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The Systems Biology Markup Language (SBML): Where It’s Been and Where It’s Going

Michael Hucka¹

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1. BNMC, California Institute of Technology

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Presentation

Date:

Received 22 January 2007 04:39 UTC; Posted 22 January 2007

Subjects:

Biotechnology, Bioinformatics

Tags:

• systems biology
• structured data formats
• standards
• modelling
• XML
• SBML

Abstract:

A cornerstone of systems biology is the use of computational modeling, by which hypotheses can be cast into a quantitative form that can be tested systematically. The use of computational modeling by biologists promises to pave the way for more rigorous analyses of biological functions, and ultimately will lead to new and better treatments for disease.

A crucial enabler for more widespread use of computational modeling in biology is reaching agreement on how to represent, store, and communicate models between software tools. The Systems Biology Markup Language (SBML) project is an effort to create a machine-readable format for representing computational models in biology. By supporting SBML as an input and output format, different software tools can operate on the same representation of a model, removing chances 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 systems supporting it today.

In this presentation, I will discuss the current state of SBML, including recent developments such as this year’s finalization of Version 2 of SBML Level 2. I will also survey some of the software tools that support SBML, and related projects that have arisen to support more effective use of computational models. Lastly, I will discuss expected future developments in SBML.

Presented at:

ICSB 2006, 11 October 2006

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This document is licensed to the public under the Creative Commons Attribution 2.5 License

How to cite this document:

Hucka, Michael. The Systems Biology Markup Language (SBML): Where It’s Been and Where It’s Going. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2007.21.1> (2007)

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