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SBML and the BioModel Database
Jamais Cascio, 11 Apr 05

SBML.jpgToday sees the opening of BioModels, an online database of annotated open biological models. BioModels is a collaborative effort of the UK's European Bioinformatics Institute, the Keck Graduate Institute in the US, Japan's Systems Biology Institute and Stellenbosch University in South Africa, along with the Systems Biology Markup Language (SBML) team. SBML is a standardized, open source language for describing the behavior of biological systems, allowing biologists to share models and results easily.

Even the simplest living organisms perform a mind-boggling array of different processes, which are interconnected in complex ways to ensure that the organism responds appropriately to its environment. One ofthe 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.

This is a good example of how open standards and open access can facilitate scientific understanding. SBML can function as a Rosetta Stone for bioinformatics, translating the results of research across myriad modeling packages, making it possible for researchers around the globe to share in each other's work. The BioModels database, in turn, parallels the work at BioForge in making tools for discovery freely and openly available.

Computer modeling is widely used in the natural sciences; translational markup languages and model repositories would clearly be of value across a wide spectrum of research fields. We have quite a few readers doing scientific research -- do similar efforts exist in other fields?

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This project seems to me quite close to so-called "Semantic Grid" projects, which try to improve collaboration between computing resources, not only on a technical basis (computing the same kind of data the same way), but on a semantic basis (computing about the same kind of objects).
See for various projects.
Quite far away from bio-science, astronomers community is also involved in a similar project called International Virtual Observatory Alliance

Posted by: Bernard Vatant on 13 Apr 05



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