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Software Infrastructure for Enabling Greater Collaboration in Computational Modeling: The Systems Biology Markup Language (SBML) Project: 

Software Infrastructure for Enabling Greater Collaboration in Computational Modeling: The Systems Biology Markup Language (SBML) Project Michael Hucka, Andrew Finney, Ben Bornstein, Bruce Shapiro, Ben Kovitz, Sarah Keating, Jo Matthews, Akira Funahashi, Herbert Sauro, John Doyle, Hiroaki Kitano California Institute of Technology (USA) University of Hertfordshire (UK) ERATO-SORST Kitano Symbiotic Sytems (Japan)

SBML = Systems Biology Markup Language: 

SBML = Systems Biology Markup Language A machine-readable format for representing computational models in systems biology Expressed in XML Intended for software tools—not for humans (Although it is text-based and therefore readable) Think HTML Intended to be a tool-neutral exchange language for software applications in systems biology Simply an enabling technology

What Kind of Models Can You Express in SBML?: 

What Kind of Models Can You Express in SBML? Focus: systems of biochemical reactions Models can also include: Compartments Rules/constraints Discrete events Compartment Molecular species Reaction

Structure of Models Expressed in SBML: 

Structure of Models Expressed in SBML Basic structure of SBML is straightforward: Beginning of SBML model definition List of function definitions (new in Level 2) List of unit definitions List of compartments List of molecular species List of parameters List of rules List of reactions List of events (new in Level 2) End of SBML model definition

Acceptance of SBML: 

Acceptance of SBML Over 60 software packages world-wide support SBML today See sbml.org

Software from the SBML Team: 

Software from the SBML Team Embeddable software library for using SBML LibSBML 2.1.0 Provides API for C, C++, Java, Python, others Supports Linux, Mac, Windows ° GNU LGPL Interfaces to popular general math environments MathSBML 2.3.38 for Mathematica SBMLToolbox 1.0 (forthcoming) for MATLAB Conversion tools KEGG2SBML 1.1.0 CellML2SBML 1.0 (forthcoming) Web-based facilities Validation, visualization, example models

Publications: 

Publications SBML specifications are online at http://sbml.org Also have FAQ, community wiki, discussion forums Hucka et al., Bioinformatics 2003; 19(4): 524-531 "Fast-breaking paper" for June 2004, ISI-Thompson Finney & Hucka, Biochem. Soc. Trans., 31, 2003 Hucka et al., Systems Biology, 1(1): 41-53, 2004 MIME type for SBML (RFC 3823) application/sbml+xml

SBML Process: 

SBML Process "Editors": Andrew Finney and Mike Hucka Organize & manage activities, meetings, development Seek funding for same Guide (but do not dictate) technical proposals Integrate & edit final proposals into coherent spec. SBML Forum: informal community of modelers, researchers, software developers Open: no official membership, no dues, etc. Main channels for discussions: Forum meetings (next: Oct. 14-15, ICSB Heidelberg) sbml-discuss@caltech.edu

Currently in Development: SBML Level 3: 

Currently in Development: SBML Level 3 Addition of "modules" providing facilities for representing more information, including: Graphical diagrammatic visual layout of models Model composition (submodels) Multistate complex species Arrays of elements Representing 2-D & 3-D spatial geometry And several others… If interested, please join discussions at http://sbml.org!

Acknowledgments: 

Acknowledgments National Human Genome Research Institute (USA) National Institute of General Medical Sciences (USA) International Joint Research Program of NEDO (Japan) ERATO Kitano Symbiotic Systems Project (Japan) ERATO-SORST Program of the Japan Science and Technology Agency (Japan) Ministry of Agriculture (Japan) Ministry of Education, Culture, Sports, Science and Technology (Japan) BBSRC e-Science Initiative (UK) DARPA IPTO Bio-Computation Program (USA) Air Force Office of Scientific Research (USA)

Slide11: 

http://sbml.org