Systems, synthetics and semantics

As those of you who have been paying attention well know, I am currently attending this year’s International Conference on Systems Biology (#ICSB) meeting in either Heidelberg or Mannheim (there’s ongoing debate about the meeting locale).

The meeting opened yesterday with a plenary talk by Jean Peccoud talking about DNA “grammar,” making linguistic models of yeast cell cycle regularly network genetics, and the open source application (with a database too) GenoCAD, which I really recommend you check out. It was a great opening act.

Continuing on the language theme, today I really enjoyed two talks that both had a bit of a semantics bent. The first was Frank Bergmann’s “Emerging Standards in Systems Biology.”He gave an overview on markup languages for systems biology (such as the Systems Biology Markup Language, SBML) and other  standardized notation efforts. He then went on to describe a framework of tools, the Systems Biology Workbench, that were developed to make SBML associated standards more accessible. Frank also runs a blog on these topics.

The other talk I wanted to highlight was Dagmar Waltemath’s on concepts for model management for model re-use and the reproducibility of model results. She stressed the importance of good meta-data in model storage for future localization and retrieval, tracking model evolution, and linking simulation experiments with the model. She discussed some tools and techniques developed at Rostock for handling these issues, the code of which is freely available:

And the conference is not even half over…