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A new way to share models of biological systems

Today sees the launch of BioModels, the world's first database of annotated biological models. BioModels is the result of a collaboration led by the European Bioinformatics Institute (UK) and the SBML Team, an international group that develops open-source standards to describe biological systems. Other contributors include the Keck Graduate Institute (USA), the Systems Biology Institute (Japan) and Stellenbosch University (South Africa).

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 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 Novère. "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
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Source:European Molecular Biology Laboratory


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