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Model Repositories

SBML models for KEGG

All SBML files in this directory were converted from KEGG (Kyoto Encyclopedia on Genes and Genomes) by using our conversion script kegg2sbml with the permission of Professor Minoru Kanehisa (Kyoto University).
The conversion was performed by Akiya Jouraku, Nobuyuki Ohta, Akira Funahashi and Hiroaki Kitano, as part of the JST ERATO-SORST Kitano Symbiotic Systems Project. Publication of papers and other documents based on this database must include proper acknowledgment of this fact.

BioModels Database

biomodels_75x50.pngBioModels Database is a 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 XPP-Aut, and BioPAX 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 repository

cellml_logo_s.gifThe 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.

PANTHER Pathways

PANTHER Pathways consists of over 165, primarily signaling, pathways, each with subfamilies and protein sequences mapped to individual pathway components. A component is usually a single protein in a given organism, but multiple proteins can sometimes play the same role. Pathways are drawn using CellDesigner software, capturing molecular level events in both signaling and metabolic pathways, and can be exported in SBML format. Pathway diagrams are interactive and include tools for visualizing gene expression data in the context of the diagrams.

Reactome

The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. The information in this database is authored by biological researchers with expertise in their fields, maintained by the Reactome editorial staff, and cross-referenced with the sequence databases at NCBI, Ensembl and UniProt, the UCSC Genome Browser , HapMap, KEGG(Gene and Compound ), ChEBI, PubMed and GO. In addition to curated human events, inferred orthologous events in 22 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, two plants and E.coli are also available. A description of Reactome has been published in Genome Biology.

JWS Online

JWS Online is 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)

The Database of Quantitative Cellular Signalling (DOQCS)  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]

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]

ModelDB

ModelDB is being 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.

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.

CellDesigner models

Here are the models created by CellDesigner.

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. Such cellular signaling and regulatory pathways are commonly hand-drawn in biological literature as an aid to intuitive understanding. Pathway databases can provide the same assistance in the context of attempts to achieve a quantitative understanding of cellular processes by numerical simulation. They can also serve as an aid to capturing and querying both expert knowledge and heterogeneous data sets pertaining to pathways. Cell model databases are a subject of current research. SIGMOID works at the interface of these two areas.

Toll-Like Receptor signaling network

The model and the description is available at Molecular Systems Biology

Oda,K.; Kitano,H.;
A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol : msb4100057. Apr. 18, 2006

Graphical Notation Samples

SBML files for some of figures appeared in Kitano, et al., Nature Biotechnology, August 2005.

graphical.gif
Sample Files used in Figures:
  • CellDesigner 3.0 alpha version [ziped .xml files] *new graphical notation preview version.
  • CellDesigner 2.2 version [ziped .xml files]
  • EGFR Pathway Map

    Epidermal Growth Factor Receptor Pathway Map Ver.2 (2005/5/24) The model and the description is available at Molecular Systems Biology

    Oda,K.; Matsuoka,Y.;Funahashi,A.;Kitano,H.;
    A comprehensive pathway map of epidermal growth factor receptor signaling. May,2005.

    Macrophage Map

    Molecular Interaction Map of Macrophage

    A team of researchers at the Systems Biology Institute (SBI), Tokyo Medical and Dental University (TMDU), and Keio University jointly created a large scale molecular interaction map of macrophage. The map is intended to serve analysis framework for the Alliance for Cellular Signaling (AfCS), a large scale NIH-funded project lead by Professor Alfred Gilman (Univ. Texas Southwestern Medical Center). The map and description of the map is available from

    Nature Signaling Gateway
    .

    Metabolic Syndrome

    A molecular interaction map that describes most interactions involved in the metabolic syndrome for adipocyte, hepatocyte, skeletal muscle cell, and pancreatic beta cell.
    The map is prepared for the following paper:

    Kitano, H., Oda, K., Kimura, T., Matsuoka, Y., Csete, M., Doyle, J., Muramatsu, M..
    Metabolic Syndrome and Robustness Tradeoffs, Diabetes 53, S6-S15, 2004
    >Full text [PDF]