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.)

Bio::Blogs 19 - A look at Bioengineering

Duncan is hosting the 19th Bio::Blogs issue and wrote down some thoughts about bioengineering.

Pedro will take care of the next one that might cover data integration.

Good physics phun

Phun - A fun 2D physics sandbox by Emil Ernerfeldt - seems to be an awesome program that can be a black hole for planned working hours. You can draw physical objects and switch on gravity and friction etc. Have a look at the video. It reminds me on the video MIT sketching which showed a more natural interface (draw your stuff on a board and make it run) but is less powerful. Phun is not (yet) open source but according to the FAQ the author is planning to make the source code available at some point.

[via Bad Science]

The STRING and STITCH blog

For the bio crowd: If you want to be informed about news regarding the web tools STRING (proteins and their interaction) and/or STITCH (protein-chemicals interactions) you should have a look at the blog that Michael set up recently for that purpose.