid=owner option:sudo mount -t smbfs -o username=michael,password=here_goes_my_password -o uid=500 //paula/michael /mnt/smbIf you don’t want to type your password, you can save it in a file like this:username=susannepassword=0sdf7band then you can refer to this “credentials” file:sudo mount -t smbfs -o username=susanne,credentials=/home/susanne/.smbpasswd //patolmac217/susanne /mnt/smbIn order to unmount use:sudo umount /mnt/smbThis mostly fails as you are likely to have some open windows/terminals that keep the connection active. Close them and try again. You also might try umount -f.Making smb mounts permanentWhen you mount an SMB share, it will be gone upon system restart. To make it mount automatically during system bootup, you have to create a new entry in the /etc/fstab file. In my case e.g.://paula/michael /mnt/smb smbfs credentials=/home/jeltsch/.smbpasswd 0 0In the .smbpasswd file is my username and my password. Probably not very safe, but who cares? .smbpasswd should be anyway only readable by yourself!

Mounting disk image files and encrypted filesystems/partitions

Sat, 26 May 2007 00:00:00 +0000

To dump a disk (or a partition) into a file, you use the following command:dd if=/dev/hda3 of=file.binThis command writes the complete data on the hda3 partition into the file file.bin.To mount the filesystem that is in the file, you need to create a loopback device:losetup /dev/loop0 file.binNow you can mount the filesystem as usual:mount -r -t filesystemtype /dev/loop0 /mnt/mountpointApparently, one can combine the last two commands into one:mount -t filesystemtype -o loop ./file.bin /mnt/mountpointIf you want to encrypt the data on a file, that contains a whole filesystem, it is getting a bit more complicated:sudo mkdir /mnt/secure (create mount point for the filesystem)dd if=/dev/zero of=path/to/file bs=1k count=409600 (create an empty file with 400 MB size) sudo /sbin/losetup -e xor /dev/loop0 path/to/file/sbin/mkfs -t ext2 /dev/loop0 409600 (format the device as ext2)sudo mount -t ext2 /dev/loop0 /mnt/secure (mount the device file)cd /mnt/securechown username . (change the owner of the top level directory of the filesystem)If you want to unmount the filesystem:sudo umount /dev/loop0If you want to get rid of the filesystem, you have to un-associate it from the loop device 0: /sbin/losetup -d /dev/loop0For some reason RedHat 9 doesn’t come with DES support, so for the time being (until I patch the kernel or move to Suse Linux) I am using the faster, but much weaker xor encryption.Suse 9 comes with inbuilt strong encryption and offers already during the installation the possibility to create an encrypted partition. Suse 9 asks during booting for the passphrase to mount the encrypted filesystem. The boot process stops and waits for 2 minutes before continuing if you don’t type in the password. In order to reduce this time, you can edit the file /etc/init.d/boot.crypto. Change in the following line 120 to e.g. 10::${TIMEOUT:=120}If you have missed your chance to type in the passphrase during boot time, you can mount the encrypted partition as follows:/sbin/losetup -e twofish /dev/loop0 /dev/hda7 mount /dev/loop0 /media/confBTW: The information about encrypted filesystems resides in /etc/cryptotab.

rio500-0.7-1.i386.rpm works under RedHat 9

Sat, 26 May 2007 00:00:00 +0000

I again tried to compile rio500-0.8.1, but without success. Compiling fails under kernel 2.4. This is an unresolved issue and mentioned in the discussion forums. So I installed the Rio500 package rio500-0.7-1.i386.rpm. Interestingly I managed via the command line to a) format the internal memory: rio_formatb) create a folder (which is necessary before one can upload a song): rio_add_folder c) upload mp3s: rio_add_song ). That’s a big advantage to the crappy Windows Rioport interface. Next time I try to install the Gnome GUI.When listening to the first songs on the Rio500 that I transferred under Linux, they appeared very silent. When I encode next time some songs I should try the lame option –scale . However, I don’t know what argument to use to get some decent amplification of the sound.

Some partition rearrangements under Linux

Sat, 26 May 2007 00:00:00 +0000

The Linux installation is as follows:/dev/hdb1 100 MB /boot/dev/hdb2 8 MB /home/dev/hdb3 8 MB //dev/hdb4 Extended partition/dev/hdb5 1 GB Linux swap/dev/hdb6 100 GB NTFSThe idea was to use the 100 GB partition (/dev/hdb6), which has been formatted with the NTFS (= Windows 2000) file system to store large files under Linux. NTFS file systems cannot be used by Linux yet. The only DOS/Windows filesystem, that is compatible with Linux is FAT32. Unfortunately FAT32 is a quite inefficient system and has a maximal partition size of 32 GB (actually Windows can use FAT partitions up to 127 GB, but it cannot format them itself, one needs a third party utility to format them). Anyhow, Linux can only read and write to FAT partitions up to 32 GB. An additional requirement is that /dev/hdb6 should be mounted to two different mount points. Therefore we have to split this partition into 2 smaller ones. Now this appeared to be impossible under Linux. The reason of this is - like with so many other things that suck - Bill Gates. Similar to his “640KB RAM is enough for everybody” decision, he decided that only four primary DOS-type partitions can be on one physical hard drive. Soon this appeared to be too little and thus a work-around was introduced: “Extended Partitions”. One of the four primary partitions of a disk can be a so-called “extended partition” and contain several (actually I think unlimited amount of) logical partitions. Thus in the above layout of the hard disk /dev/hdb partition number 4 (/dev/hdb4) is an extended partition. It contains two logical partitions: /dev/hdb5 and /dev/hdb6. The problem is the following: The Linux utilities cfdisk and fdisk cannot access these two logical partitions separately. If we want to split /dev/hdb6 into two smaller partitions, we first have to delete this partition and then create two new ones in its place. But both cfdisk and fdisk can only delete /dev/hdb4 as a whole. That would delete the Linux swap partition (quite a disaster while you are running the operating system).The way how to solve the problem is the following: Boot into Windows 2000, delete the 100 GB NTFS partition and created two smaller ones instead (/dev/hdb6 and /dev/hdb7). You have to format them FAT32 or NTFS as Windows cannot do anything else. If you have Partition Magic 8 or higher (preferably on a boot floppy), you can immediately format the two new smaller partitions as Linux partitions (that is: ext2 or ext3). Reboot into Linux. Funnily when mounting the partitions that were formatted using Partition Magic 8, already 5 percent of the space is already occupied although there are no files anywhere (at least this is what the Hardware Browser/Hard Drives utility shows). To reclaim this lost space you have to reformat them under Linux using the command mkfs.ext3 /dev/hdb6. If you want to use the newest (and probably one of the best) file system for Linux, you can format them with the ReiserFS file system (command: mkfs.reiserfs /dev/hdb6). Reboot and add those partitions into the fstab file to automount them on startup.

Startup script for VNC server

Sat, 26 May 2007 00:00:00 +0000

To start up the VNC server automatically as a service during booting, you need this shell script . You probably also can write a much simpler shell script yourself, that does the same job. In fact you will have to as this script is broken on RedHat 9. The simplest shell script is of course the command “vncserver” alone… This script goes into the folder /etc/init.d. Then you make a symbolic link in the directory /etc/rc5.d that points to the script. The /etc/rc5.d directory contains a bunch of links to scripts in the init.d file which are executed when the system is entering runlevel 5 (runlevel 5 is the one where you have the gui and multiple users enabled, the one you most likely use in 95% of all cases). There are other directories for other runlevels (e.g. /etc/rc3.d for runlevel 3, etc.).

The ls command

Sat, 26 May 2007 00:00:00 +0000

I have been using is for years, but hardly have used its “advanced” options. That is:ls -t to sort the content of the directory according to modification date. ls -d to display the directories and not their contents. ls -alh lists the complete content of the directory in long, human-readable form (that means file sizes are given in B, K, M or G and not in bytes).The -d option I mostly use as: ls -d .* This shows me all “hidden” directories which are located in the current directory. If I just typed ls .* I would get a recursive listing of all contents of all hidden directories.

The sticky bit, bzip2 and automatic start of programs upon login

Sat, 26 May 2007 00:00:00 +0000

The sticky bitI am still wondering what exactly the “stick bit” in the file permissions is doing. My suspicion is that if the sticky bit is set for a directory in the group field (chmod g+s foldername) that the permissions are inherited (that is all newly created files in that folder and below will have the same permissions as their parents. But maybe I am wrong as there is still the weird “umask” command that influences permissions of newly created files. I have to figure out how to automatically set the permissions of a specific directory (which is going to be shared among different users to g+rw.bzip2 and bunzip2To uncompress a bzip2 file, execute the following command:bunzip2 filename.txt.bz2 (where filename.txt.bz2 is the name of the file you wish to uncompress). The result of this operation is a file called filename.txt. By default, bunzip2 will delete the filename.txt.bz2 file.Automatic start of programs upon loginTo start up automatically a program upon login, e.g. gaim, I just added the following line to the end of my .bash_profile: “gaim &”. I don’t know whether it’s a good way to implement it like this but it works. I then did the mistake to start the vncserver with this method. What happend was, that upon logging in, the vncserver started up. And of course .bash_profile got executed within the first xdisplay of the vncserver (which happens in case of Red Hat 9 to start up KDE as window manager). So from within this session another instance of vncserver was started. this repeated itself until I had about 80 vncservers running on my machine and the speed slowed down dramatically.

VNC (Virtual Network Computing) via ssh

Sat, 26 May 2007 00:00:00 +0000

I am sitting at home and want to use the GUI of my Linux at work. But my work computer which is running the VNC server (mcblpc2.hi.helsinki.fi) is behind the University firewall. The only connection I can get into the firewall is via one of the university mainframes, e.g. vesuri.helsinki.fi. In order to connect using VNC, I need just two commands:ssh -L 5901:mcblpc2.hi.helsinki.fi:5901 mjeltsch@vesuri.helsinki.fivncviewer localhost:1To make the connection faster, you can use compression (helps only if you have a slow connection, e.g. a modem). When using VNC with ssh, the vncviewer really thinks you make a connection to the local machine and therefore chooses a wrong encoding. So the second command actually should be: vncviewer localhost:1 -compresslevel 0 -encodings "copyrect hextile"When you run the vncserver on a computer that has its own firewall, you need to have sshd running and to open the ssh port (22). Then you establish a tunnel from that ssh server on that computer to a port on your local computer:ssh -L 5901:remotemachine:5901 username@remotemachine vncviewer localhost:1When you run KDE desktop sharing on Suse 9.0, you share the physical screen (:0). Thus, if you are logged out, you cannot connect using desktop sharing. You have to start up additionally a vnvserver instance:vncserverThis server will use by default the :1 session and that’s why the forwarded port must be 5901 and not 5900 (like for the first session).

What corresponds to the Windows ipconfig /all command in Linux?

Sat, 26 May 2007 00:00:00 +0000

I think /sbin/ifconfig displays at least the ip address, the hardware address and the subnet mask and some other stuff. But not much about anything else like DHCP or DNS addresses…

Wine and Crossover Office

Sat, 26 May 2007 00:00:00 +0000

Being fed up with VMware (because it’s so slow and using half of my memory) I turned to Wine . But Wine appears to be very difficult to set up. Typical Linux. It will work but unless you spend a whole week you don’t get it working. That’s where the Corssover Office application comes in. It’s just a bunch of helper applications to make setting up wine easy. That is with certain Windows applications and most Windows applications are not supported. So I got a demo version of Crossover Office and started installing (as root). The application installed without problems. After installation I started the Crossover Office Setup application. That is the place from where you install your Windows applications. So I wanted to try Microsoft Office XP (as it is licensed for the whole university). I made the mistake to select “Install everything”. The installer forced me to install also Microsoft’s Internet Explorer and a bunch of other crap. Than the Office XP installer stopped to respond in the middle of the process. Waited for 2 hours but the progress bar didn’t move and there was no disc activity. So I had to cancel the setup and leave a mess behind. A second attempt to install failed as well. So I thought to use the Windows uninstaller. Failed as well. Uninstalling from within crossover office failed also. So I thought to uninstall the whole crossover office (there is an uninstall script in the bin directory of crossover office which is hardly mentioned anywhere in the documentation). That worked but apparently didn’t uninstall everything. I still had to manually remove several directories, but worst of all the Gnome menu entries were not deleted. The gnome menu entries are quite a tricky thing since they are not located in one place. Gnome uses some “virtual folder” (vfolder) system to create the menus. That is the menus are assembled on the fly based on several xml files located in several places. But I guess I found all of them and removed the entries manually. I must have made a coding mistake since after this the whole menu was gone. Apparently the mistake was in my ~/.gnome2/vfolders/applications.vfolder-info file. Of course I didn’t have a backup, so I copied the same file from /root/.gnome2/vfolders into my home folder.After that I reinstalled crossover office and only installed Microsoft Word XP and that worked! An nice entry was visible in the menu “Windows Applications/Programs/”. Then I installed Adobe Photoshop 6.01. Installation was painless, but after that, the Microsoft Word entry in the menu had disappeared. Also there was no Photoshop entry under “Windows Applications/Programs/Adobe”. There was only an ImageReady entry. It appears that every newly installed application erases the menu entries of the previously installed application. However the hierarchical folder structure remains, only the last entry ins gone and replaced by a dot in the last menu folder. BTW Photoshop worked as one can start it up from within ImageReady.Both Office XP and Adobe Photoshop are applications that are “supported” by the Crossover Office. Now I tried to install an unsupported application, i.e. the Gene Construction Kit 2.5 (GCK2.5). The first thing was that the Crossover Office complained that the installer CD has some hidden files and that I have to make some changes to the fstab entries as root to enable reading these files. I did that and continued installation. The installer finished and there was a menu entry under “Windows Applications/Programs/Gene Construction Kit 2.5” which was named “Uninstaller”. I concluded that the Uninstaller program had been installer after the GCK2.5 application and thus erased the latter entry. Even more strangely after logging out and in again even the Uninstaller item was gone from the menu. Also all other program entries had disappeared.I figured that all the menu entries are single files in the directory /home/jeltsch/.gnome2/applications. They have the extension .desktop and are xml files with a relatively easy structure. One example:> more Internet\ Explorer.desktop[Desktop Entry]Name=Internet ExplorerType=ApplicationComment=Internet ExplorerExec=/opt/cxoffice/bin/wine “C://Program Files//Internet Explorer//IEXPLORE.EXE” X-Created-by=cxoffice Icon=/home/jeltsch/.cxoffice/dotwine/fake_windows/Windows/Icons/9d75_iexplore.-32528.xpm [jeltsch@mcblpc2 applications]$ more CXTree-Windows_Applications-Programs-Internet_Explorer.desktop[Desktop Entry]Name=Internet ExplorerType=ApplicationComment=Internet ExplorerExec=/opt/cxoffice/bin/wine “C://Program Files//Internet Explorer//IEXPLORE.EXE” X-Created-by=cxoffice Icon=/home/jeltsch/.cxoffice/dotwine/fake_windows/Windows/Icons/9d75_iexplore.-32528.xpm Categories=Application;X-cxoffice;X-CXTree-Windows_Applications-Programs;It appears that all entries that were made by the Crossover Office Installer are still present in this directory. Now I just have to figure out why they don’t show up. Of course I can start the applications by just typing the entry under Exec into the command line but that is somehow cumbersome. To test GCK2.5 I started it from the command line and it really came up. First it asked for the installer CD (some kind of copy protection mechanism). It was in the drive but somehow I had to eject it and insert it again to make it visible. That worked fine and the dialog appeared where I entered my name and organization. But then it miraculously complained: “Could not start the application because there is not enough memory”.Now I have to tackle this problem, because GCK2.5 is probably the most important application for me that has not Linux equivalent.

