title: Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.
abstract: Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.
authors.affiliation: Control and Dynamical Systems, California Institute of Technology, Pasadena 91125, USA. mhucka@caltech.edu
authors.forename: M
authors.initials: M
authors.lastname: Hucka
authors.forename: A
authors.initials: A
authors.lastname: Finney
authors.forename: B J
authors.initials: BJ
authors.lastname: Bornstein
authors.forename: S M
authors.initials: SM
authors.lastname: Keating
authors.forename: B E
authors.initials: BE
authors.lastname: Shapiro
authors.forename: J
authors.initials: J
authors.lastname: Matthews
authors.forename: B L
authors.initials: BL
authors.lastname: Kovitz
authors.forename: M J
authors.initials: MJ
authors.lastname: Schilstra
authors.forename: A
authors.initials: A
authors.lastname: Funahashi
authors.forename: J C
authors.initials: JC
authors.lastname: Doyle
authors.forename: H
authors.initials: H
authors.lastname: Kitano
mesh_terms: D001671:Biochemistry / Q000379:methods / Q000592:standards; D002468:Cell Physiological Phenomena; D019295:Computational Biology / Q000379:methods / Q000592:standards*; D005786:Gene Expression Regulation / Q000502:physiology; D017408:Guidelines as Topic; D038622:Internationality; D008954:Models, Biological; D011381:Programming Languages; D012015:Reference Standards; D012984:Software; D049490:Systems Biology; D009626:Terminology as Topic