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Standards > model/format > bsg-s000052


ready Systems Biology Markup Language

Abbreviation:SBML


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General Information
The Systems Biology Markup Language (SBML) is a machine-readable exchange format for computational models of biological processes. Its strength is in representating phenomena at the scale of biochemical reactions, but it is not limited to that. 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.



This record is maintained by skeating  ORCID

Record added: May 14, 2015, 11:14 a.m.
Record updated: May 4, 2017, 1:39 p.m. by skeating.





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Implementing Databases (15)
MetaCrop 2.0
The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated information on reactions and the kinetic data associated with these reactions. Ontology terms are used and publication identification available to ease mining the data.

Integrated Pathway Analysis and Visualization System
iPAVS provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provides several tools to manipulate,filter, browse, search, analyze, visualize and compare the integrated pathway resources.

BRENDA
BRENDA is the main collection of enzyme functional data available to the scientific community.

A repository of mathematical models of biological and biomedical systems
BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-linked to publicly available reference information.

Reactome - a curated knowledgebase of biological pathways
The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.

SABIO-RK Biochemical Reaction Kinetics Database
SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.

YEASTNET: A consensus reconstruction of yeast metabolism
YEASTNET is a resource of the yeast metabolic network as reconstructed from a combination of genomic data and publications.

Experimental data repository for KInetic MOdels of biological SYStems
KiMoSys is a user-friendly platform that includes a public data repository of relevant published measurements, including metabolite concentrations (time-series and steady-state), flux data, and enzyme measurements in order to build ODE-based kinetic model. It is designed to search, exchange and disseminate experimental data (and associated kinetic models) for the systems modeling community.

SIGNOR, the SIGnaling Network Open Resource
SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. The core of this project is a collection of more than 11000 manually-annotated causal relationships between proteins that participate in signal transduction. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.

Physiome Model Repository
The Physiome Model Repository (PMR) is the main online repository for the IUPS Physiome Project, providing version and access controlled repositories, called workspaces, for users to store their data. PMR also provides a mechanism to create persistent access to specific revisions of a workspace, termed exposures. Exposure plugins are available for specific types of data (e.g., CellML or FieldML documents) which enable customizable views of the data when browsing the repository via a web browser, or an application accessing the repository’s content via web services.

FAIRDOMHub
The FAIRDOMHub is a publicly available resource build using the SEEK software, which enables collaborations within the scientific community. FAIRDOM will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.

JWS Online
JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.

BiGG Models
BiGG is a freely compendium of published genome-scale metabolic networks, combined into a single database. NCBI genome annotations are used to map genes, and metabolites are linked to many external databases such as KEGG, PubChem as well as others..

MetaNetX
MetaNetX/MNXref is a database for reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. The tools developed at MetaNetX are useful for accessing, analysing and manipulating metabolic networks. MetaNetX goal is to automate model construction and genome annotation for large-scale metabolic networks.

Virtual Parts Repository
A repository of reusable, modular and composable models of biological parts.

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Credit

Record Maintainer

Funds

Maintains

Grant Number(s)

  • R01 GM070923 (US National Institute of General Medical Sciences, (NIGMS))


Publications

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

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 JH,Hunter PJ,Juty NS,Kasberger JL,Kremling A,Kummer U,Le Novere 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
Bioinformatics 2003

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