BackupPC (and MacOS X)

Fri, 25 May 2007 00:00:00 +0000

BackupPC seems to be a cool application. Except for the fact that it is not easy to start working with in the first place. I downloaded BackupPC-2.0.0.tar.gz and installed it into the directory /usr/local/backuppc. Then I executed the config.pl and answered all I could. The place where I want to backup my stuff is my second hard drive /dev/hdb5 which is formatted as reiserfs and mounted at /mnt/hdb. After the config script there was a new directory in /mnt/hdb: backuppc, which contained 6 other directories: conf, cpool, log, pc, pool and trash.BTW you cannot use a smbmount to store the backup data (at least not easily). The configure.pl script tries to chown the stuff on the smbmount and this leads to the abortion of the perl script (could be modified and the chown could be done manually by defining the correct uid and gid in the fstab). I struggled with this for a day (gave the smbmount even fmask=777,dmask=777 and the correct owner/group), but to no avail as apparently the scripts wants to execute the chown command. I probably need to solve this problem as I need to backup via the network to a Macintosh running OS X and thus need to use samba (or nfs…).I use tar over ssh to backup my client (actually server and one of the clients are in my case physically the same machine). Anyway I have to setup ssh. As I have RH9, it’s OpenSSH (ssh2).Another client is running MacOS X (10.3). Works quite well after I figured out that the tar command on MacOS X is neither in the PATH nor in its normal location, but in /usr/bin/tar. I just made a link and BackupPC worked:sudo ln -s /usr/bin/tar /bin/tar

Changing environment variables (env, csh, bash)

Fri, 25 May 2007 00:00:00 +0000

I just install BackupPC. The perl install script complains that my environment variable LANG is set to en_US.UTF-8 and that it should be en_US. This setting is specificed in RedHat 9 Linux in the file /etc/sysconfig/i18n. To check what is the current value of the LANG variable type echo $LANG. To change or set the variable to en_US type LANG=en_US To show all environment variables, just enterenvat the command line.If you want to set an environment variable, you need to know what shell you are using. Many instructions still assume that you are using csh, but I guess it’s maybe only 1% of Linux users that use it. E.g. in the bash shell use the following command to set the environment variable DESTDIR to /usr/localexport DESTDIR=/usr/localwhile in csh typeDESTDIR = /usr/local

Connecting the external hard drive to my computer (Maxtor One Touch 200GB, FireWire & USB 2.0/1.1)

Fri, 25 May 2007 00:00:00 +0000

The hard drive was connected to Redhat9 Linux via firewire and the hard drive had a reiserfs filesystem. It was supposed to be used for backups, but suddenly stopped working (it was not anymore recognized during system startup). Probably that had something to do with the external USB zip drive. Both are apparently visible to the system as SCSI devices and the zip drive might have (via automount) occupied the sda number that was manually added to /etc/fstab to enable the Maxtor hard drive. To check whether everything is OK with the drive itself, I connected it to my work computer. My work computer, however doesn’t have a fire wire card, so I had to use the USB port. This shouldn’t make any difference as both USB and firewire are somehow treated as SCSI devices.I only edited /etc/fstab adding the following line:/dev/sda1 /mnt/usbhd1 reiserfs defaults 1 2I first forgot to create the directory /mnt/usbhd1. Thus after restarting the drive was not mounted. I checked with /sbin/fdisk -l and there was the following entry/dev/sda1 Windows 95 (or something like that)Funnily the resiserfs file system shows as a fat filesystem. I changed the “reiserfs” entry in /etc/fstab to “vfat” and created the directory /mnt/usbhd1. During startup there was an error (something like “no fat filesystem could be found on the partition”). So I changed it back to reiserfs, rebooted and the external drive was mounted during startup without problems.

Debugging GCK2.5 under wine

Fri, 25 May 2007 00:00:00 +0000

GCK2.5.9 works with wine (crossover office 2.01 version). The 2.5.9 update doesn’t show the “Could not start the application because there is not enough memory” error. GCK starts up without any trouble and is partially usable. In fact it seems to be fully functional (including Deluxe import) with one big exception: new files cannot be created (quits upon selecting “File - New”. The empty window box where you can select what type of GCK file you want to create (sequence, illustration, etc) is drawn with the title “New Window”, but its not filled with content and the application quits.

Dubugging GCK2.5 under wine

Fri, 25 May 2007 00:00:00 +0000

The new window that fails to be displayed, contains (when run natievly under W2K) the following text (and radio buttons for the four different file types):Select File Type Contruct (Ctrl-C)Illustration (Ctrl-I)List (Ctrl-L)Gel (Ctrl-G)New File NameOKCancelThe text associated with the different radio buttons appears first in the debug file in the following lines (as determined by the command “grep -n “List” all_output > List_output”, etc): 3890577 Gel3885836 Illustration3881107 List3876329 ConstructThat is within the range where we predicted the error to be. Let’s now look at what happend shortly before and after these commands were issued. After using GCK2.5 under wine a little bit more, I noticed that there is another function that causes the program to crash without error message, namely the “find sequence” function. Also in this case a dialog is displayed in which the user is supposed to type in a nucleotide sequence. Maybe there is something in common for these two crashes which could help to identify the crucial system call that makes the program to crash.

Gnome & KDE sessions autostart items

Fri, 25 May 2007 00:00:00 +0000

Always when I logged into a Gnome session, automatically several application started up without me wanting them to start up (two terminal sessions and a nautilus windows). To get rid of them (at least I think so, I will see at the next login), you have to go to Main Menu - Preferences - More preferences - Sessions. Under the “Current Session” tab, one can remove the programs that are automatically started upon login and also specify in which order the programs are started that are started automatically.In KDE, item in the /home/user/.kde/Autostart directory get executed upon session start. Just place a .desktop file into that directory to have it auto-executed.

grep to search for file content or rpm -qa output

Fri, 25 May 2007 00:00:00 +0000

In order to search a specific directory (path_to_directory) and all its subdirectories (-r for recursive) for files that contain a specific text string, use the following command:grep -r "textstring" path_to_directoryAlso very useful is to pipe the output of another process into grep. E.g. you want to know whether a specific rpm package is installed on your system, but you don’t remember the exact name. Thus you cannot use the “rpm -q packagename”. In that cast you can ask rpm for all installed packages (rpm -qa) and then pipe this output to grep and let grep look for a substring from the packagename that you do remember:rpm -qa | grep substringE.g. when the package modutils-2.4.22-8 is installed you have to ask rpm:rpm -q modutils OR rpm -q modutils-2.4.22in order to get an answer. The request rpm -q modutils-2.4 would be: The package modutils-2.4 is not installed. Thus if you don’t know the exact name of the package, it is a safe bet to grep the rpm output for something you remember exactly.

Location of launchers, panels, etc. in Gnome

Fri, 25 May 2007 00:00:00 +0000

The files that specify the different folders and buttons of the Gnome user interface are somehow really badly distributed all over the place. Here are just a few of the more common locations:Icons in the panel: ~/.gnome2/panel2.d/default/launchers/Contents of Start Here: ~/.gnome2/vfolders/start-here/user’s Home, Trash and Start Here: ~/.gnome-desktop/

Loosing your Windows softly

Fri, 25 May 2007 00:00:00 +0000

I have two hard drives and the partitioning is as follows:hda1 120 GB/dev/hda1 100 MB Linux ext3 /boot/dev/hda2 95 GB Linux ext3 /home/dev/hda3 1 GB Linux swap/dev/hdb4 Extended partition/dev/hdb5 17 GB Linux /hdb1 32 GB/dev/hdb1 100 MB Linux ext3 /boot/dev/hdb2 1 GB Linux swap/dev/hdb3 Extended partition/dev/hdb4 12 GB NTFS Windows2000/dev/hdb5 18 GB Linux reiserfsBoth boot partitions had grub installed (there used to be an old Linux Red Hat 7 install on hdb1). The bios was set to use the first hard drive (hda1) to boot. In order to boot Windows 2000, one needs apparently a Windows-written MBR (master boot record), which is to my understanding something like a hidden partition which is in any case the first partition of any drive (something like hda0). Since there was never Windows 2000 installed on hda1 (is was put later into the machine and put into the bios boot priority first), there was also no Windows 2000-like MBR written into its MBR. The other hard drive (hdb) has a Windows install (Linux was installed later), so there must have been a functioning Windows 2000-like MBR. That MBR most likely was destroyed at some time. This distruction did not happen during the first Linux Red Hat 7 install, as after that one could still boot into Windows 2000 via grub. It must have occurred later somehow (maybe during a grub update?). Then I put the 2nd hard drive in, installed Red Hat 9 and during this install the Red Hat installer put the second grub install onto its boot partition, which did contain a Windows entry (as I specified during the Red Hat 9 installation). Booting into Windows 2000 (which was on the other hard drive) was still possible. But as I never used to boot into Windows (I started to use vmware and then wine), I just recently realized that the Windows entry in the grub.conf had disappeared. Consequently I couldn’t boot into Windows anymore. I entered manually the Windows entry like everywhere advised:title Windows 2000rootnoverify (hd1,1)chainloader +1But no go. I always received an error (Error 13 invalid device). I thought I had chosen the wrong partition and tried all possible partitions from (hd1,0) to (hd1,5). Still no go. Although the error messages were different. For the:/boot partition (hd1,0): Grubloader error 25linux /home (hd1,1): Error 13 invalid or unsupported executable format linux swap (hd1,2): Error 12 invalid device extended partition entry (hd1,3): no error occurred, but I was thrown into the grub menu of the boot partition of the 2nd hard drive linux / (hd1,4): Error 12 invalid deviceany other (higher) partition that wasn’t present (e.g. hd1,5): Error 12 invalid deviceSo I booted with the Windows 2000 installation CD and tried to fix the the MBR of hdb. I went into the manual repair section and typed the fixmbr command. There was a warning: “This operation modifies your partition table and could render all your data on the hard drive inaccessible”. I had no choice, so I did it. It didn’t help. At least not much. Once thing improved, however: when I swapped the drives (made hdb the master and hda the slave and gave in the BIOS boot priority to the new master, I could boot into Windows 2000. That was already some improvement. However, I still couldn’t boot into Windows 2000 via grub. So I booted again with the Windows 2000 installation CD and executed another “dangerous” command: FIXBOOT. This was the end of my Windows. After that I couldn’t boot into Windows at all. I always received the error: ntldr is missing (NT loader is missing). I still managed to use this Windows 2000 installation together with VMware, but otherwise there was no possibility to boot it up. The Microsoft Knowledge Base Article 318728 describes many possible solutions to the “ntldr is missing” error, which I tried all, but without any positive results. Microsoft apparently admits, that this error is unrecoverable in some instances as the last method to rescue such a situation is: “Perform a Parallel Installation of Windows 2000 and use the Windows Explorer to copy the data you want to recover”.

Self-extracting compressed files

Fri, 25 May 2007 00:00:00 +0000

Today I created a self-extracting, compressed file from a pdf document (disclosure.pdf). First I compressed the pdf file:

bzip2 disclosure.pdf

Then I create a text file (header.txt) with the following content:

sudo is not only to sudo (execute files as another user)

Fri, 25 May 2007 00:00:00 +0000

If you want to execute a command with root privileges, you normally use the command “sudo”. But of course you can execute a command also as any other user. E.g. I need to execute some script for my backup as user “backuppc”. then I just type:sudo -u backuppc /usr/local/backuppc/bin/BackupPC_serverMesg status infoInstead of the username (backuppc) one can also use the user id (uid).

