Helsinki University on Michael’s Domain

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:

Internationalization in everyday operations at Meilahti campus

Mon, 22 Oct 2018 00:00:00 +0000

Meet the rectors at MeilahtiLast Thursday (18.10.2018), the new rector of Helsinki University Jari Niemelä and the four vice-rectors (Sari Lindblom, Paula Eerola, Hanna Snellman, Tom Böhling) visited the Meilahti campus for an open question and answer event. Hardly any foreigners were present during the event. Consequently, the language of communication was Finnish. Obviously, foreigners won’t participate if they do not understand and speak the language of the event. And since foreigner’s don’t participate, there is no reason to change the language of the event, and so the circle continues… Traditionally Finnish and Swedish onlyThe Meilahti campus holds a special position when it comes to language use since until very recently, it was impossible to receive a degree from Meilahti without knowing Finnish or Swedish since the only degree programs were not offered in English. However, the situation has been changing (e.g. with the move of the Psychology Department to Meilahti and the establishment of new degree programs like TRANSMED ), but old habits die hard. Trailblazers RPU and HiLIFEThe trailblazers for internationalization at the Meilahti campus are the Research Programs Unit and HiLIFE. The postgraduate students and postdocs of the Research Programs Unit (RPU) and the HiLIFE recruitments are the two most internationalized parts of the Meilahti campus and consequently, Hannu Sariola (previous vice dean for research at Meilahti) and Tomi Mäkelä (the HiLIFE director) brought up the topic of internationalization pointing out that the rules of the university allow for more language flexibility than is actually implemented. To date, the only official languages at the University of Helsinki are Finnish and Swedish, although more English-speaking than Swedish-speaking students are enrolled. English is also the de-facto language of almost all scientific endeavors. Balancing the domestic languages with English likely has no perfect solution. If the university wants to optimize its international impact and success, the role of Finnish and Swedish inevitable has to decline unless massively more resources become available.**Separate events?**In order to engage the foreign staff as well, the dean of the faculty recently organized the faculty staff meeting twice: once in English and once in Finnish. I am not sure whether such separation is a long-term good idea, but it addresses the issue pragmatically and gets the job done. If someone suggested separating the faculty X-mas party according to language, that would be considered discriminatory, but for a working meeting, nobody seems to object…**PS:**I am not the only one who is aware that internationalization has a long way to go. There is a nice article on the Helsinki University intranet portraying the new vice rector Hanna Snellman and her take on the issue: https://flamma.helsinki.fi/en/HY377022 . However, the university keeps most of its interesting web content behind locked doors (inside their Flamma service), inaccessible to the general public, who is paying the university’s bills… What does the university fear? More transparency?

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:

