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ST NetWatch: Modeling Tools

Action Potential Simulation View Action Potential Simulation Save to My Folders
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) View AgentCell (Digital E. Coli) Save to My Folders
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 View Arkin Lab Homepage Save to My Folders
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)
AVIS View AVIS Save to My Folders
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)
BioModels Database View BioModels Database Save to My Folders
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 View CellDesigner Save to My Folders
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)
Cellerator View Cellerator Save to My Folders
Cellerator is a tool that allows users to model interactions between components of a signal transduction network or between multiple networks. It is a plugin for Mathematica, a commercially available mathematical computation and visualization software package. Cellerator translates reaction data into differential equations that Mathematica can use for simulations and analysis. The Cellerator site has a list of suggested reading materials pertaining to systems biology and mathematical modeling and includes a gallery of images and movies generated by Cellerator. xCellerator is the second-generation version of the software that uses a different algorithm for translating data, which makes it faster than Cellerator, and is compatible with systems biology markup language (SBML). The xCellerator site includes sample models for NF-kB signaling, MAPK cascades, G protein activation, and circadian rhythms. Both Cellerator and xCellerator are open-source and freely available for academic use, although they will only function if users already have the Mathematica software.
(Free Site)
Computational Cell Group in Physiology, Development, and Neuroscience View Computational Cell Group in Physiology, Development, and Neuroscience Save to My Folders
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 View Cytoscape Save to My Folders
Cytoscape is an open source software platform for visualizing and annotating 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. Because Cytoscape is open source, users are encouraged to develop and share their own plugins to expand the software’s capabilities, and the site includes a tutorial for writing plugins. Many user-developed plugins are freely available, although many require users to register for a free license before downloading. These plugins enhance the functionality of Cytoscape by enabling the user to analyze network properties, apply filters to complex networks, add gene expression data to a network, or identify new networks. A description of each plugin, information about any restrictions that may apply to its use, and links to the site where it may downloaded are provided. Users can also subscribe to an email service that will notify them when new plugins become available.
(Free Site)
MCell View MCell Save to My Folders
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)
ModelDB View ModelDB Save to My Folders
ModelDB is part of SenseLab, which consists of several interconnected databases: the Cell Properties Database (CellPropDB), Neuron Database (NeuronDB), Model Database (ModelDB), Olfactory Receptor Database (ORDB), Odor Molecular Database (OdorDB), Olfactory Bulb Odor Map Database (OdorMapDB), Microcircuit Database (MicrocircuitDB), and BrainPharm. ModelDB is a collection of published computational neuroscience models that users can download and execute with the free, open source simulator Neuron.
(Free Site)
NEURON View NEURON Save to My Folders
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)
Simmune Project View Simmune Project Save to My Folders
The Simmune Project from the National Institute of Allergy and Infectious Disease (NIAID) aims to develop systems biology tools that bridge the gap between the different modeling approaches taken by experimental and theoretical biologists. The Simmune software was originally developed at the University of Hamburg for simulating immunological events, but can be used for modeling events in other biological contexts. Users may incorporate data describing biological phenomena at different scales -- the molecular, cellular, and tissue levels. The Simmune software package consists of three components: the modeler (Simmod), the simulator (Simmune), and the Network Browser. Users define the components of the model with Simmod, including such information as the properties of individual molecules, how individual molecules interact, their rates of association and dissociation, properties of the cells and their environment, and other parameters for the in silico experiments. After the parameters of the model have been defined, the Simmune simulator runs simulations during which users can collect data from individual cells at specific time points. Users can explore the data captured during the simulation with the Network Browser. The software package is free for noncommercial use, and licenses are available for commercial users.
(Free Site)
Systems Biology Markup Language (SBML) View Systems Biology Markup Language (SBML) Save to My Folders
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 View Systems Biology Workbench Save to My Folders
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 View The Virtual Cell Save to My Folders
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)

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