Suse 9

Fri, 25 May 2007 00:00:00 +0000

I switched to Suse 9. I can’t figure out from RedHat’s announcements what they are really up to. So I better get used to an alternative right now. I also switched from Gnome to KDE and at least on Suse 9, I like KDE more than Gnome on Red Hat 9.

Changing job priority under Linux

Thu, 24 May 2007 00:00:00 +0000

If the job is already running use:renice 19 -p 2478This gives the job 2478 (as identified with ps -aux) the lowest possible priority. renice -20 would give it highest priority. If the job is not yet running you can execute it with nice command:nice +19 amuleto execute amule with lowest possible priority) andnice -20 amuleto execute it with highest priority.

Editing the crontab

Thu, 24 May 2007 00:00:00 +0000

We have a shared directory (/home/shared) on our computer and a usergroup called “shared”. The purpose is that we put things there that should be accessible (including writable) to several users of the system. If one user puts a file there, it can be read by others but not e.g. deleted. In order to fix this, we edited the crontab to execute every 5 minutes the following two commands: chgrp -R shared /home/sharedchmod -R 744 /home/sharedIn order to do this we edited (as root of course) the /etc/crontab file by adding the line: */5 * * * * root run-parts /etc/cron.minutelyThis means execution every 5 minutes, every hour, every day, every month, every weekday the script run-parts should be executed as root taking all scripts from the /etc/cron.minutely as argument (we created this directory newly in addition to the already existing /etc/cron.hourly, etc.). We restarted crond (the crontab deamon) via the GUI (under RedHat 9 Menu-System Settings-Server Settings-Services).

Installing Staden 2003b on Suse 9

Thu, 24 May 2007 00:00:00 +0000

Download the sources .
cd into /usr/local and become su.
tar -xvzf /home/jeltsch/Documents/staden_linux_2003.0b1.tar.gz (jeltsch is my usename, thus has to be replaced for other users!!!!)

More about GCK2.5 under wine

Thu, 24 May 2007 00:00:00 +0000

After working with GCK2.5 under wine I have identified more bugs that make the program quit unexpectedly. However, now I have not been using cross-over office (as its evaluation period has expired and of course my boss wouldn’t spend a cent for Linux programs). So I am using the default installation of wine that comes with Suse 9. I copied over the fake windows directory from the former .cxoffice directory. The following bugs do exist (they always appear when a window opens that requires you to enter alphanumeric values via the keyboard):1. Create new file (I knew about that before). Interestingly the (empty) new file that opens upon program start can be saved without problems…2. Find sequence (one shortly sees the window “Find occurence” and then the program quits)3. Sometimes (not always), when changing the color of a selected sequence the program quits.4. Features -> Make Region5. When selecting a sequence and getting info

No chown or chmod on samba mounts

Thu, 24 May 2007 00:00:00 +0000

I figured out (hopefully correctly) that owner, group and accession rights to files and directories on an smbmount are not changeable, not even by root. Thus you have to specify everything at mount time, e.g.:sudo mount -t smbfs -o username=jeltsch,credentials=/home/jeltsch/.smbpasswd5 -o uid=backuppc,gid=users,fmask=644,dmask=755 //patolmac217/jeltsch /mnt/jeltsch@patolmac217.hi.helsinki.fi

Problem to access X desktop from a root terminal

Thu, 24 May 2007 00:00:00 +0000

It never happened to me under Red Hat 9, but when I am working in KDE as a normal user and try to execute emacs from a terminal, in which I am su, I occasionally get the following error message:jeltsch@mcblpc2:~> suPassword:mcblpc2:/home/jeltsch emacs test.txtXlib: connection to ":0.0" refused by serverXlib: Invalid XDM-AUTHORIZATION-1 key (failed key comparison)emacs: Cannot connect to X server :0.0.Check the DISPLAY environment variable or use -d’.Also use the xhost’ program to verify that it is set to permit connections from your machine. In order to allow root to access X, you need to execute the following command: mcblpc2:/home/jeltsch export XAUTHORITY=/home/jeltsch/.Xauthoritymcblpc2:/home/jeltsch emacs test.txtOf course, I can use emacs without its GUI and just type:emacs -nw test.txt

ps2pdf

Thu, 24 May 2007 00:00:00 +0000

I got a bit confused about the ps2pdf conversion utility. Some people claim, that it invariably creates pdf files with letter pagesize. However there is the argument -sPAPERSIZE=a4 and that should make pdf files with a4-sized pages. It apparently works. If one uses eps files as input files, ps2pdf puts the eps image directly to the border of the pdf file which gets cut off during printing. There should be some utilities to correct this.

RPM management

Thu, 24 May 2007 00:00:00 +0000

Example: The quanta packagerpm -q quanta Check whether and which version of quanta is installedrpm -ql quanta List all files (and their installation location) that are provided by the quanta packagerpm -ivh quanta Install quantarpm -e quanta Erase (deinstall) quantarpm -aq | grep quanta If you don’t know exactly what you are looking for you can list all packages and grep them with a substring.rpm -q -f filename Search for rpm packages that provide filenameA good manual for rpm managemant: http://www.rpm.org/max-rpm/ .If you want to query an RPM that is not installed, you need the following syntax:rpm -qpl --requires quanta.rpm This would list all requirements and all files that are in the package.cat package.rpm | rpm2cpio | pax -r Extract a file from an rpm package.

Starting up and shutting down network cards

Thu, 24 May 2007 00:00:00 +0000

STARTING:(/usr)/sbin/ifup eth0 (or eth1)STOPPING:(/usr)/sbin/ifdown eth0 (or eth1)STATUS:(/usr)/sbin/ifconfig -a

Using Riositude under VMware

Thu, 24 May 2007 00:00:00 +0000

I have to admit, that there is no really functioning GUI for the rioutils. Meaning that if I want to upload mp3 files to my Rio500 under Linux I have to use the command line (and even the command line seems to be somehow instable as the rpm was created a while ago and compiling fails under the recent Linux releases (Red Hat 8,9, Suse 8, 9). So I used first the Rioport AudioManager 3 under VMware. It is slow and the GUI is as bad as it gets (bloatware). A really cool replacement program for Windows is Riositude . It’s much faster, easier to use and takes not even 200 KB disk space. It works great from VMware provided I start it up immediately after plugging in my Rio500. Otherwise the Linux takes over (I guess a usb kernel module is loaded automatically upon plugging in the Rio). The kernel module has to be removed manually by “sudo /sbin/rmmod rio500” to allow VMware to control the Rio. To check which kernel moduls are loaded, use “/sbin/lsmod”. I should somehow get rid of this module if I want to stick to Riositude/VMware to operate my Rio. There are of course other programs for Windows, that can do a similar job, e.g. Rio FXP . Unfortunately this one didn’t work for us under WindowsXP. A listing of Riosoftware can be found at rioworld.org .

VNC server (aka KDE Desktop Sharing) under Suse 9

Thu, 24 May 2007 00:00:00 +0000

Suse 9 has an inbuilt VNC server called KDE Desktop sharing (under the System -> Remote Access menu). It can be configured in the Control Center -> Internet & Network. Unlike when you start up VNC via the command line (“vncserver”) this tool doesn’t start a new X desktop, but connects to your already existing X desktop. It is possible to run in addition to the inbuilt KDE Desktop Sharing a normal vncserver that starts its own X sessions.

VNC server under Suse 9

Thu, 24 May 2007 00:00:00 +0000

I tried to use vncserver on Suse 9, but to my surprise upon starting up with “vncserver” and then connecting with the “vncviewer” command I only saw the grey screen and an X terminal. I tried to execute xclock and gaim and they start up nicely. However I would also like to bee able to start up KDE. So I looked into the xstartup file (in the .vnc directory in your home folder) from my old Red Hat 9 install and compared it to the one from my Suse 9 install:Suse 9:!/bin/shxrdb $HOME/.Xresourcesxsetroot -solid greyxterm -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" &twm &Red Hat 9:!/bin/shRed Hat Linux VNC session startup scriptunset SESSION_MANAGERexec /etc/X11/xinit/xinitrcI figured out that twm is a window manager; thus it replaces KDE in this context. If I replace the Suse script by the Red Hat script, KDE starts up upon starting vncserver.

What Text Editor for Linux?

Thu, 24 May 2007 00:00:00 +0000

I have been using emacs (or Xemacs) so far, but now I started to use Nedit . Seems to be quite powerful and fast (although nothing comes close to BBEdit, unfortunately only for Macs).

A good introduction to shell scripting

Wed, 23 May 2007 00:00:00 +0000

http://www.freeos.com/guides/lsst

Adding a Suse 9 to a Red Hat 9 (two different distros on the same computer)

Wed, 23 May 2007 00:00:00 +0000

Red Hat 9 is installed and the following partitioning is present:hdd1 /boot (ext3) 100MBhdd2 /home (reiserfs) 7.8GBhdd3 / (ext3) 7.8GBhdd4 EXThdd5 swap 1GBhdd6 /mnt/documents (reiserfs) 12GBhdd7 /mnt/music (reiserfs) 90GBThe task is to add a second Linux OS (Suse 9) onto this hard disk without destroying anything. The root partition of this system should be 10 GB. Additionally I want to put all user-created files on one partition (now they are on three different partitions: hdd2, hdd6 and hdd7). First I got a 200 MB external USB2/firewire hard drive (Maxtor, mounted as /mnt/sdb1) and copied the data from hdd1, hdd2, hdd6 and hdd7 onto it with “cp -ax /home /mnt/sdb1”, etc. Then I rebooted using the Knoppix 3.3 CD and from a root terminal executed partimage. I tried to save the image of the root partition directly to my external usb drive, but without success: everytime the program halted somewhere during the process. I then saved the image on /mnt/music and that succeeded. I rebooted into Red Hat 9 and copied the image manually from /mnt/music to the usb drive (/mnt/sdb1). Because I didn’t trust the partimage program, I additionally copied the filesystem manually to the usb drive using the following commands: mkdir /mnt/sdb1/redhat_root cd / find . -xdev -print | cpio -padm /mnt/sdb1/redhat_root Apparently this copies everything including special files, mount points, etc. preserving all the file meta data. After this I disconnected the external usb drive (to be on the safe side), rebooted into Knoppix and wanted to try out QTParted. It should be able to resize partitions. From a root terminal: “qtparted”. However, I was not able to resize anything (the options were greyed out). I could delete and recreate though (which didn’t help much). So I decided to go for a clean sweep, popped the Suse 9 CD into the drive and rebooted into the Suse 9 installer. I choose expert partitioning and deleted all partitions that were present and recreated the following partitions. I made sure to use exactly the same amount of blocks (1019) for hdb3 as had been used for hdd3 because I knew that partimage can only restore images onto partitions that have exactly the same size or are bigger:/dev/hdb1 1 8 64228+ 83 Linux (ext3) /boot/dev/hdb2 9 1314 10490445 83 Linux (reiserfs) //dev/hdb3 1315 2333 8185117+ 83 Linux (reiserfs) /redhat/dev/hdb4 2334 14945 101305890 f Win95 Ext'd (LBA)/dev/hdb5 2334 2464 1052226 82 Linux swap/dev/hdb6 2465 14945 100253601 83 Linux (reiserfs) /homeAfter the install had finished, I rebooted into Knoppix and tried to restore the Red Hat root partition onto hdb3. Partimage told me that the partition was smaller than the image, thus a restore was not possible. So rebooted into Suse 9 and manually copied the Red Hat 9 root system back to hdb3 (with the same command sequnce that was used to copy it manually to the usb drive). Then I changed /redhat/etc/fstab to reflect the new partitioning and copied all the files from /boot (but not the subdirectories from /boot) onto the new boot partition (except those files that had already equivalents in /boot). Then I modified /boot/grub/menu.lst by adding a line for the Red Hat install:title Red Hat 9 Linuxroot (hd1,0)kernel /vmlinuz-2.4.20-19.9 root=/dev/hdb3initrd /initrd-2.4.20-19.9.imgI also create the two user folders in the /home directory (which used to be the mount point for the /home partition). But I copy all the hidden files and directories (those starting with a .) into the userfolders.Then I tried to reboot into Red Hat 9. Without success. Kernel panic. No init found. Try passing init=option to the kernel. Actually the file system check of hdb3 failed (no superblock found). There are several error messages and the important ones come first and fast (and you don’t see them) and the bad, misleading error messages come late. Something like that you should manually repair the partition. And that root is mounted read-only. And that you can make it read-write by “mount -n -o remount,rw /”. And that only with Ctrl-D one can reboot into this state. Obviously that’s what I am going to do. However there is no hint about what command to use. Several attempts to do anything while having mounted from hdb failed (if reiserfs is read-only it cannot be repaired, if it is read-write it cannot be checked). So I reboot into Knoppix and do the repair from there: fsck (which executes reiserfsck) doesn’t do the job: it only checks, but doesn’t do any repairs. I figured that flagging reiserfsck –rebuild-sb /dev/hdb3 does repair the superblock. Still no go, so I do the slow complete rebuild of the filesystem from scratch with reiserfsck –rebuild-tree /dev/hdb3. It still doesn’t boot into RH9. Then I get the idea: the RH9 kernel might not support reiserfs (or the module is not loaded). Or (alternatively) copying some special files from a ext3 partition to a reiserfs partition might simply not work. So I delete (from Knoppix) the whole hdb3 and recreate it as ext3. Copy back all the data (QTParted still complains about too small size). And it finally works. I create two directories for the two users on the /home partitons and manually copy into them the non-hidden files of the old userfolders. I don’t copy the hidden files. There are many that would screw up Suse and make it impossible to log in (I had tried that out before). I log into Suse 9 as root and create the two users with exactly the same name as on RH9. There is a warning that the directory exists and that all its content will be owned by the new user. That is OK of course.

