SBML
SBML encodes biochemical reaction networks in an XML-based, software-independent format (SBML Level 1) to support modeling of cell signaling pathways, metabolic pathways, and gene regulation.
Key Features:
- SBML Level 1: Provides the Level 1 specification for representing biochemical reaction networks.
- XML-Based Structure: Uses XML to encode models for machine processing and interoperability among computational tools.
- Software Independence: Represents models in a software-independent language to enable exchange across different platforms.
- Model Representation: Captures biochemical reactions and their interactions for standardized computational models.
Scientific Applications:
- Cell signaling pathways: Represents and exchanges computational models of cell signaling pathways.
- Metabolic pathways: Encodes metabolic pathway models for simulation and analysis.
- Gene regulation: Represents gene regulatory networks and their interactions in computational models.
- Model exchange and standardization: Standardizes information exchange to support development, evaluation, and reuse of systems biology models.
Methodology:
Defines a standardized, XML-based, software-independent format for accurately representing biochemical reactions and their interactions.
Topics
Collections
Details
- License:
- LGPL-2.1
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- library, workflow
- Operating Systems:
- Linux, Windows, Mac
- Programming Languages:
- R, Ruby, Java, C#, Python, C++
- Added:
- 1/17/2017
- Last Updated:
- 11/24/2024
Operations
Data Inputs & Outputs
Data handling
Inputs
Publications
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr J, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19(4):524-531. doi:10.1093/bioinformatics/btg015. PMID:12611808.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology. 2013;7(1):135. doi:10.1186/1752-0509-7-135. PMID:24321545. PMCID:PMC3892043.