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| Hinxton,
Pasadena, Monday 11 April 2005 |
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| A new way to share models of biological systems |
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| Nicolas Le Novère [EMBL-EBI] |
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![Michael Hucka [California Institute of Technology, USA]](../../../../../images/press/press05/mhucka.jpg) |
| Michael Hucka [California Institute of Technology, USA] |
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![Andrew Finney [University of Hertfordshire, UK]](../../../../../images/press/press05/afinney.jpg) |
| Andrew Finney [University of Hertfordshire, UK] |
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Press
Release 11 April 2005 [PDF]
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 opensource
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 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
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 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 cellbiological
systems."
Some of these systems are very simple, containing just a
few processes or reactions; others contain hundreds. The
models are checked to verify that they correspond to the
reference publication. Human curators annotate and crosslink
components of the models to other relevant data
resources. This allows users to identify precisely the
components of models, and helps them to retrieve
appropriate models, which they can then visualize and build
upon using any SBML-compatible software.
"Ultimately", says Le Novère, "we hope that publishers will
encourage any author who plans to publish a new model to
submit it to the BioModels database; this will ensure that all
the models in the public domain are freely available for
everyone to make the most of them."
The BioModels database is freely available at: www.ebi.ac.uk/biomodels/.
Press Contacts
Cath Brooksbank PhD
EMBL-EBI Scientific Outreach Officer Wellcome Trust
Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Tel: +44 [0]1223 492525,
E-mail: cath@ebi.ac.uk
Trista Dawson
EMBL Press Officer, European Molecular Biology Laboratory,
Meyerhofstrasse 1, 69117 Heidelberg, Germany
Tel: +49 [0] 6221 3878452
E-mail: trista.dawson@embl.de |
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