Adobe Acrobat 5.0.5 under wine

Wed, 23 May 2007 00:00:00 +0000

I reinstalled Acrobat 5 to run it under wine. It didn’t work. The reason appeared to be again a plugin: DocBox.api. After removing it everything went smoothly. Already before (using RedHat 9) I have had trouble with a Acrobat plugin (it was WebPDF.api at that time). Most manipulation of pdf files can be easily done with Linux tools, but one thing is tricky: cropping already existing pdf files. That’s why I need Acrobat.

Apache on Mac OS X

Wed, 23 May 2007 00:00:00 +0000

I still use one of our ancient Macintoshs (Blue/White G3) as a web server ( msbl.helsinki.fi ). I had set up some access restrictions for some of the pages containing confidential data. And of course I forgot how I did it. Now I needed to figure out as I wanted to add some new stuff. For the general server, the accession is restricted based on individual .htaccess files in directories. In my own user directory ( msbl.helsinki.fi/~michael ) only one folder is access restricted ( msbl.helsinki.fi/~michael/presentations/confidential ). This setting is done in the main configuration file of Apache (/etc/httpd/httpd.conf) and only two users (michael and mcbl) have access via the following entry: AuthType Basic AuthName "Confidental" AuthUserFile /Users/michael/.htpasswd require user michael mcbl

Burning CDs from the command line: cdrdao

Wed, 23 May 2007 00:00:00 +0000

K3b seems to be the best GUI for burning CDs on Linux. But today it failed to burn an image file (bin/cue) and I don’t know why. So I used:cdrdao write --device /dev/cdrecorder --speed 8 filename.cue

Changing sound volume or bitrate of mp3 files with lame

Wed, 23 May 2007 00:00:00 +0000

Sometimes the recording level of mp3 files is very low. If I do some jogging next to a busy road, I cannot hear anything even when the sound volume is on the max. Therefore I have to increase the volume of the mp3 file. Using lame you can do it with the following script: #!/bin/bashwhile [ $# -ge 1 ]; doinfn=$1outfn="${infn%%.mp3}_3x.mp3"echo $outfnlame --mp3input -v --scale=3 $infn $outfnshift 1doneThe only problem is that filnames with blank spaces make this script to collapse. Have to figure out something else. Also the bitrate can be modified in this way:#!/bin/bashwhile [ $# -ge 1 ]; doinfn=$1outfn="${infn%%.mp3}_LQ.mp3"echo $outfnlame --mp3input -V 9 $infn $outfnshift 1done-V 9 is the lowest bitrate/quality -V 0 is the highest.

Changing specific ownerships: chmod --from

Wed, 23 May 2007 00:00:00 +0000

I copied a bunch of preference files (those files and directories whose name starts with a dot) from my old RedHat home directory into my new Suse install. I had backed up the files being root and so all of them were owner:group root:root. In order to only change those files, that had root:root into jeltsch:users I executed from within my home directory:sudo chown -R --from=root:root jeltsch:users .*If you wanted to change all files on the system that belong to one user you could use:sudo chown -R --from=username newowner /

Creating a boot floppy for RedHat 8

Wed, 23 May 2007 00:00:00 +0000

Get the boot floppy image from the RedHat site and write it to a floppy. The floppy should not be mounted while writing:dd if=boot.img of=/dev/fd0That’s actually the command to write any floppy image back to a floppy.

Creating groups and changing group membership in Mac OS X

Wed, 23 May 2007 00:00:00 +0000

I want to store some files on a Macintosh (OS 10.2). They should be in the Public folder, but only accessible (= only readable) by certain people. Thus I would like to create a new group that has accession rights to these files. Strangely, the group command doesn’t exist on MacOS X (chgrp does exist though). I downloaded the User Manager application. But the version for OS 10.2 was not really easy to use. Thus I used the NetInfo Manager. I duplicated an existing group, changed its name to “gck” and id number and added two users (if you have more than one entry, you have to add them in brackets and comma-seperated). Then I created a directory in my Public folder and changed its group to “gck”. Permissions for this directory are drwxr-x—. The files inside this directory also belong all to the “gck” group and have -rwxr—– permissions.

Creating Konqueror Service Menus (aka contextual menus)

Wed, 23 May 2007 00:00:00 +0000

Konqueror Service Menues are additonal options that are displayed when you right-click on a file in Konqueror. They are file-type specific, meaning you can define which options are displayed depending what type of file you are right-clicking. Mac-people call these “contextual menues”. A good tutorial is https://techbase.kde.org/Development/Tutorials/Creating_Konqueror_Service_MenusIn short: In the directory /opt/kde3/share/apps/konqueror/servicemenus there is a buch of desktop files. Just duplicate one, rename it and edit its content to please you. In the following example I have created a new file (pdfpic.desktop), that adds a menu option that is displayed when I right-click jpg files and it starts an editor with which I can add or modify the embedded rdf (resource description framework) information of a jpeg file. The editor is a java application and the %U sais, that if many files are simultaneously right-clicked they should be opened in one instance of the program.[Desktop Entry]ServiceTypes=image/jpegActions=openInRdfpic[Desktop Action openInRdfpic]Name=Edit metadataIcon=backgroundExec=/usr/lib/java2/jre/bin/java -jar /usr/local/rdfpic-2.1/rdfpic.jar %U

Editing (resizing, format converting, compressing) images in the command line with ImageMagick (mogrify, convert)

Wed, 23 May 2007 00:00:00 +0000

Resize all tif images in the current directory:mogrify -resize 25% 25% *.tifResize all jpeg images in the current directory to a width of 614 pixels and keep the image ratio constant:mogrify -resize 614 *.jpgAs above, but resize the hight to 614 pixels:mogrify -resize x614 *.jpgConvert all bmp imgaes in the current directory into tiff images:mogrify -format tiff *.bmpCompress all tiff images in the current directory with ZIP compression:mogrify -compress ZIP *.tiffI tried to convert also pict files (from Macintosh), but without success, although the pict file format appears to be supported by Imagemagick. In order to make sure that ImageMagick knows that the file to convert is a pict file I used this command:convert pict:Photo0024.PICT tiff:Photo0002.tifThere is also a picttoppm utility in the netpbm package, but it was not anymore included in the version that Suse 9 uses; so I couldn’t check that out…Interestingly PixiePlus can display pict files, where does it take the routines from?If you have very large images, the default limits of ImageMagick are resulting in an error(e.g. mogrify-im6.q16: width or height exceeds limit) and you need to edit /etc/ImageMagick-6/policy.xml!

GRAMPS and Suse Linux 9

Wed, 23 May 2007 00:00:00 +0000

At first I thought there is no way to get the GRAMPS genealogy software running on Suse 9. Apparently GNOME support by Suse sucks; the GRAMPS developers even say there are several things broken in the GNOME support of Suse. But finally there is a Suse Linux 9 RPM, that works (at least for us): http://apt.bygden.nu/SuSE/9.0-i386/RPMS.suser-rbos/gramps-0.98.0-rb1.i586.rpm . Here also my favourite way to make a graphical report from GRAMPS (you need to have the graphviz package installed):If you want to make a pdf file:

How to import sequences from SRS into GCK2.5

Wed, 23 May 2007 00:00:00 +0000

Obviously you can import sequences into GCK2.5 directly from Genbank. But usually you are working with a web tool like SRS and end up having your sequences displayed in your browser. From SRS version 7 the import goes as follows: From your fancy display, click SAVE. From the pull-down menu “Use view” select * Complete Entries *. Then “Output to” FILE (TEXT). Check under “Save as type” SAVE TABEL AS ASCii TABLE/TEXT WITH. Click SAVE and save it somewhere with the file extension .ebl. Then from within GCK2.5 select IMPORT and select the file. Ready.

How to mount a NFS export

Wed, 23 May 2007 00:00:00 +0000

sudo mount -t nfs -o rw server:/var/www /webserverormount server:/var/www /webserverThe mount can be put into /etc/fstab, e.g.:server:/var/www /webserver nfs rsize=8192,wsize=8192,timeo=14,intr,userThis doesn’t mount the nfs export automatically during startup, but any user can mount it by executing “mount /webserver”. Be aware that if you have mounted another filesystem under /var/www (e.g. if you keep all html data on a seperate partition like /var/www/htdocs), these won’t be available unless you export the partition’s mountpoint seperately!

How to rescue a bad X configuration during Suse 9 install

Wed, 23 May 2007 00:00:00 +0000

During my first Suse9 install I screwed up X. During the configuration of X the installer suggested to me: vesa 1600x1200@75. I thought I was smarter and went to the manual configuration and selected my Nokia 445Xi monitor from the list. Then it tried to switch into the new mode and gave me buttons to adjust the settings (centering, width, etc.). I did that and after I was satisfied continued the installation. When X was supposed to start up for the first time, my screen showed only “out of synch”. The way how to repair this is: Reboot in safe mode; change in /boot/grub/menu.lst vga=xxx into vga=normal and remove the “showopts” entry. Reboot again in safe mode, change to runlevel 3 (“init 3”) and execute sax2 –vesa 0:1024x768@75. Then I again selected my Nokia monitor but didn’t do the adjustments (I centered and sized the image only via the front panel knobs on the monitor). And everything is fine again.

MySQL install

Wed, 23 May 2007 00:00:00 +0000

After installing the Suse 9 rpm, execute the following commands:sudo /usr/bin/mysql_install_db(Creating default databases & permissions. Apparently the same can be done by “sudo rcmysql start”)sudo /usr/bin/mysqld_safe --user=mysql &(Start the server for the first time)REMEMBER TO SET A PASSWORD FOR THE MySQL root USER ! This is done with: /usr/bin/mysqladmin -u root password 'new-password' /usr/bin/mysqladmin -u root -h hostname password 'new-password'Give all privileges to root and user:/usr/bin/mysql -u root -p Enter password:Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 6 to server version: 4.0.15 Type 'help;' or '\h' for help. Type '\c' to clear the buffer.mysql> GRANT ALL PRIVILEGES ON *.* TO user@localhost IDENTIFIED BY 'Password' WITH GRANT OPTION; Query OK, 0 rows affected (0.00 sec)mysql> GRANT ALL PRIVILEGES ON *.* TO user@'%' IDENTIFIED BY 'Password' WITH GRANT OPTION;Query OK, 0 rows affected (0.00 sec)mysql> GRANT ALL PRIVILEGES ON *.* TO root@localhost IDENTIFIED BY 'Password' WITH GRANT OPTION; Query OK, 0 rows affected (0.00 sec)mysql> GRANT ALL PRIVILEGES ON *.* TO root@'%' IDENTIFIED BY 'Password' WITH GRANT OPTION; Query OK, 0 rows affected (0.00 sec)mysql> quit Bye``/usr/bin/mysqladmin version(later “/usr/bin/mysqladmin -u root -p version” is necessary)/usr/bin/mysqladmin variables(later “/usr/bin/mysqladmin -u root -p variables” is necessary)/usr/bin/mysqladmin -u root -p shutdown(can you shutdown the server?)sudo /usr/bin/mysqld_safe --log &(can you start the server?)ps -A | grep mysql(check whether the server process is running)/usr/bin/mysqlshow -u root -p(show all databases)/usr/bin/mysqlshow -u root -p mysql(show the tables of database “mysql”)To start the mysql daemon at system startup, you should go to the runlevel editor (advanced mode) and toggle the status for the mysql entry of init.d

Piping the output of find into a new command (find, xargs)

Wed, 23 May 2007 00:00:00 +0000

E.g. to change the permissions of all directories:find . -type d -print | xargs /bin/chmod ug+rxTo be able to handle directory names with special charactersfind . -type d -print0 | xargs -0 /bin/chmod ug+rxIn order to find all tif files in the current directory or below and to compress them (using the ImageMagick “mogrify” command and LZW compression):find . -name '*.tif' -print | xargs mogrify -compress LZWApart from the “xargs” method, some command (including find) accept the “-exec” argument. The following finds all files in the current directory that are smaller than 4k and deletes them:find . -size -4k -exec rm {} \;

Problems with vhosts on RedHat 8

Wed, 23 May 2007 00:00:00 +0000

We have httpd-2.0.40-11.9 installed and configured at our domain registrars site that jeltsch.org, marzidesign.com and sundayscam.com are forwared to our IP address (62.18.133.129). However, whatever site we requested from within our browser, the index.html files from vhost jeltsch.org was loaded. First it seemed that the browsers request didn’t include the name of the server. Because in such cases the webservers serves the first vhost in the list (which is jeltsch.org). However, the problem was another one: Under the vhosts directives we had the following configuration:NameVirtualHost *:80ServerAdmin webmaster@jeltsch.orgDocumentRoot /var/www/html/vhosts/jeltsch.orgServerName jeltsch.orgServerAlias www.jeltsch.orgErrorLog logs/jeltsch.org-error_logCustomLog logs/jeltsch.org-access_log combinedand then all the other vhosts. When we changed these settings to the following ones, things started to work:NameVirtualHost 62.78.133.129ServerAdmin webmaster@jeltsch.orgDocumentRoot /var/www/html/vhosts/jeltsch.orgServerName jeltsch.orgServerAlias www.jeltsch.orgErrorLog logs/jeltsch.org-error_logCustomLog logs/jeltsch.org-access_log combinedThis is not nice as it requires us to change the IP number in the httpd.conf file every time our dynamically assigned ip address changes. In theory the * should work.

ps2pdf versus pstill and password protection of pdf documents

Wed, 23 May 2007 00:00:00 +0000

While reading about ps2pdf (which is just a commandline front-end to ghostscript), I realized that despite its simple appearance, ps2pdf has almost all capabilities of Acrobat 5. ps2pdf14 outputs Acrobat 5-compatible files. According to the documentation strong password protection should be possible, however, I never managed with that.In theory the following commands should work:-sOwnerPassword= and -sUserPassword=In order to set the key length to 128 you have to useps2pdf14 -dEncryptionR=3 -dKeylength=128Another thing that I don’t know how to handle easily with ps2pdf is the cropping of documents.For the password protection, a very good alternative seems to be PStill ( http://www.pstill.com/ ). The command:pstill -Muserpassword=testpassword testfile.psdoes the trick.

