Open Source on Michael’s Domain

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:

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”.

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

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

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