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Nicolas Le Novère, UK

What Invited talk
When 2010-02-01
from 13:00 to 14:00
Where Ulmenstrasse 69, Haus 1, room 118
Contact Name Dagmar Waltemath
Contact Email dagmar.waltemath@uni-rostock.de
Contact Phone 4987440
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last modified 2010-11-16 18:29

Toward a consistent set of interoperable standards to represent models and simulations

A decade ago, the creation of the Systems Biology Markup Language (SBML) changed the way people exchanged, verified and re-used models in systems biology. The robustness and versatility of this standard format, coupled to a wide software support fostered the emergence of a whole area of research centred on model processing such as encoding, annotation, merging, comparison and integration with other datasets.
Other community standards of representation were created in computational systems biology, and a vertical organisation is emerging, with different layers of descriptions. While the model structure is covered by SBML and similar efforts, the biological semantics can be described using BioPAX while models and pathways can be graphically represented using the languages of the Systems Biology Graphical Notation (SBGN). Computing glues permit to relate the components of the different layers. For instance one can generate SBGN maps from SBML using the Systems Biology Ontology (SBO) and convert SBML into BioPAX using the controlled MIRIAM annotations.
Independently to the systems biology community, other scientists developed their own standards of representations, such as CellML (physiology), NeuroML (neurophysiology), SimileXML (ecology), with more on the way. More recently, new languages appeared that complement the model description, such as SED-ML to describe the simulation experiments or SBRML to encode the numerical results. The developers of all those initiatives are now in contact, and try to improve the interoperability of the languages.
One can hope to see, in a not too elusive future, the creation of a coherent set of non-overlapping standards, similar to the W3C standards for the World Wide Web, that will cover the various modeling approaches and scales, but also the different levels of discourse and representation in Systems Biology.


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