Another move

Despite the fact that nobody should follow this feed anymore: The blog moved again. Now you can find it at http://thedaoofflow.fluxionary.net/

Konrad's considerations moved - update your RSS readers

I finally moved my blog so please update your bookmarks and RSS readers: The new URL is http://konrad.foerstner.org/blog/

The design is not yet set up properly and there will be a change of the categories, but I am very busy these days and want to avoid to post here and in the new blog.

DiSo - the distributed social network

The DiSo project is a promising attempt to create a distributed social network - so is not following the "silo" approach as other social networks do. The blog of the project offers a short (4 min) introductionary video in which Chris Messina explains the vision and ideas behind this solution. The project will make use of open standards like OpenID, XMPP and different microformats. Code is available as open source. Really looking forward to see this stuff in action soon.

The WWW is not the Internet

Yes, maybe I am little bit too nitpicky, but this bugs me: April 30th 1993 the World Wide Web became officially accessible for the general public and libwww became open source. Some media saw this as a reason to celebrate yesterday the 15th birthday of the WWW. Due to this "birthday" I stumbled across a common mistake more often then usually: Mixing up WWW with the Internet.

The WWW is not the Internet!

As an analogy - a car is not a highway. The WWW is one of many internet-based services like email, IRC or p2p networks. The Internet is the underlying network that is using the Internet Protocol (IP). I personally would like to see a little bit more awareness of this issue.

OpenBSD 4.3 released

After 6 months of hard work the OpenBSD project released version 4.3 of the great, (non-)fishy operating system. As usually there is a collection of micro-interviews with some of the developers about new features at the O'Reilly's BSD DevCenter.

Ready to register - The 10th International EMBL PhD Symposium

This year the well known EMBL PhD Symposium will cover fields belonging to the topic "Decision Making in Biology - Nature at the Crossroads" and you can already register. It is still some time until October (23rd - 25th) so the program is not yet available but the list of speakers looks very promising.

Blossum62 error - Never stop questioning

Outch! Styczynski et al. [1] found an error in the BLOSSUM62 - THE substitution matrix used since 16 years in bioinformatics for protein database searches.

Lessons learned:

• Don't stop questioning even fundamental laws/tools/assumptions/etc.
• Transparency - in bioinformatics the access to the source code and the data - is essential for proper science

[Via Suicyte Notes]

[1] BLOSUM62 miscalculations improve search performance. Styczynski MP, Jensen KL, Rigoutsos I, Stephanopoulos G Nat Biotechnol. 2008 Mar ; 26(3): 274-5

Petition - Open the GCG and SeqLab code

Steven M. Thompson has initiated a petition to make Accelrys' GCG and SeqLab available under an open source software. He wants to prevent the loss of these bioinformatics tool sets after Accelrys' recent decision to stop the support and development of them.

Synthetic biology against global warming and energy crisis

Craig Venter gave a talk at the TED conference this year in which he presented a synthetic biology approach to create an organism that might solve two major problems of mankind: The increasing CO₂ concentration in the atmosphere and limited fuel resources. Venter claimed that the project will take further 18 month. The video of the talk is now available.

The iTOL toolbar for Firefox

Ivica just created a Firefox toolbar for iTOL which might be handy if you manage your phylogenetic trees with this cool web tool.

(Yes, looks like I became the unofficial announcer of new tools etc. from the Bork group) ... that wasn't planned.)