Running wine from a real windows install

Wed, 23 May 2007 00:00:00 +0000

I thought wine might run better from a real windows install. So I resized my partitions to free some 8 GB space. Unfortunately the partitioning software was not really great as I lost one of my partitions (the one where I had stored all of my downloads…). So I decided to go for a clean start and formatted the whole hard disk. First I partitioned the disk using cfdisk. Then I installed Windows98 from the installer CD onto the FAT32 partition, after that Windows2000 from the installer CD to another FAT32 partition (I wanted to install WindowsXP, but the installer CD refused to boot my computer). After that I reinstalled Suse 9 and copied back my home folder from my backup disk. So far wine works fine (after some minor adjustments in $home/.wine/config and mounting the Windows98 partition withmount -t vfat -o uid=jeltsch,gid=users,fmask=644,dmask=755 /dev/hda1 /media/win98Without giving the uid, gis, fmask and dmask options you won’t be able to write anything to the partition.

Samba trouble (smb, smbadduser, smbpasswd)

Wed, 23 May 2007 00:00:00 +0000

If your samba is unreliable, there can be a number of reasons. I got the impression that YAST overwrites configuration data you have manually edited (e.g. in the password and user files) when you try to change settings via the YAST samba setup procedure. Here follows a checklist in case samba is again not responding or not visible in the network neighborhood. It could be that the unreliability is due to a PDC shutting down. Maybe I should make my Linux the PDC as it is always running. Anyway even if I manage to connect from W2K (using map network drive) I couldn’t connect from W98 by clicking the visible icon of my computer in the MCBL workgroup (“network path not found”). And in MacOSX my computer was not visible at all (but I could connect via the manual command “smb://128.214.186.42/homes”). Strange…In /etc/samba/smb.conf:

Spin down the harddisk with hdparm

Wed, 23 May 2007 00:00:00 +0000

The command to spin down the hard disk after 50 seconds (5x10) being idle: /sbin/hdparm -S10 /dev/hda

ssh host keys

Wed, 23 May 2007 00:00:00 +0000

When reinstalling an ssh server, one should keep the ssh key files from the old system. Otherwise ssh clients will receive messages of like “IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!”. If you didn’t keep the files, the clients can of course delete the entries from the host key file (usually /home/user/.ssh/known_hosts). When the user connects after that again to the server, the new, changed host key files are added to the host key file.

The new iPod (3rd generation) and Suse Linux 9

Wed, 23 May 2007 00:00:00 +0000

I have bought an iPod. And it appears that the 3rd generation iPod is substantially different from the previous models. E.g. in its file system. In previous models you could convert the HFS+ file system into a FAT32 filesystem. HFS+ is the filesystem used by the new MacOS X OS. It cannot be read by Windows OS (unless you buy commerical third party software such as MacOpener or MacDrive). There are several Linux-interfaces for the iPod, but they all require that the iPod is mounted as a regular mass storage device. Suse Linux 9 luckily has support for HFS+ filesystems although it is still experimental. In order to be able to mount HFS+ formatted file systems, you have to load the hfsplus kernel module:sudo /sbin/modprobe hfsplusAfter that you can just plug in the iPod. After a while you will hear a beep meaning that it was recognized. To determine which device number it got you should check the system messages:tail -30 /var/log/messagesAs it is handles like a SCSI device it will get probably sda if it is your first usb/firewire device. If you have already usb or firewire devices connected to your computer it will get maybe sdb or sdc (and so on). Create a mount point:sudo mkdir /media/ipodThe 3rd generation iPod has apparently two partitions. The first must be for the firmware/system software (sdx1) and the second is for the data (sdx29. Funnily when I tried to mount it withsudo mount -t hfsplus /dev/sdc2 /media/ipodthe system complained that something is not OK with the device. However, when I tried:sudo mount -o umask=000 /dev/sdc2 /media/ipodeverything went smoothly. The umask option is necessary in order to give everybody read-write access. Otherwise only root can write. I installed gtkpod to move my mp3s to the iPod. There is even a Suse 9 rpm around.

Reading Macintosh Standard-formated disks (hfs)

Tue, 22 May 2007 00:00:00 +0000

Apparently the kernel module to read hfs-formated disks is less functional than the one for hfsplus-formated disks. I managed to crash my system mounting an hfs-formatted CD. A good alternative are the hfs utilities (hfsutils). There is also an easy GUI for them called xhfsutil.UPDATE (25.12.2023): I needed to mount an HFS+ formatted partition from a 2011 MacbookPro (macOS Sierra) to copy some data before disposing of it. Strangely, my Ubuntu 20.04 still cannot automatically manage to mount these if they are wrapped in a CoreStorage volume (which started in macOS 10.10). In order to mount these, you need to specify a size limit (for details, see https://superuser.com/questions/961401/mounting-hfs-partition-on-arch-linux/1088110#1088110) . To figure out the exact size limit, you use testdisk. You need to find out the size of the partition (which testdisk gives you in sectors). You need to multiply the sector number with the sector size (which you can figure out with fdisk; it’s usually 512). The command for mounting the partition is:mount -t hfsplus -o ro,sizelimit=N /dev/sdXn /mnt

autofs, automount, auto.master and mounting samba shares

Mon, 21 May 2007 00:00:00 +0000

First I added a symbolic link to /etc/init.d/rc5.d/:cd /etc/init.d/rc5.d sudo ln -s ../autofs S21autofsThen I added to the /etc/auto.master the following line:/media/automounts /etc/auto.smbmountsThen I created the file auto.smbmounts with the following content:michael_msbl.helsinki.fi -fstype=smbfs,username=michael,password=## ://paula/michael Then I created the mountpoint:sudo mkdir /media/automounts/michael_msbl.helsinki.fiThen I activated the autofs daemon:sudo /etc/init.d/autofs startNow whenever one tries to access the directory /media/automounts/michael_msbl.helsinki.fi, the autofs daemon will mount the smb share automatically and unmount after a certain period of inactivity.

Changing the host name with Yast2 (overriding the DCHP server)

Mon, 21 May 2007 00:00:00 +0000

I couldn’t figure out how to change the host name. The host name is e.g. displayed by default (Suse 9) in the command prompt and used by several applications. If you move your computer between different networks, this name changes as the default (Suse 9) is, that the host name is assigned by the DHCP server. But you can override these setting using Yast2: Control Center -> Yast2 modules -> Networ Devices -> Network Card -> authenticate! -> Edit already configured network cards -> Host name & Name server -> Uncheck the box “Change hostname via DHCP” and write the desired host name into the box. I presume you have to reboot for the settings to take effect. However, this doesn’t change e.g. the name of your computer that is visible on the windows network. To change this, you have to add an entry to /etc/samba/smb.conf like this: netbios name = “michael-laptop” (Is this correct?: The "" is necessary, otherwise you will only see the first part of the name (that is: michael).) This will change your name as it appears e.g. when you browse the network from a Windows NT computer. However, the samba implementation of MacOS 10.2 will still continue to display some generic name (in my case the name the DHCP server wants to give me: mcblmj-2).

Duplicating Macintosh-formated (hfs and hfs+) CDs under WindowsXP with Nero Express

Mon, 21 May 2007 00:00:00 +0000

Although a standard Windows XP Professional OS cannot read (= mount) Macintosh-formatted CDs (neither hfs nor hfs+), the burning program Nero Express can duplicate such CDs!

Editing names of desktop entries

Mon, 21 May 2007 00:00:00 +0000

How to change the name of items on the desktop (e.g. the Trash bin) Go to the directory ~/Desktop. There are .desktop files, which you can edit. To change the name of directories (e.g. the trash bin) edit the hidden file called .directory.

Formating an mounting an external firewire reiserfs disk

Mon, 21 May 2007 00:00:00 +0000

I didn’t know how to format an unformatted drive under Linux. I attached a firewire case with an old 12 GB Macintosh-formatted HD to my computer. In order to format it with reiserfs, I used Yast2. I had to go to expert mode and rewrite the partition table. By this action Yast2 puts an entry into the fstab, that I modified to:/dev/sda1 /media/firewire reiserfs noauto,user 0 0since I don’t want to have it connected every time I boot up. Instead I can now mount it as a regular user manually with:mount /media/tmp/To make the drive writable to normal users (or to whomever you want to grant access) you need to change the ownership and/or permissions of the mountpoint:chmod -R a+rwx /media/firewire

Good rpm repositories for Suse Linux 9

Mon, 21 May 2007 00:00:00 +0000

You can search specifically for suse 9 rpm packages under http://rpm.pbone.net/ but there are two good sites that have specialized on Suse Linux rpm packages: http://guru.linuxbe.org http://packman.links2linux.de/

Reiserfsck and repairing the root partition using the Knoppix CD

Mon, 21 May 2007 00:00:00 +0000

When I booted my laptop today, I got the following error message:Fsck failed. Please repair manually and reboot. The root file system is currently mounted read-only. To remount it read-write do: bash mount -n -o remount,rw / Attention: Only CONTROL-D will reboot the system in this maintainance mode. sgutdown or reboot will not work. Give root password to log inI logged in and executed:reiserfsck --fix-fixable /dev/hda7Several error messages appeared, among them in the end:reiserfs_open: the reiserfs superblock cannot be found on /. Failed to open the filesystem.Then it said somthing like that the superblock is corrupted and if I am sure that I am dealing with a reiserfs partition, I can rebuild it using the command:reiserfsck --rebuild-sbThen I realized, that /dev/hda7 is my encrypted filesystem and therefore no superblock was found. I repeated the command:reiserfsck --fix-fixable /dev/hda6It told me that the option “–fix-fixable” will be ignored. I don’t know why. Maybe because I have mounted the system from the same partition I am about to fix. Anyway, the message in the beginning The root file system is currently mounted read-only. To remount it read-write do: bash mount -n -o remount,rw /tempted me to remount it in read-write mode and to execute the command again. But with no result. So I booted from the Knoppix CD and executed from there. The filesystem replayed, but no errors were found.Then I remembered that I had modified the fstab yesterday by adding: /dev/sda1 /media/firewire reiserfs noauto,user 1 2I thought that the noauto option prevents the partition from being accessed during bootup. Apparently not and the problematic entry a the two numbers in the end (1 2). They determine whether a filesystem is checked on bootup. I set them to “0 0” and tried to reboot.Voila, everything is fine again.Otherwise I might have tired to rebuild the superblock from Knoppix:reiserfsck --rebuild-sb /dev/hda6

Rio500 drivers for W98 and W2K under VMware

Mon, 21 May 2007 00:00:00 +0000

VMware W2K and W98 do not recognize my Rio500. As I run not from a physical disk, I cannot reboot into W2K or W98 and install the driver from there. I checked, however where the drivers go during the install under W98: the driver consists of two files: riousb.inf and RioUSB.sys. The riousb.inf goes to two places: to C:\windows\INF and (under the new name of RioPort.Comriousb.inf) to C:\windows\INF\OTHER. The RioUSB.sys goes to C:\windows\system32\drivers. I couldn’t check where W2K puts the drivers, becasue when I tried to start up W2K I got the following error: Cannot find file system32\ntoskrnl.exe. Please reinstall.

smb mounts via fstab or automount?

Mon, 21 May 2007 00:00:00 +0000

I have many computers I need to connect to from my Linux box. Network browsing works, but is terribly slow, so I want to create some shortcuts, that I can mount with a single mouseclick what I need from a list. First I thought to modify the fstab and put there entries that would allow me to easily mount smb shares as a normal user. E.g.://paula/michael /media/smbmounts smbfs noauto,user,credentials=/home/jeltsch/.smbpasswd1 0 0This works if I have the entry mounted at system startup (without the “noauto” entry). If the “noauto” entry is present, the smb share is not mounted at system startup, but must explicitely be mounted by the following command:mount /media/smbmountsBecause of the “user” option in the fstab, every regular user should be able to do this. Not so! First I had to enable the “suid” for the smbmnt command (it appeared to be in /usr/bin/smbmnt, but was linked to a link that linked to /usr/lib/samba/classic/smbmnt:chmod +s /usr/lib/samba/classic/smbmntThen I found contradicting information whether the mountpoint (in my case /media/smbmounts) has to owned by the mounting user or not. To be safe it did:chown jeltsch /media/smbmountsStill I got an error which I couldn’t figure out and I decided to use automounts.

