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Exchanging stoichiometric models: interoperability at genome scale

Presented by: 
B Olivier Vrije Universiteit Amsterdam
Date: 
Tuesday 4th November 2014 - 13:00 to 13:15
Venue: 
INI Seminar Room 1
Abstract: 
Advances in the methods used to construct genome scale constraint based models and the wider adoption of constraint based modeling in biotechnological and medical applications have led to a rapid increase in both the number of models being constructed and the tools used to analyze them.

Faced with such growth, both in number and diversity, the need for a standardized data format for the definition, exchange and annotation of constraint based models has become critical. As the core model components (e.g. species, reactions, stoichiometry) can already be efficiently described in the Systems Biology Markup Language (SBML) the Flux Balance Constraints (FBC) package aims to extend SBML Level 3 core by adding the elements necessary to encode current and future constraint based model.

In this presentation, focusing on how they might be utilized in modelling microbial ecosystems, I will introduce the SBML Level 3 FBC package and two related standards, SED-ML and the COMBINE archive.

I will also explain the need for the consistent use of reaction/species identifiers and a tool that is being developed to address this issue.

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University of Cambridge Research Councils UK
    Clay Mathematics Institute London Mathematical Society NM Rothschild and Sons