Autarchy of the Private Cave

It has been quite a time since my last serious and long post. On the one hand, summer is vacations time – so I’ve been to one in Turkey; on the other hand – the long-awaited ICSB-2008 conference finally took place in Gothenburg, Sweden, on August 23-27 (or 22-28, counting in tutorials and workshops).

Update: it appears that conference domain name http://www.icsb-2008.org/ was not maintained after the conference, so I had to remove all the links to that website (which now appears to be owned by someone not related to ICSB). However, there seems to be a mirror of ICSB-2008 at http://www.gmm.gu.se/groups/icsb08test/.

Synopsis: in this post I present a personal-perspective report on the 9th ICSB (with a condensed ICSB-2008 photo-report in my gallery).

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I’m planning to reconstruct (based on literature and some original research) a specific cellular regulatory network. For this I decided to use some specialized biological modelling software. The requirements I had were pretty simple:

• must have SBML support. SBML appears de-facto standard for biological model notation;
• must be fairly frequently updated;
• should be feature-packed and easy to use. However, this requirement can only be checked after some use, and I was pre-selecting, not reviewing.

Software put into the title of the post was found to be the most mature and interesting from the usage perspective. However, there are more than those mentioned software tools reviewed. Reviews are based primarily on the information from official websites and documentation; some tools (like VirtualCell) are reviewed somewhat more thoroughly.
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