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A List of Model Repositories
Here are the different models available in this repository.

BioModels.net BioModels Database

Part of the international initiative BioModels.net, the resource provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and give the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML, CellML, SciLab and XPP-Aut formats.

[Le Novre N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems. Nucleic Acids Res., in the press]

CellML CellML repository
The CellML.org model repository is part of the international Physiome Project, and is a resource containing hundreds of computational biology models encoded in the CellML format. These models cover a wide range of electrophysiological and cellular processes and are actively maintained and curated to high standards. CellML.org is working with other groups, including Biomodels.net, to establish standards for curation.

JWS Online
One of the first resources offering curation of the models it distributes, and online simulation. It is linked to journals such as Microbiology, FEBS Journal and IEE Proceedings in Systems Biology, that deposit the models upon submission of the manuscripts, so as to make them available to the reviewers. It now distributes the models in SBML and Pysces formats.

[Olivier BG, Snoep JL. Web-based kinetic modelling using JWS Online.(2004) Bioinformatics, 20: 2143-2144]

The Database of Quantitative Cellular Signalling (DOQCS)
DOCQS is a repository of models of signalling pathways present in the neurons. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. The pathways can be downloaded in the format used by the neuronal simulator GENESIS.

[Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks. (2003) Bioinformatics, 19: 408-415]

ModelDB
Developed as part of the SenseLab effort, the resource distributes models encoded in the many different formats, mainly those used by the GENESIS and NEURON simulators, but also format used by generic simulation environments such as Octave, MatLab, Octave or XPP-Aut.

SigPath
SigPath is an interesting project to develop an open knowledgebase of qualitative pathways and quantitative models related to signalling. An interesting feature is the possibility of annotating model components.

[Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H. Quantitative information management for the biochemical computation of cellular networks. (2004) Science STKE, 248: PL11]

SBML models for KEGG

SBML Model Repository @ sbml.org

SBI Model Base
A series of molecular interaction maps created by SBI using CellDesigner.

Metabolic Syndrome
Molecular Interaction Map of Macrophage
EGFR Pathway Map
Yeast Map
Graphical Notation Samples


PANTHER Pathways by Applied Biosystems

PathArt
PathArt is a comprehensive collection of manually curated information from literature as well as public domain databases on more than 1000 signaling and metabolic pathways.

Reactome

Sigmoid
The SIGMOID project is intended to produce a database of cellular signaling pathways and models thereof, to marshall the major forms of data and knowledge required as input to cellular modeling software and also to organize the outputs.



last updated: 2007 August
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