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| Hinxton,
Tuesday 6 December 2005 |
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| Setting the standard for computer models of life |
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| The creators of MIRIAM |
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Press
Release 6 December 2005 [PDF]
In the December 6 issue of Nature Biotechnology,
scientists from 14 different organizations around
the world, including the EMBL-European Bioinformatics
Institute, propose a new quality standard for biochemical
models. MIRIAM [for Minimum information requested
in the annotation of biochemical models] will help
researchers to reuse, modify and combine computer
models of biochemical processes to gain a fuller
understanding of life at the molecular and cellular
level.
Biologists are making a concerted effort to catalogue
all the molecular components of living things, from
the smallest molecules and ions to the genetic code.
These 'parts lists' help them to build computer
models that simulate living processes. By combining
models of simple processes they hope to understand
and faithfully represent how entire biological systems
– be they cells, organs, organisms or ecological
niches – work. As well as contributing to
the understanding of biology, this approach has
numerous applications: for example, diseases can
be simulated, and treatment regimens optimised.
"The computational systems biology community has
made enormous progress in improving access to models,"
explains the EMBL-EBI's Nicolas Le Novère, lead
author of the paper. "We've begun to share programming
languages for encoding them [e.g. systems biology
markup language, www.sbml.org] and to build public
repositories so we can share them [e.g. www.ebi.ac.uk/biomodels].
The current challenge is quality control: systems
biologists won't use publicly available models if
they can't search them properly, of if a model's
reuse is hampered by a tiny mistake in the way that
its encoded. MIRIAM is an attempt to address these
issues."
MIRIAM has two parts: [1] a set of checks
that match a model to its description ['reference
correspondence', often a publication in a scientific
journal], and [2] a set of 'annotation schemes'.
The first of these documents the model's provenance:
who created it, whether it's been modified, and
a stable link to its full description; the second
scheme links the components of the model to relevant
bioinformatics resources: for example, a model of
alcohol metabolism in the liver would be annotated
with links to the protein databases for all the
enzymes involved in this pathway, and database links
to all the relevant metabolites. The aim of these
annotation schemes is to make it easier for researchers
to search models on the basis of their components,
to contact the creators of the model if they need
more information, and to track the history of a
model if it has been modified.
MIRIAM's creators
include representatives of four major repositories
for models [BioModels Database, CellML Model Repository,
DOQCS and SigPath], all of which are now in the
process of making the models in their repositories
MIRIAM compliant. "By adopting MIRIAM as a voluntary
code of conduct, we will be able to provide our
users with a reasonable level of quality assurance,
so they'll be able to get on with the business of
generating and testing new hypotheses instead of
recoding someone else's old hypothesis," continues
Le Novère. "We also hope that journal editors will
adopt MIRIAM as a quality control measure for papers
that describe models. This approach has worked very
well for other fields – for example the microarray
community, by enabling authors, publishers and data
providers to work together to improve access to
meaningful biological information." The creators
of MIRIAM. Clockwise from bottom right: Benjamin
Bornstein, Akira Funahashi, Pedro Mendes, Jacky
Snoep, Upinder Bhalla, Barry Wanner, Julio Collado-Vides,
Andrew Finney, Hugh Spence, Nicolas Le Novre and
Matt Halstead. Photo taken by Michael Hucka.
Source article
Minimum information requested in the annotation of biochemical models [MIRIAM]
N. Le Novère et al.
Nat. Biotechnol., 6 December 2005
Press contact
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 |
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