Around the web, week of March 21, 2008

Journals
Big science from Andrei Sali and David Baker
• The molecular architecture of the nuclear pore complex
• De Novo Computational Design of Retro-Aldol Enzymes

Blogs

• Nature archive visualized – a Processing sketch to visualize the keywords from Nature over the last 30 years. Some of the more spurious terms could probably be cleaned up but even as a draft the effect is pretty neat.
• Research streaming is born. Mike from Bioinformatics Zen is auto-publishing his svn commit messages and uploading figures he generates to Flikr. This would be well suited to someone like me who has too many projects going on to stop and dedicate time to blog about them here.
• Universal Parallel Computing Research Centers are being heavily funded by Microsoft and Intel. One at University of Illinois at Urbana-Champaign, well known for the CHARMM++ parallel library and the super-scalable NAMD molecular dynamics package built on top of it. The other will be located at UC Berkeley.
• The End of the Relational era, is SQL dying? Bill McColl of Computing at Scale says it is. I would argue that relational databases have received the golden hammer treatment over the years. But I totally agree with his prediction that SQL will ultimately be replaced by DSL’s having implicit data-parallelism.
• The Youtube API has been updated with some significant improvements for developers. Uploads, comments, and video playlists can all be manipulated outside of youtube. This makes a convincing case to leverage the massive youtube userbase if your site deals with video content.

Tech

• I’ve finally moved most of my projects from SVN to Git. I’m now a ‘branch-a-holic’ and git definitely fits my workflow better than subversion now that I’m used to it.
• Capistrano is typically used for Rails deployment, but I’m finding it’s good for just about anything you want to run across multiple remote hosts. This is a great mini-language for cluster admins who don’t want to struggle with something like mpirun

Around the web, week of March 7, 2008

• Bio::Blogs #19, the engineering edition!
• BuzzClouds in science, a very cool vizualization of scientific buzzwords and trending. (service)
• Backward compatibility ≠ Forward Scalability, Intel places some caveats on the free-lunch, legacy software won’t take advantage of future architectures unless they’re redesigned. This shouldn’t be a surprise but it hasn’t always been the case. The trend of adding more cores and changing memory architectures means that some applications may get left in the dust unless they’re optimized for these new paradigms.
• DSL specification and behavior, a great example of building a DSL in Groovy for bioinformatics.
• BioRuby on Rails, some good examples of how to fetch EBI records on the web using ActiveRecord for persistance.
• Ruby-Processing, a bridge to use the Processing API in the Ruby language.