BNMC Seminar:  SBML, SBGN, and BioModels.net

Michael Hucka

Systems biology by its nature requires collaborations between scientists with expertise in biology, chemistry, computer sciences, engineering, mathematics, and physics. Successful integration of these disciplines depends on bringing to bear both social and technological tools: namely, consortia that help forge collaborations and common understanding, software tools that permit analysis of vast and complex data, and agreed-upon standards that enable researchers to communicate and reuse each other’s results in practical and unambiguous ways. In this presentation, I will discuss several international projects (SBML, SBGN, and BioModels.net) aimed at addressing the last issue.

An important prerequisite for effective sharing of computational models is reaching agreement on how to communicate them, both between software and between humans. The Systems Biology Markup Language (SBML) project is an effort to create a machine-readable format for representing computational models at the biochemical reaction level. By supporting SBML as an input and output format, different software tools can operate on the same representation of a model, removing chance for errors in translation and assuring a common starting point for analyses and simulations. SBML has become the most successful effort in this direction so far, with over 100 software tools supporting it today.

A recently-created sister project is the Systems Biology Graphical Notation (SBGN) project. It addresses the issue of consistent human communication, by attempting to add more rigor and consistency to the graphical network diagrams that often accompany published research on models of biological reaction systems. The real payoff will come when more people and software adopt such a common visual notation and it becomes as familiar to them as circuit schematics are to electronics engineers.

Finally, when developing and publishing computational models, it is only natural to want to put them into a database. The BioModels.net project is an effort to (1) provide a free, centralized, publicly-accessible database of human-curated computational models in SBML and other structured formats; (2) define agreed-upon standards for model curation; and (2) define agreed-upon vocabularies for annotating models with connections to biological data resources.
About the speaker

Dr. Michael Hucka is a Senior Research Fellow at the California Institute of Technology. He is currently the co-director of the Biological Network Modeling Center, an initiative to bring together a number of efforts at Caltech in the area of computational systems biology. He is also one of the principal developers of the Systems Biology Markup Language (SBML), an international standard format for representing computational models in a way that can be used by different software systems to communicate and exchange those models. More recently, he has been involved in starting the SBGN effort, the BioModels Database, and the BioModels.net consortium. Dr. Hucka was previously a postdoctoral scholar in the Division of Biology at Caltech, where he worked on the GENESIS neural simulation package. He is also one of the creators of NeuroML. His formal training is in computer science and engineering.