The recently launched BioModels Database (April 11,2005), by the European Molecular Biology Laboratory and the SBML Team, promises to be a great resource for quantitative modeling of complex systems. Using a the widely accepted, Systems Biology Markup Language (SBML), an open-source computer language, this database, for the first time, will allow for an open exchange of biological models while providing cross-referencing.
The official press release explains:
Even the simplest living organisms perform a mindboggling array of different processes, which are interconnected in complex ways to ensure that the organism responds appropriately to its environment. One of the best ways of ensuring that we really understand how these processes fit together is to build computer models of them. If a computer model behaves differently than the real organism, we know that we’ve neglected an important component of the system. Quantitative models can also reveal previously unappreciated properties of complex systems, paving the way towards new drug treatments. This approach, known as ‘computational systems biology,’ is becoming increasingly popular now that scientists are accumulating detailed parts lists for many organisms, thanks to genome sequencing projects and other efforts to comprehensively document the components of living entities.
“Until now, computer modellers had no defined way of exchanging descriptions of biological systems, and there was no accepted place to deposit and share new models when they were developed,” explains the EBI’s Nicolas Le Novere. “The BioModels database aims to address these issues.”
The first step was to develop a standard way of describing such models. The Systems Biology Markup Language (SBML), an open-source computer language developed by the SBML Team, is now widely accepted and is supported by over 75 different software systems worldwide. This allows computational systems biologists to write models using the tool of their choice, and then to share them so that others can build on their work.
Michael Hucka of the California Institute of Technology continues: “The next logical step was to build a community resource that would allow anyone to submit, download and reuse the models. That’s the purpose of the BioModels database. BioModels provides access to published, peerreviewed, quantitative models of biochemical and cell-biological systems.”
The press release (.pdf)…
(hat tip: FutureFeeder. Also, while you are there, check out ‘Superatoms : Alchemy and the 3-D Periodic Table’, and then start visiting FutureFeeder q day — Che-Wei Wang is too cool to miss.)