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Links to other resources for databases and simulators of signaling pathways

Some of these entries have been borrowed from the computational cell biology project at the University of Cambridge.

Computational cell biology resources

  • SCIENCE's Signal Transduction Knowledge Environment Large resource for signal transduction, needs subscription for full access.

  • TRANSPATH signal transduction database Maps of signal transduction pathways.

  • CSNDB: Cell Signaling Networks DataBase Cell Signaling Networks Data base (CSNDB) is a data- and knowledge- base for signaling pathways of human cells.

  • Biomelecular Interaction Network Database The Biomolecular Interaction Network Database (BIND) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the BIND 2.0 data model has led to the incorporation of virtually all components of molecular mechanisms including interactions between any two molecules composed of proteins, nucleic acids and small molecules.

  • WIT Metabolic reconstructions for sequenced (or partially sequenced) genomes

  • Cytocom Network A network of laboratories working on signaling and analysis.

  • DIP: Database of Interacting Proteins The DIP(TM) database catalogs experimentally determined interactions between proteins.

  • BioCarta The BioCarta site has a Pathways section with many good-looking pathway diagrams and some annotations for each.

  • SigPath This is a developing site on quantitative signaling. "SigPath is an information system designed to support quantitative studies on the signaling pathways and networks of the cell."

E. coli databases

  • GenProtEC E. coli Genome and Proteome database

  • CGSC E. coli Genetic Stock Center

  • EcoCyc Encyclopedia of E. coli Genes and Metabolism

  • ECDC E. coli database collection

  • Colibri

Enzyme databases

  • NC_IUBMB The Nomenclature Committee of the International Union of Biochemistry and Molecular Biology has an exhaustive database of enzymes and their nomenclature.

  • KEGG Kyoto Encyclopedia of Genes and Genomes.

  • DBGET/LinkDB Integrated database retrieval system of the GenomeNet, Japan.

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

  • AfCS The Alliance for Cellular Signaling has databases of molecules involved in signaling, a listing of relevant proteins proteins and signaling maps.

Cell biology modeling and specification language projects

  • CellML The CellML markup language for signaling pathways, anatomy, and many more aspects of cell biology.

  • ERATO/SBML Systems Biology Workbench

Simulators for signaling pathways.

  • Kinetikit version 7
    This is the standard release for the kinetikit simulator. The release includes the kinetikit source scripts and the binaries for Linux for the GENESIS simulator.

  • Kinetikit version 8 (Developmental)
    This is the developmental release for the kinetikit simulator. The release includes the kinetikit source scripts and the binaries for Linux for the GENESIS simulator. This version handles high-level specification of pathway interactions but its format is planned to be superseded soon. If you do not use the high-level specification stuff it is provides several features beyond kinetikit 7. It requires a custom version of genesis, which is part of the release.

  • GENESIS This is a mirror of the official release of GENESIS.

  • Biospice A biological data analysis and modeling workspace and database

  • DBsolve Software for metabolic, enzymatic and receptor-ligand binding simulation

  • E-Cell A simulation platform for the modelling of cells at a molecular level

  • Gepasi A software package for modelling systems of biochemical reactions

  • Jarnac A language for describing and manipulating cellular system models

  • MCell A general Monte Carlo simulator of cellular microphysiology

  • Triple-J Java web simulation project A Java/Mathematica simulator and database of metabolic and oscillatory biochemical models.

  • Virtual Cell A general computational framework for modeling cell biological processes

  • WIT Metabolic reconstructions for sequenced (or partially sequenced) genomes

Running models on-line. (To be implemented)

This forthcoming feature will initially allow predefined signaling models in the database to be loaded and run. Subsequently it will be extended to allow construction of the model on-line as well. The Virtual Cell site already allows this kind of on-line model definition and simulation.

Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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