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ST NetWatch: Modeling Tools

AVIS: AVIS is an AJAX (Asynchronous JavaScript and XML) viewer for cell signaling networks, gene regulatory networks, or protein interaction networks, which provides web-based visualization of cellular networks with dynamic zooming, panning, and linking capabilities. AVIS will render data describing interaction networks in various text file formats. There are samples on the site or you can read the manual to find out how to format your own network into a compatible file. A detailed user manual explains the acceptable file formats (SIG, Pajek NET, AVIS, or SBML), how to run AVIS on a server, how to add the AVIS Gadget to web pages, and how to configure AVIS for customized web display of networks. The tool can also be used directly on the Iyengar lab's web site to visualize networks, by uploading a file in an acceptable format (choose the link "Upload and visualize network text files from your client machine"). AVIS uses the GraphViz, ImageMagic (PerlMagic), and overLib libraries.
(Free Site)
Action Potential Simulation: Especially useful for those teaching molecular neurobiology, this site allows students to alter various parameters to determine their effects on action potential propagation.
(Free Site)
AgentCell (Digital E. Coli): This site provides access to a simulation tool for studying bacterial chemotaxis in the absence and presence of a gradient to understand how intracellular signaling events control cellular behavior. The software is freely available and the site includes several animations showing digital chemotaxis using AgentCell.
(Free Site)
Arkin Lab Homepage: The Arkin lab is developing modeling and simulation tools for the analysis of biological signaling networks. The Stuff section provides particularly useful information from tutorials and excerpts from presentations on applying mathematical analysis to biological questions to actual software available to download to perform analysis. Arkin's group provides information for both novices and experienced biological computational scientists.
(Free Site)
BioModels Database: The BioModels Database, part of the EMBL-EBI collection of databases, is a repository for published mathematical models of biological pathways. Biochemical and signaling pathways are both included, but biochemical pathways are more highly represented. Some models (curated models) have been checked for accuracy by database curators, and others (non-curated models) have had only their mathematical elements verified. Users can search models in the database by author or contributor names, by InterPro or KEGG pathway ID, or by gene ontology terms. The models are annotated with links to publications, protein sequences from UniProt, and other information relevant to the pathway components. Models may be downloaded individually as needed, or the entire database of 244 models may be downloaded at once. The models are in Systems Biology Markup Language (SBML) format and ready for use in SBML-compatible simulators.
(Free Site)
CellDesigner: CellDesigner allows users to create and annotate graphical models of gene regulatory and biochemical networks from experimental interaction and kinetics data. You can build models from scratch or start from existing models that are available from the BioModels Database. CellDesigner can connect to databases such as PubMed, Entrez Gene, and the Saccharomyces Genome Database to retrieve information about pathway components. The CellDesigner software is available free of charge from its developer, the Systems Biology Institute, and is compatible with Systems Biology Markup Language (SBML) and the Systems Biology Workbench, a software platform that integrates diverse modeling tools so that they can be used together.
(Free Site)
Computational Cell Group in Physiology, Development, and Neuroscience: This group at the University of Cambridge has developed several tools for studying bacterial chemotaxis in E. coli. The three different computational biology tools are BCT, StochSim, and Smoldyn. BCT is a text-based, deterministic simulator of the chemotaxis signal transduction pathway in E. coli. StochSim was originally designed as a stochastic simulator to study bacterial chemotaxis and can now be used for simulation of biochemical processes. Smoldyn stands for Smoluchowski dynamics and is a biochemical simulator in which the diffusion of molecules in 1-, 2-, or 3-dimensions can be computed and displayed graphically. Each of the programs is available for downloading and the algorithms are described in detail. The site also provide data related to the biochemical events associated with E. coli chemotaxis and pages discussion various aspect of bacterial chemotaxis.
(Free Site)
Cytoscape: Cytoscape offers an array of bioinformatics software for visualization of complex molecular interaction networks. The software supports the import of data in multiple file formats and various options allow the user to customize the output graphs. Plug-ins allow analysis of network properties, allow the user to apply filters to limit complex networks, or add gene expression data onto a network.
(Free Site)
MCell: MCell is "A General Monte Carlo Simulator Of Cellular Microphysiology" and is simulation software designed to incorporate high resolution ultrastructure into models of ligand diffusion and signaling. The software was developed by Thomas M. Bartol Jr. at the Salk Institute and Joel R. Stiles at the Pittsburg Supercomputing Center.
(Free Site)
NEURON: NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons. Michael Hines and John W. Moore at the Department of Neurobiology, Duke University have collaborated in its creation. The software is freely available for downloading.
(Free Site)
Systems Biology Markup Language (SBML): SBML is an XML-based language for representing models of biochemical reaction networks, including signaling pathways, in computer-readable format. STKE has chosen an SBML-compatible file format for machine-readable versions of the Connections Maps database. The website provides assistive documents, schemas, and presentations, as well as a comprehensive FAQ list and two SBML discussion forums. Other highlights are an extensive model repository and a community-editable SBML Wiki area, where users can describe their own experiences with the software and make suggestions for future development. SBML tools include those for validation, visualization, and conversion of SBML files.
(Free Site)
Systems Biology Workbench: One difficulty in mathematical modeling of pathways is integrating information from multiple sources, which are often in incompatible formats. The Systems Biology Workbench (SBW) is a software platform that allows users to integrate data from different types of programs and modeling tools. SBW provides a framework that enables applications that are normally incompatible to share information. SBW was designed to speed the time it takes to build new models from aggregated information or add to existing models without starting from scratch. SBW is especially useful because it allows users to take data from models in one format and put them into a model in a different format. SBW uses Systems Biology Markup Language (SBML), the format that is becoming the standard for modeling tools.
(Free Site)
The Virtual Cell: The Virtual Cell is unique software environment based on Java's Remote Method Invocation (RMI) for cell biological research that is being developed at the National Resource for Cell Analysis and Modeling. Experimentalists can use the software to create models, define cellular geometry, specify simulations, and analyze simulation results. Version 3.0 was released June 2001.
(Free Site)