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…

½ year and 1000+€ for Win7 & Office 2010

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

In the beginning of 2011 I bought a netbook ( Lenovo IdeaPad S10-3t ). I bought it with my own money. It was preloaded with Windows 7 Starter Edition. Because I prefer to use Ubuntu , I shrank the Windows 7 partition and installed Ubuntu as my primary OS. I installed the University-licensed Microsoft Office XP, for which there were still installation media around in our research program. There are only two occasions when I boot into Windows: when I needed to work on collaborative publications or grant applications at home with my co-authors using Microsoft Word or when there is a program that has no equivalent on Linux (which has rarely happened during the last years).However, last October, more and more compatibility problems appeared between the aging Office XP and the newer versions of Office, that use the new XML format (.docx). On one occasion, after my boss had opened a Word file (created by Office XP), modified it and send it back to me (using compatibility mode), it became uneditable in Office XP. Word would crash whenever I tried to edit two of the three embedded images. In fact, I spent hours of recreating an editable version of that document from scratch.That was when I decided to upgrade my privately owned computer’s Windows and Office versions. Helsinki University’s license agreement with Microsoft allows staff and students to run Windows and Office on their home PC. To university researchers, it happens all the time that they need to work from home. In fact, I wrote almost a complete research paper ( Jeltsch et al, JBC 2006 ) from home. Thus it should not be difficult and not expensive to upgrade from Windows 7 Starter to Windows 7 Ultimate and from Office XP to Office 2010, right? Helsinki University wants to get higher and higher in the [Alma intranet pages]( http://www.topuniversities.com/university-rankings/world-university-rankings/2011?page=1>international rankings. Therefore, one might think the University would have made sure their researchers have easy access for the right tools to do their job. WRONG!Helsinki University has provided instructions on their Ohjelmistojakelu page of the university. Under the <a href=) (Home Use Program) link hides the “Microsoft Home Use Program and software delivery to members of the staff”. I downloaded the file (“koodi.txt”) which is a text file cotaining a code (something like “XXX0000”). With this code I went to the Microsoft Home use Program site. I had to type in my work e-mail address and the code and I received the following error message: “We are sorry, but we are unable to complete your request. the following problem(s) exist: - Please contact your benefit administrator to learn if you are eligible and to retrieve your program code.“I phoned the helpdesk of the University to ask what is wrong. The answer: “The University and Micorsoft are negotiating a new licensing deal and the old code doesn’t work anymore and the new code is not yet there.” How long will it approximately take for the new working codes codes to appear? “A few weeks.” I waited a few weeks. To be precise: I waited six weeks. I went through the same procedure as before. But the code still did not work. Retrospectively, I suppose that the helpdesk’s first answer was wrong: The codes were probably still fine, but the instructions on the university’s pages were wrong (they sent me to the wrong page to type in the code and at the time of this writing - 5 months later - the university’s pages are still wrong).In the beginning of the new year I submitted a formal support request to the helpdesk. I received the following answer:Hi MichaelUniversity of Helsinki has made a new agreement with Microsoft (moved from MSCA to EES) starting this month and now that our agreement is changing codes won't work. I assume we get new codes to our new agreement from Microsoft after all paper work is done, and this will take approx. couple of weeks or so.All we can do now is wait, you can check in february if Home Use Program -option is working. Sorry for the inconvenience.Best regards,Tommi also send me the Alma link with the instructions . I tried several of the links in the document (which were links to sites where one could order Windows and Office installation media/downloads), but already the first link was broken: Microsoft Windows operating systems: e-Academy (no CD/DVD option, only downloadable versions). It is still broken at the time of this writing.The other option (“Microsoft Home Use Program HUP (Digital River, also installation medias)”) linked only to the instructions that I already knew (and which do not work). Because apparently nobody had ever tried before to leaglly aquire Windows and Office for home use via this program, I went in March together with my computer to our physical help desk at Meilahti campus. Iivari was very friendly, but the only thing he managed to do was to replicate the problem and to convice somebody that there is a problem that should be looked at. A few days later he sent me the link to a page from where I could order Windows and Office for 20€/DVD: https://hup.atea.fi/ .This link I have never found anywhere in the university’s online instructions (as I learned later, it is somewhere there, but almost impossible to find). I am not surprised that otherwise law-abiding citizens of this country use illegal versions of Windows/Office at home if it is so difficult to be legal.I received the DVDs via Post a week later (I had to go to the post office and to pay there the 20€/DVD).Before I installed anything, I made a disk dumpdd if=/dev/sda of=/dev/sdbof my entire hard drive (250 GB hard disk, it took 20 hours via USB). Because I had Windows 7 Starter installed on my computer, I first tried to use the anytime upgrade . For this I actually only would have needed the license key, but not the physical installation disks. When I typed in the key, it started the upgrade, but failed without any details. So I decided to run the upgrade advisor (a program from Microsoft that determines whether your computer is “good” enough for the upgrade). The only thing it found was that I was short on disk space. So I freed another 5 GB by uninstalling software (mostly the bloatware that was put there by Lenovo). The second attempt also failed without any specific error message. I had no way of knowing what was the reason.So I tried a clean custom install. First I needed to transfer the Windows 7 install DVD to a USB stick (my computer has no CD/DVD drive and I or my lab doesn’t own an external CD/DVD drive). Fortunately this is easier with Windows 7 than with Windows XP. However, not all USB sticks seem to be equal and the first USB stick I tired (Verbatim) was rejected by the tool I used. I followed these instructions . Then I booted from the 4GB stick and started the upgrade. Everything went fine until the very end, when I needed to reboot and I was greeted with “Your Windows 7 install is broken. Do you want Windows to fix it?” Then I made a bad decision: I said yes. After fixing, nothing worked anymore. Upon rebooting, there was only a blinking black cursor.OK, if I cannot upgrade, I can do a fresh install. I wiped my hard drive clean and started the install. Everything went fine until I had to type in the product key. It complained that it is not a valid product key. Of course I had not thouroughly read and understood the pages at www.atea.fi . Probably because they are only in Finnish. Apparently, the University’s deal with Microsoft does not provide the staff with full installers, but only with upgrade installers. Consequently I need to keep my old Windows version around for the install. Luckily I had my diskdump. I wrote it back to the hard drive. This took only about 6 hours.This Monday I went (together with my laptop) to the local computing support. Perttu enlightened me about the possible upgrade paths to Windows 7 and tried to do the custom install using an external DVD drive. And it worked! Hallelujah! It took several reboots, but finally I had a running Windows 7 Ultimate. Installing the drivers took also about three hours. It took an eternity to download the drivers from Lenovo’s site, despite them being akamaized. Maybe they didn’t pay their bills. Now I just needed to create an iso image from the Office 2010 DVD, move it over to the computer and start the install, which went flawlessly this time.I presume that the first time I tried the custom install, the system was somehow compromised by the failed anytime-upgrade. Who knows. 500 Million lines of code, that nobody really understands anymore. It’s close to a miracle, that Microsoft is managing to keep Windows afloat.Of course the Windows installer had screwed up my grub boot loader and I had to start the machine from a System rescue CD on a USB stick and write back the MBR from my disk dump:dd if=/dev/sda of=/dev/sdc bs=512 count=1I still don’t exaclty know now, whether the Windows 7 Starter Edition does or doesn’t qualify for an upgrade using the University licensed upgrade plan. I stupidly assumed that if a 10 year old Windows XP Home qualifies, a Windows 7 Starter edition would too.The whole procedure lastet about half a year and taken together, I spent maybe seven to ten days of work for it (about half of this time during working hours, the other half during my weekends). Let’s estimate the real costs including the hours I had to put into this Windows 7 & Office 2010 installation: conservatively at least 1000€. The system is broken and the worst thing is, that there is nobody to blame and nobody who can fix it. Maybe Helsinki University should invest some energy and time into the development and adoption of open source Operating Systems. After all, the most popular one (Linux) was started by somebody from Helsinki University .

HBGS course

Mon, 10 May 2010 00:00:00 +0000

All documents related the the HBGS course Tags in protein expression, detection and purification. Most documents are available in both PDF and OpenOffice format. Feel free to repurpose the documents. They are licensed under the Creative Commons Attribution-Noncommercial-Share Alike 1.0 License .