Staden 1.4 and Suse 9

Mon, 21 May 2007 00:00:00 +0000

I installed today the new Staden package (version 1.4) to my Suse 9. I included the lines:export STADENROOT=/usr/local/staden-linux-rel-1-4 . $STADENROOT/staden.profilein my ~/.bashrc file.After this kprinter broke with the following error:kprinter: /usr/local/staden-linux-rel-1-4/lib/linux-binaries/libstdc++.so.5: no version information available (required by /opt/kde3/lib/kprinter.so)Apparently the usual file (/usr/lib/libstdc++.so.5) is not anymore used because the staden linux-binary directory is listed in the PATH variable in the very beginning and thus overrides all other entries. Thus I replaced /usr/local/staden-linux-rel-1-4/lib/linux-binaries/libstdc++.so.5 and libstdc++.so.5.0.1 by symbolic links to /usr/lib/libstdc++.so.5.0.5:cd /usr/local/staden-linux-rel-1-4/lib/linux-binariessudo ln -s /usr/lib/libstdc++.so.5.0.5 libstdc++.so.5.0.1sudo ln -s /usr/lib/libstdc++.so.5.0.5 libstdc++.so.5So far at least printing works without error messages, but I have not tried staden yet…

suid and executing programs as root without need of typing the root password

Mon, 21 May 2007 00:00:00 +0000

If you have executables (programs, scripts), that need root privileges to run (e.g. that mount something), you don’t need to type in the su password everytime.You can set the suid for that file and change its owner to root:chmod u+s filename chown root filename

VMware and nonstandard screen resolutions of laptops

Mon, 21 May 2007 00:00:00 +0000

My laptop screen is a 1280x800. This resolution is not supported by the graphic driver of VMware. Under Windows 98, I unchecked the autofit option, resized the VMware window to a weired size, went to the Windows registry (in Windows 98 it’s three hidden files called system.dat, user.dat and policy.pol) and changed the Resolution entry (which was something like 966,558) to 1280,800. After rebooting the resolution was OK when I selected fullscreen. However, in windowed mode the resolution does not become adjusted to the smaller size, but instead you get scroll bars. But in Windows 98, networking doesn’t want to work. I am connected (webbrowsing, etc. works) but whenever I try to browse the local area network I gt the error: “Unable to browse the network”. In Windows 2000, the same trick with the resolution didn’t work. The registry entry is also called differently “Resolution.KVM”. Before that entry there are different other entries called resolution. But as they consist of complex number series, I don’t know how to edit them. So I am using the 1078x768 resolution although it obviously locks fuzzy on my 1280x800 screen. After updating to VMware 4.5.2 (build 8848) I am able to adjust to 1200x800 also with the Windows 2000 guest OS. In full screen mode everything is fine, but when I run in windowed mode and “fit guest to window”, the settings are lost from the windows registry and I have to manually edit them, and reboot to be able to get full screen resolution back to 1200x800.

VMware and Samba

Mon, 21 May 2007 00:00:00 +0000

VMware can interfere with Samba. When you are running a samba server on your computer and install VMware, you might break your samba server. You can check that by:sudo /etc/init.d/smb statusIf the result is “dead” and if VMware is running its own samba server (which you can check by ps -aux and then looking for an entry like vmware-smb), then you have to rerun vmware-config.pl. In RedHat, there is an easy way to remove the vmware samba server from starting up (system Settings -> Server Settings -> Services; just stop the service and uncheck the box if you don’t want it to start up upon system boot). In Suse 9, I just re-run the vmware-config.pl script. When it asks something like: do you want vmware to set up file access to the host computer, then you should say no.

VMware setup error (libpopt)

Mon, 21 May 2007 00:00:00 +0000

The error message during VMware setup (vmware-config.pl) is due to the fact that Suse 9 has a too new package for the requested library:/usr/bin/vmware-smbpasswd.bin: error while loading shared libraries: libpopt.so.0: cannot open shared object file: No such file or directoryThe following fixes the problem:ln -s /usr/lib/libpopt.so.1 /usr/lib/libpopt.so.0

Where do man documents live?

Mon, 21 May 2007 00:00:00 +0000

When you install the Stuffit Expancer for Linux, you get not only the binaries, but also the man pages. I put the two files (named unstuff and stuff) into the following directory: /usr/local/man/man1. They are now available when I type: man stuff or man unstuff.

Wine and Adobe Illustrator (can't find AIRes.dll)

Mon, 21 May 2007 00:00:00 +0000

Adobe Illustrator didn’t want to start up under wine, because it couldn’t find the file AI90Res.dll. This file is located after the Illustrator install in:~/.cxoffice/dotwine/fake_windows/Program Files/Adobe/Illustrator 10/Support Files/Contents/Windows/SystemI just moved it up one directory and everything started working.

BSPlayer and corrupted DivX files

Sun, 20 May 2007 00:00:00 +0000

I have a couple of scratched CDs with DivX video files. Both VLC and DivX Player were not able to play these files beyond the first corrupted frames. They tried to resume, but because the damage was too much, they did get stuck completely. But I found a player that handles most of these problems quite well: BSPlayer . It is only available for Windows though…

Couldn't find MIME type application/octet-stream (Konquerer/Kdesktop)

Sun, 20 May 2007 00:00:00 +0000

This is copied from [http://users.pandora.be/Ice9/Linux stuff/Linux_tips.html]( http://users.pandora.be/Ice9/Linux stuff/Linux_tips.html). I have used the second method as the desktop file appeared to be disfunctional judging from its content and had been created during the time when the error appeared first (that was when I was playing with the File associations section of the control center).

File Associations in KDE

Sun, 20 May 2007 00:00:00 +0000

I have many files in strange formats that can be opened by applications that are not installed by default on any Linux distribution. How do I teach KDE to recognize these files based on their endings (like .ab1) and to open them - when clicked - with the correct application? Go to Control Center -> KDE Components -> File Associations -> Add -> Leave Group “all” and type in some short, descriptive name (e.g. ABI trace file) -> Under “Filename patterns” put the file extension (or any other pattern that enables KDE to recognize the file; e.g. *.abi1) -> Write something descriptive into the “Description” field -> Under “Application Preference Order” click “Add” and type the name of the application (if it is in the path) or browse and select the executable (for the .ab1 example it would be e.g. trev, the trace file viewer from the Staden package) -> Click “Apply” -> I have the feeling that you have to log out and log in again to make the changes active. For the above example you will see that Konqueror list for files with the .ab1 ending the File Type “ABI trace file” and when you click them, they are opened with the trev application.

Installation and configuration of disc-cover on Suse 9.0

Sun, 20 May 2007 00:00:00 +0000

libcdaudio libcdaudio-devel (for cdaudio.h) perl-audio-cd module disc-cover configuration: create all the configuration files, otherwise segmentation fault add servers to .cdserverrc ( http://www.freedb.org/modules.php?name=Sections&sop=viewarticle&artid=9 )

Quick edits of jpg files from within Konqueror (jhead, jpegtran)

Sun, 20 May 2007 00:00:00 +0000

I wanted to have a quick way to rotate the images I take with my digital camera. The Olympus Camedia C-4000 always writes “1” als orientation into the EXIF data (either it doesn’t have an orientaiton sensor or it is broken), therefore I cannot rotate the images automatically by the commandjhead -autorot *.jpgSo I created a desktop file ~/bin/rotate90clockwise.desktpop with the following content[Desktop Entry] ServiceTypes=image/jpeg Actions=rotate90clockwise [Desktop Action rotate90clockwise] Name=Rotate 90 clockwise Icon=/opt/kde3/share/icons/crystalsvg/22x22/actions/rotate_cw.png Exec=/usr/bin/jhead -cmd "jpegtran -rot 90 &i > &o" %UThen I made a symbolic linksudo ln -sf ~/bin/rotate90clockwise.desktop /opt/kde3/share/apps/konqueror/servicemenus/rotate90clockwise.desktop Now when I browse files in Konqueror, I get by right-clicking a jpeg file the additonal option of rotating it. The rotation is lossless BTW and the EXIF information in maintaned. It is also possible to integrate rotation commands into image viewing software. E.g. if the following script is located in ~/bin!/bin/sh jhead -cmd "jpegtran -rot 90 &i > &o" $*you can call it from within GQView by adding the scriptname in one of the free slots below the “big” image editors:Menu name Command line Rotate clockwise rotate_clockwise %fEdit -> Options -> Editors

Automatization of Sequence Handling (Staden's pregap4 and gap4)

Sat, 19 May 2007 00:00:00 +0000

Already a while ago I wrote a script, that tries to automatize most of the work involved in getting sequences from our ABI sequencer into a gap4 database. The script is far from perfect and looks like this:!/bin/sh rm *.seq *.log Log\ file.txt for i in ls .ab1; do echo "Renaming $i" mv $i echo $i | sed “s/ $.\{27\}$ ./\1.ab1/" done ls *.ab1 *.txt > tracefile.list pregap4 -nowin -config /home/jeltsch/bin/pregap4_gap4.conf -fofn tracefile.list gap4 test.0.auxI put the script into ~/bin; and this script is supposed to be invoked from within the directory where the sequences are located. Typically the ab1 trace files from a single sequencing run from our machine are stored in one directory together with some (for me) meaningless log files, etc.First the script deletes unnecessary files from the directory; then it truncates filenames to 27 characters plus .ab1 ending. Funnily pregap4 handles longer filenames well, but gap4 has problems. Then all the remaining files are put into a list (tracefile.list) that is read by pregap4. pregap4 is used non-interactively. It gets its instructions (the setup of the modules) from a configuration file (which in my case is also stored in ~/bin).pregap4 calls the gap4 shotgun assembler and puts the readings into a gap4 database. Unfortunately I havn’t figured out how to automatically assign a descriptive name for this database. At the moment they will all have the same names and can be only identified based on their location in a different directory. It would be good to give them automatically a unique name, e.g. the date when the assembly was done or something similar.After all this has been done, gap4 is called and loads the newly created database for manual inspection and editing.Most of our sequencing is done to check newly made vectors. Therefore we usually know exactly what sequence we expect. If (which is unfortunately not the case) people use any program to document their constructs that included full sequence information (such as the Gene Construction Kit), the trace files should be automatically compared to such “expected” sequence.At the moment I achieve this by exporting the DNA sequence from the Gene Construction Kit program (GCK) as plain text file (apparently I could also use EMBL format) and putting this file together with the ab1 trace file into the same directory before starting the script. Thus it is handles just as any other sequence and the sequence readings are aligned to it.However, there are several things that I would like to be set automatically when invoking gap4 because I always perform the same sequence of clicks when manually inspecting in gap4 the alignment:Displaying all forward reading frames: I presume that because the “expected sequence” is the longest, it is always present in forward orientation in the assembly and the reading frames are allways forward. This results from the fact that I maintain (for ease of reading) the vector sequence in GCK allways in such orientation that the CDS of the GOI is in a forward frame.Highlighting disagreements by background color should be switched on.Upper/lower case character differences should be not handled as disagreementsBecause the quality of our sequencing is modest, mostly the default values are to strict for gap4 to enter the readings into the same contig. Thus I usually end up finding internal repeats and entering them manually. This should be possible to set automatically in the gap4 assembly, but I haven’t got around to figure out how.

Changing the default to tree view in Konqueror

Sat, 19 May 2007 00:00:00 +0000

Make the changes how you want to window to appear.
Right-click on title bar, click “Store Window Settings”.
Click “Settings” -> “Save View Profile” ->Select “File Management” from the list of available profiles -> “Save”.
Close the window and reopen it to see that your settings stick.

Desktop Integration of the Staden Package in KDE on Suse Linux 9

Sat, 19 May 2007 00:00:00 +0000

I have installed the Staden package on my laptop. In order to convince other people from my lab to use it, it must be very easy to use. Ideally, they should just need to select some sequences, click and the preprocessing and assembly should be done automatically. In order to achieve that I did the following:

Installation of Duplicate File Finder

Sat, 19 May 2007 00:00:00 +0000

I was making order among my 50000+ files in my home directory and realized that I had multiple copies of the same file in different directories. Therefore I was looking for some convenient way to find those duplicates and to delete them.There are several applications that do something like this. However, none is perfect. E.g. mp3 files of the same song, but with a different id3 tag will be recognized by most programs as being different, whereas they might be essentially the same apart from the metadata in the id3 tag.I settled for Duplicate File Finder , a java application. Installation required JavaUnix , which appeared to be tricky to install.First of all, I needed to install the java2 SDK. The default on Suse Linux 9 is that only the runtime environment (java3-jre) is installed.For configuration and compilation to succeed (thanks to Ian Ballantyne) one needs to append the current install directory to the path:export PATH=$PATH:.But now the program crashes complaining thatjava.lang.UnsatisfiedLinkError: no javaunix in java.library.pathAgain I got some help:export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$JAVA_HOME/jre/lib/ext/Linux/makes it work. The LD_LIBRARY_PATH is not set on my system. When you install the Staden package, it sets this variable to “/usr/local/staden-linux-rel-1-4/lib/linux-binaries”. You can copy the javaunix.so file to the location that is given in the environment variable LD_LIBRARY_PATH.

kaptain on Suse Linux 9

Sat, 19 May 2007 00:00:00 +0000

I am currently trying out several graphical front ends for the molecular software package EMBOSS and I have read good reviews of kaptain . However, because there are no rpm packages of kaptain for Suse Linux 9 available, I tried to compile it myself. First problem was that the configure script couldn’t find the libraries and headers for qt3:> checking for Qt… configure: error: Qt (>= Qt 2.2.2) (headers and libraries) not found. Please check your installation!Thus I executed ./configure with the option:> ./configure --with-qt-dir=/usr/lib/qt3 Now the configuration script proceeds to the end. However, the make still fails, the last lines of output are like this:Making all in kaptain make[2]: Entering directory /home/jeltsch/downloads/kaptain-0.71/kaptain’ g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/lib/qt3/include -I/usr/X11R6/include -D_REENTRANT -O2 -fno-exceptions -fno-check-new -c kaptain.cpp kaptain.cpp: In constructor Kaptain::Kaptain(Intermediate*, Kaptain*, QWidget*, QBoxLayout*, QDialog*, bool, const char*)': kaptain.cpp:99: error: assert’ undeclared (first use this function) kaptain.cpp:99: error: (Each undeclared identifier is reported only once for each function it appears in.) kaptain.cpp: In member function void Kaptain::button_pressed()': kaptain.cpp:1576: error: ostream_iterator’ undeclared (first use this function) kaptain.cpp:1576: error: parse error before >' token kaptain.cpp:1598: error: parse error before >’ token make[2]: *** [kaptain.o] Error 1 make[2]: Leaving directory /home/jeltsch/downloads/kaptain-0.71/kaptain' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory /home/jeltsch/downloads/kaptain-0.71’ make: *** [all-recursive-am] Error 2I got help from the author of the software Zsolt Terek. I had to insert at the beginning of kaptain.cpp:include include `.

The PATH in Suse Linux 9 (/etc/profile.local)

Sat, 19 May 2007 00:00:00 +0000

Several software installations modify the PATH environment variable. There are many different file that are read during bootup that contribute to the final PATH variable. Several software installs, however, break exisiting PATH entries. Among them is the Staden package. The staden installation instruction advise to include the following lines in ~/.bashrc:export STADENROOT=/usr/local/staden-linux-rel-1-4 . $STADENROOT/staden.profileIn order to quickfix PATH problems, you can give the full path that you need in /etc/profile.local:PATH=/home/jeltsch/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/sbin/:/sbin:/opt/gnome/bin:/opt/kde3/bin:/usr/lib/java/bin:/usr/local/bio/bin/If you leave the entry in ~/.bashrc, the staden path will be inserted before all the entries in /etc/profile.local, thus will take precedence over other entries. This breaks certain programs as some of the libraries Staden uses are older than the ones on Suse Linux 9 (see some older posting).

DCOPserver error during KDE login

Thu, 05 Apr 2007 00:00:00 +0000

Yesterday my laptop ran out of power and during the emergency shutdown stuff got apparently screwed up. When I tried to log into KDE this morning, I got the following error message: There was an arror setting up inter-process communication for KDE /home/jeltsch/.DCOPserver_michael-laptop__0 could not read network connection list Please check that "dcopserver" is running This is again a very non-informative error message. The way to fix this was as follows: rm ~/.kde/socket-michael-laptop rm ~/.kde/tmp-michael-laptop rm -rf /tmp/kdesocket-jeltsch rm -rf /tmp/kde-jeltsch There were errors while removing the directories in /tmp. Even as root I couldn’t remove the directories; the error message claimed they were not empty. But there were no files when listed with ls -al. As a workaround a renamed the directories: mv /tmp/kdesocket-jeltsch /tmp/kdesocket-jeltsch.old mv /tmp/kde-jeltsch /tmp/kde-jeltsch.old After this I could again log in, but the items from my Panel had disappeared.

Desktop Integration of Staden into KDE 3.2

Thu, 05 Apr 2007 00:00:00 +0000

Two things have to be accomplished: 1. The menu should contain appropriate entries. 2. The files should be clickable and have appropriate “Open with” entries. 1. is easy to do. The (systemwide) entries for the menu are in /opt/kde3/share/applnk. I just added an addiitonal directory structure under this directory:Science – Staden |– Gap4.desktop |– Pregap4.desktop |– Spin.desktop |– Stadenlaunch.desktop -- Trev.desktop If you edit the menu as a regular user, the entries are only valid for yourself. Additionally Suse messes between two locations for user-defined menu entries: ~/.kde/share/applnk and ~/.local/share/applications. Once you have the entries in the systemwide /opt/kde3/share/applnk additonal changes made by individual users will replicate the directory under the users home directory. Because entries in the users home directory take precedence over systemwide entries, these will be valid then.

Extracting files from rpm archives (rpm2cpio)

Thu, 05 Apr 2007 00:00:00 +0000

The command rpm2cpio finger-0.17-9.i386.rpm | cpio -imVd extracts all files from the rpm archive finger-0.17-9.i386.rpm. It creates the directory structure relative to the current directory.

Farfalle with Gorgonzola Cream

Thu, 05 Apr 2007 00:00:00 +0000

Serves 4 3 cups farfale (‘motylki’) 180 g gorgonzola cheese, any rind removed, diced 2/3 cup of heavy cream pinch of granulated sugar 2 teaspoons finely chopped fresh sage, plus fresh sage leaves to garnish salt and ground balck pepper Cook the pasta until al dente: 8-10 minutes or according to the instructions on the package. Meanwhile, put the gorgonzola and cream in a medium saucepan. Add the sugar and plenty of ground black pepper and heat gently, stirring frequently, until the cheese has melted. Remove the pan from heat. Drain the cooked pasta well and return it to the pot in which it was cooked. Pour the sauce into the pot with the pasta. Add the chopped sage to the pasta and toss over medium heat until the pasta is evenly coated. Taste for seasoning, adding salt if necessary, then devide among four warmed bowls. Garnish each portion with sage and serve immediately.

How to add comments to HTML code

Thu, 05 Apr 2007 00:00:00 +0000

Identifying your kernel version (ver)

Thu, 05 Apr 2007 00:00:00 +0000

To figure out what kernel you are running just type ver Of course you can also just look into /boot and look to which kernel the default links are pointing to.

Installing Windows95 under VMware

Thu, 05 Apr 2007 00:00:00 +0000

You need: the Windows95 installation CD and a Windows 95 version B boot floppy . As I don’t have a floppy drive I have to create a floppy image of the boot floppy. Under VMware boot from the Windows95 boot floppy. Create a primary partion that fills the virtual disk completely (options 1 and then 1 again and then yes). Reboot Windows95. Format the virtual disk and install Windows95: format C: /S R:\WIN95\SETUP /IS I couldn’t get my installation CD to work. So I made an image of it dd if=/dev/cdrom of=w95oem.iso Then the rest should be a routine install…

KMail, multiple SMTP servers and the alternative sendmail

Thu, 05 Apr 2007 00:00:00 +0000

KMail has always problems with multiple smtp servers. As a solution I installed sendmail. Then I just created a new outgoing mailserver and selected the sendmail option. No further configuration was necessary and it seems to work.

Making a Suse RPM for the Staden Package

Thu, 05 Apr 2007 00:00:00 +0000

As the binaries work on all Suse distributions, I though to skip the build process and just have the binaries unpacked by rpm and then add the suse-specific files to the correct places. These additional files are mainly kde.desktop files, icons andexport STADENROOT=/usr/local/staden-linux-1-4-1and sourcing /usr/local/staden-linux-1-4-1/staden.profilein ~/.bashrc.Thus the unpacking would be justtar --extract --verbose --gzip --absolute-names --file=staden-linux-1-4-1.tar.gzandchown -R root:root /usr/local/staden-linux-1-4-1

Making the Staden applications clickable in MacOS X

Thu, 05 Apr 2007 00:00:00 +0000

I have installed Staden on MacOS X and have been playing around with it. I used the ebiotools package created by Anders Nisters described in issue 10/1 of the embnet.news for the installation. It works, although not according to the Mac philosophy:

Manually uncompressing backup files creating by BackupPC (Zzzz)

Thu, 05 Apr 2007 00:00:00 +0000

The perl script /usr/local/backuppc/bin/BackupPC_zcat does it, but you need BackupPC installed for this purpose. There is a standalone frontend for the compression libraries available called Zzzz… made by the same guy who is behind mplayer.

Mexican Chilli Corn Pie

Thu, 05 Apr 2007 00:00:00 +0000

Serves 4 1 tbsp corn oil 2 garlic cloves, crushed 1 red pepper & 1 green pepper, deseeded and diced 1 celery stalk, diced 1 tsp hot chilli powder 400g can chopped tomatoes, 325g can sweetcorn, drained 215g can kidney beans, drained and rinsed 2 tbsp chopped fresh coriander salt and pepper tomato and avocado salad, to serve Topping: 125g cornmeal 1 tbsp plain flower 1/2 tsp salt 2 tsp baking powder 1 egg, beaten 100ml milk 1 tbsp corn oil 125g grated mature Cheddar Heat the oil in a large frying pan and gently fry the garlic, peppers and celery for 5-6 minutes or until just softened. Stir in the chilli powder, tomatoes, sweetcorn, beans and seasoning. Bring to the boil and simmer for 10 minutes. Stir in the coriander and spoon into an ovenproof dish. To make the topping, mix together the cornmeal, flour, salt and baking powder. Make a well in the center, add the egg, milk and oil and beat until a smooth batter is formed. Spoon over the pepper and sweetcorn mixture and sprinkle with the cheese. Bake in a preheated oven, 220C for 25-30 minutes until golden and firm. Serve immediately with a tomato and avocado salad.

Paglia e Fieno with Walnuts and Gorgonzola

Thu, 05 Apr 2007 00:00:00 +0000

Serves 4 300g paglia e fieno (‘flattened spaghetti’) 2 tablespoons butter 1 teaspoon finely chopped fresh sage or 1/2 teaspoon dried sage, plus fresh sage leaves to garnish (optional) 120 g gorgonzola 3 tablespoons mascarpone cheese 5 tablespoons milk 1/2 cup walnut halves, ground 2 tablespoons freshly grated Parmesan cheese freshly ground black pepper Cook the pasta in a large pot of salted boiling water, according to the instructions on the package. Meanwhile, melt the butter in a large skillet or saucepan over low heat, add the sage and stir it around. Sprinkle in the diced gorgonzola and the add the mascarpone. Stir the ingredients with a wooden spoon until the cheeses start to melt. Pour in the milk and keep stirring. Sprinkle in the walnuts and grated parmesan and add plenty of black pepper. Continue to stir over low heat until the mixture forms a creamy sauce. Do not allow it to boil or the nuts will taste bitter, and do not cook the sauce for longer than a few minutes or the nuts will discolor it. Drain the pasta, turn it into a warmed bowl, then add the sauce and toss well. Serve immediately, with more black pepper ground on top. Garnish with the sage leaves, if desired.

Pinnacle PCTV Deluxe and Linux support

Thu, 05 Apr 2007 00:00:00 +0000

I bought a USB TV card; a Pinnacle PCTV Deluxe. There is only one program for Linux available: dunerec . Here is how I got it working: Download and untar (tar -xvzf) dune2-linux.tar.gz After untarring you have two directories: dunetools and dunelib, two shell scripts (which function escapes me) and one README.txt with some installation instructions. You don’t need to compile anything, you just need to copy the executables (and some other files) into the correct directories: dunetools/dunerec/dunerec goes to /usr/local/bin dunetools/duneinit/duneinit goes to /usr/local/bin You need to create the directory /usr/local/lib/dune Now you need some files from the Windows program, that came together with the TV card. Obviously you need to have a Windows system and install the Program there first. You find the files yu need in “C:\Program Files\Pinnacle\Pinnacle PCTV Deluxe\Driver". You need to copy the files ending with .v (k2.v, etc.), DuneNTSC.sys and DunePal.sys to the newly created directory /usr/local/lib/dune As I am living in Europe, I need to use Pal.sys; therefore I rename it to dune.sys chown root /usr/local/bin/dunerec chmod u+s /usr/local/bin/dunerec chown root /usr/local/bin/duneinit chmod u+s /usr/local/bin/duneinit Scanning for channels is done with the command /usr/local/bin dunerec -i 0 -S 1 -d 1 Dune at 001/002 VID 2304 PID 061E Loading ezusb2 firmware… dune.sys: FWOff: 77736 FWLen: 10296 You have to restart the program! The “-d 1” option is only to print debugging information. You need to execute the command again, this is normal: dunerec -i 0 -S 1 >> /usr/local/lib/dune/channels.txt This command puts the output of the scanning into the file /usr/local/lib/dune/channels.txt; you still have to remove from this file the lines starting with . The error message “Cannot find dune!” occurs when the TV card is not plugged into the computer. I had it also occur when the TV card was present and I needed to remove the card, restart and hotplug it again to make it working. You should test whether the card is working: dunerec -R test.mpg -i 0 -a 479250 This records the TV signal on frequency 479.250 MHz into the file test.mpg. You can stop the recording with Ctrl-C and watch this mpg file with the video player of your choice. However, in order to watch live streaming TV, you need to pipe the data to a player. The only player I managed to get accepting the data is mplayer . There is a great rpm for Suse Linux 9.1 from Packman . Don’t forget to download the rpm with all the codecs! Here are some commands that I have used for piping: dunerec -R - -i 0 -a 479250 | mplayer -cache 8192 - You can adjust the cache size to reduce the waiting time to start playback. dunerec -R - -i 0 -a 479250 | mplayer -framedrop -vo x11 - Without cache you need to allow the player to drop frames. dunerec -i 0 -a 479250 -t dvd -R - | mplayer -ao arts -vo xv -double -cache 4096 -framedrop - This is the complete command that I use now. I copied it from the gtk2 GUI.GTK2 GUI for TV card “Pinnacle PCTV Deluxe” http://pctvgtk.sourceforge.net” . The installation work according to the instructions and the stuff really works. I had some problems with the scanning. it didn’t find all programs. I had to do the scanning under Windows (using the Pinnacle program) and then write down the frequencies and add them manually to the channels.txt files. But that went also without problems.

Problems installing VMware tools (manual installation)

Thu, 05 Apr 2007 00:00:00 +0000

For some reason VMware 4.5.2 didn’t manage to update the VMware tools using the regular option under “VM -> Install VMware tools…”. So I had to install them manually: sudo /sbin/losetup /dev/loop1 /home/your_username/vmware-distrib/lib/isoimages/windows.iso mkdir /home/your_username/temp sudo mount -r -t iso9660 /dev/loop1 /home/your_username/temp/ As my home directory is visible under VMware, I started the setup.exe manually. Everything went OK, although VMware still complains after the reboot that my VMware tools are out of date…

Quanta crashes during start-up (moving my account to a new user)

Thu, 05 Apr 2007 00:00:00 +0000

When I start Quanta as a regular user, it crashes. The output of the terminal is: jeltsch@michael-laptop:~> quanta QGDict::hashKeyString: Invalid null key Invalid entry (missing '=') at /opt/kde3/share/apps/quanta/doc/javascript.docrc:241 TagAction::property( "accel" ) failed: property invalid or does not exist TagAction::property( "accel" ) failed: property invalid or does not exist TagAction::property( "accel" ) failed: property invalid or does not exist jeltsch@michael-laptop:~> However, when started as root, things work OK, although the error messages are the same. At the moment I changed the desktop entry from the start menu so that Quanta starts up as root. Of course, I have to allow access to my X windows, e.g. by executing xhost +. I created a new regular user (mjeltsch9 and executed quanta as mjeltsch, quanta worked also fine. Apparently something is fishy with some user-specific settings. I tried to figure out what, but to no avail. Therefore I decided to make a clean start. As root, I chowned recursively all files in my home directory to mjeltsch and moved them (excluding hidden files) into /home/mjeltsch. All hidden files I put into a new directory which I called old_dot_files. I might need some of these. Then I deleted my /home/jeltsch. Using Yast2, I deleted account “jeltsch” and changed the /home/mjeltsch into /home/jeltsch. Then, also in Yast2, I renamed the user mjeltsch into jeltsch and changed his home directory from /home/mjeltsch into /home/jeltsch. I also had to chown -R /tmp/mcop-jeltsch. Apparently everything works again, but all my desktop configuration is of course lost.

Recursive grep

Thu, 05 Apr 2007 00:00:00 +0000

grep (case-insensitive, recursive) grep doesn’t offer any possibility to recursively descent down the directory tree. The following command searches e.g. just thru all the files in the current directory:grep bacteria *To make the search case-insensitive, one can use the i flag:grep -i bacteria *But if you want to do a recursive search you have to use a quite complicated construction of UNIX commands to achieve this goal:find ~/Mail -type f -exec grep 'bacteria' {} \; -printThis command searches recursively thru the Mail directory of the current user and prints all the lines that contain the word bacteria.

Reference Sequences (Staden)

Thu, 05 Apr 2007 00:00:00 +0000

To make one sequence a reference sequence, just select its name from the gap4 Edit Contig window and right click and select as reference sequence. If the file is in embl format, the features will show up as Staden tags in the alignment.

Removing PDF password protection

Thu, 05 Apr 2007 00:00:00 +0000

I recently bought a pdf book. It was password-protected (40bit security). Unfortunately some of the PDF viewers on Linux cannot open password-protected pdf files. So I decided that I can remove the password protection for private use.A quick lock at the web showed two very easy methods of password removal:

Resetting the MySQL root password

Thu, 05 Apr 2007 00:00:00 +0000

If you have forgotten your MySQL root password, you can reset it if you have physical access to the machine mysql is running on: Find the .pid file of the mysql process. It is either called mysql.pid or machinename.pid. Kill the mysql process. On my MacOS X server e.g. kill cat /usr/local/mysql-standard-4.0.16-apple-darwin6.6-powerpc/data/localhost.pid`` Restart the mysql server /usr/local/mysql-standard-4.0.16-apple-darwin6.6-powerpc/bin/mysqld_safe --skip-grant-tables & Set the new root password (replace newpassword with the new password!) /usr/local/mysql-standard-4.0.16-apple-darwin6.6-powerpc/bin/mysqladmin -u root flush-privileges password "newpassword" Done!

scp (secure copy)

Thu, 05 Apr 2007 00:00:00 +0000

In order to copy the file index.html from the local machine to vesuri.helsinki.fi the following command is needed:scp -p /Volumes/Documents/michael/Sites/index.html jeltsch@vesuri.helsinki.fi:./public_html/index.htmlThe p flag preserves modification times, access times, and modes from the original file. The full path of the original file (/Volumes/Documents/michael/Sites/index.html) is of course not needed if the file is in the current directory.In order to copy the directory “/Multimedia/TV Shows/Kids & Family” from a remote server with the IP address 192.168.0.16 to the current directory of the local machine, use the following command:scp -r root@192.168.0.16:"/Multimedia/TV\\ Shows/Kids\\ \&\\ Family" .Note the double back slashes to escape the white spaces in the file path! The r flag is needed because you want the complete content of the directory (recursive).If you need to specifiy a port number, you need the capital P flag:scp -P 22222 -v TVSeriesXY_S01E* mnmplus@192.168.0.16:/Volumes/MultimediaSometimes, scp is inefficient (e.g. when transferring massive amounts of small, uncompressed files). In that case, one solution is to use tar (to concatenate and compress) and then pipe the output through ssh to the other machine and decompress/untar it there:tar cpf - server.helsinki.fi | ssh jeltsch@othermachine.helsinki.fi "tar xpf - -C /home/jeltsch/"

Sequence trace files in tar archives (Staden)

Thu, 05 Apr 2007 00:00:00 +0000

I want to store all sequence traces of a sequencing project (using Staden) in one file. You can do that if you simply tar all the *.ztr files: tar -cvf ./test.tar *.ztr Then you have to specify in gap4 Options -> Configure menus -> Expert And then you need to specify Options -> Trace file location -> TAR=./test.tar

Software development projects for Molecular Biology

Thu, 05 Apr 2007 00:00:00 +0000

GCK2.5-related

GCK2.5 debug under wine** There are still some bugs that make using gck2.5 sometimes a pain under wine. Especially the inability to annotate regions, to search for a sequence and to open a new file.
GCK2.5 export** GCK2.5 is not able to export in embl format with the regions converted into features. It can, however, export comments to text file and plain sequence to a text file. It should be trivial to write a perl script that takes these two files and converts them into one embl file, EMBOSS cirdna/lindna or pDRAW32 file.
GCK2.5/wine desktop integration** When clicking on files that are associated with Windows programs (using wine), the Linux file manager (e.g. Konqueror) passes the file as an argument to the associated Windows application and the file is opened under wine. However GCK2.5 refuses to accept the file as an argument. When clicking on a .gcc file, GCK2.5 starts up, but opens an empty window and I have to open the .gcc file from within GCK2.5. Unnecessary clicking, especially when I need to navigate over several folder hierachies. When GCK2.5 is running natively under Windows, is it possible to start GCK2.5 with a construct file as a command line argument? I should check that out.

pDRAW32-related

Specifying a default working directory (Path) for Acrobat via acroread.desktop file

Thu, 05 Apr 2007 00:00:00 +0000

Acrobat starts always with ~ as the working directory. Because I keep all my pdf files in a seperate directory, I have to do quite some navigation before I can save them. This is especially bad as the Acrobat save as window displays all files including hidden files.

Staden Help Function (no Netscepe, no help)

Thu, 05 Apr 2007 00:00:00 +0000

Because I don’t have Netscape installed on my computer, the help function of Staden doesn’t work automatically. During the staden course James told be to look into /usr/local/staden-linux-rel-1-4/lib/tk_utils/help_netscape.tcl I might do so, but as a quick fix I made a symbolic link to mozilla: sudo ln -s /usr/bin/mozilla /usr/bin/netscape And this really works. I also tried it succesfully with Konqueror: sudo ln -sf /opt/kde3/bin/konqueror /usr/bin/netscape

Staden on MacOS X (ebiotools)

Thu, 05 Apr 2007 00:00:00 +0000

Today I installed the Staden Package on Tanja’s Macintosh G4 computer (MacOS 10.3). I recommend using the ebiotools package made by Anders Nister. It includes other useful software such as EMBOSS, Blast, etc.). Installation instructions are available in the embnet news issues 9/1, 9/2, 9/3 and 10/1 or gathered into one pdf file from here .

Start netatalk as system service during bootup on Suse Linux 9

Thu, 05 Apr 2007 00:00:00 +0000

I am missing from Suse Linux 9 a nice GUI that collects ALL system services with the options “start”, “stop” and “start on every system boot”. RedHat 9 has something like that. There is Yast2, but under the services, netatalk is not even listed. To boot netatalk during system boot, I just create manually a link: cd /etc/init.d/rc5.d sudo ln -s ../atalk S22atalk After rebooting (and to my surprise) my computer froze. No Ctrl-Alt-F2, no access via ssh; the only rescue being the physical reboot button button (something I am only used to from my Macintosh times). After rebooting in safe mode and removing the link everything is fine again. When I manually start atalk, the system freezes in the same way after a couple of seconds…

Suse Linux 9.1

Thu, 05 Apr 2007 00:00:00 +0000

I bought the boxed version of Suse Linux 9.1. The update went quite smoothly. Although it reported about 1500 package conflicts, they were all just consequences of kopete 0.81 (my icq client) and vlc 0.71 (my video player). I resolved the conflicts by first unprotecting the non-Suse packages that I had installed and then risking system inconsistencies. However, after the update both kopete and vlc still functioned. On the other hand VMWare 4.0.5 broke but updating to 4.5.1 helped.

Suse Linux 9.1/9.2 and vmware

Thu, 05 Apr 2007 00:00:00 +0000

I downloaded again a VMware release to test (4.5.2). But it didn’t even wanted to be configured. Apparently Suse has screwed up the installation source directory tree structure. I found this fix: cd /usr/src/linux su make cloneconfig make prepare After this the vmware-config.pl should run ok. Before running the vmware-config.pl I also applied the vmware-any-any-update78 patch . BTW: You have to repeat this procedure everytime you update your kernel! After updating to 9.2 I had more problems. After every restart I had to execute vmware-config.pl again. This was fixed by adding for a in seq 0 9; do mknod /dev/vmnet$a c 119 $a; done to the beginning of the /etc/init.d/vmware file. After kernel updates the procedure before starting vmware-config.pl is cd /usr/src/linux make cloneconfig make modules_prepare

Syncronizing Psion3a address database with KDE's address book

Thu, 05 Apr 2007 00:00:00 +0000

I have an old Psion 3a which I use mainly as an alarm clock during vacation when I have to catch a train or plane. To make it more useful, I decided to put all my addresses to its database. The database format is some strange format (.dbf). The database application of the Psion 3a cannot import any other format and the only format it can export in is a text file where each field is seperated from the next by a delimiter character (by default linefeed) and each record is seperated from the next by an empty line (or an empty line if linefeed is the delimiter). The PsiWin application on a PC can open the dbf format and export in a variety of formats (hopefully). So the way to get all my addresses into the Psion would be (they are in MacOSX’s addressbook format at the moment) to get them first into KDE’s address book and then export from there in a format that PsiWin can read and use PsiWin to save in the dbf format that the Psion can read.

True Type fonts under Linux

Thu, 05 Apr 2007 00:00:00 +0000

True Type fonts under Linux Font handling under Linux is quite a chaos. Here is how I added true type fonts to my Suse Linux 9. In the Control Center -> System Administration -> Font Installer you have to change into Administration mode -> Advanced Mode (with embedded font selector). Then I just selected the fonts I wanted from the fonts directory of my Windows XP partition and clicked Add. By clicking Apply the fonts become available to the X Windows Server. You can do the same by manually copying the fonts into /usr/X11R6/lib/X11/fonts/truetype and then running xset fp rehash

Using multiple mouses/trackpads simultaneously (Suse Linux 9 Yast2/SaX)

Thu, 05 Apr 2007 00:00:00 +0000

I have a laptop and used Yast2 to configure an external USB mouse. However, the trackpad became inactive. When I now restart without USB mouse I am in trouble. I used for the configuration: Control Center -> Yast2 modules -> Hardware -> Select mouse model If you want to operate both external mouse and trackpad, you need to dig deeper: Control Center -> Yast2 modules -> Hardware -> Graphics Card and Monitor -> Graphical Desktop Environment -> Change -> Component: Input Devices Here you have the possibility to add an indefinte amount of mouses. You should probably test whether you new settings work (with the test button) before you restart. The settings become only active after a restart. Meaning if you want to deactivate your trackpad (because it disturbs you) you need again a restart…

What nfs and smb shares are available on a server (showmount, smbclient)?

Thu, 05 Apr 2007 00:00:00 +0000

The command to figure out what shares are available e.g. on the computer 192.168.0.2 type:For nfs: /usr/sbin/showmount -e 192.168.0.2For samba: smbclient -L 192.168.0.2

Windows NT, network browsing, mounting and disconnecting from network drives (command netuse)

Thu, 05 Apr 2007 00:00:00 +0000

Network browsing in Windows is a mystery. Sometimes some computers simply don’t show up when browsing a network. This seems to be especially true for Linux servers. Under newer versions of the Windows OS (2000, XP), you can connect to a server (if you know its IP adress) via the mount network drive command even though the network browser cannot see that server. Windows NT doesn’t have that option. The only possibility is to use the “net use” command from the command line. This is uncomfortable, although one can make .bat files for frequently used connections. The command is: net use * \\ip-adress\username The asterisk assings the share to the next available drive letter (of course you can assign manually to e.g. H:). To delete this specific network drive type: net use H: /delete Actually, even if you can browse and connect without needing the command line, you need the command line always when you want to disconnect a share from an NT server. Funnily Windows NT has no other way but to type netuse * /delete In some discussion threads it was mentioned, that one should switch on WINS support in the Linux server’s smb.conf file wins support = Yes. If you connect to Linux, make sure that Samba is running and that the user to whose home folder you want to connect to has an entry & password in the smb database (this is NOT preconfigured even in Suse 9.2): as root: smbpasswd -a username It didn’t help me, though. MacOS X computers (10.3) show up now without problems (older MacOS X versions also had problems). Maybe I should compare the smb.conf files or just copy it over to my Suse 9.1.

Windows XP guest from raw partition under VMWare 4, coLinux as rescue

Thu, 05 Apr 2007 00:00:00 +0000

So far I never was able to run a Windows XP guest OS from a raw disk partition using Linux VMWare. Here’s the discussion thread .

aMule on our server (what ports to open?)