Selected Web Sites of Interest to Kineticists, Modelers, Computational Biologists, Theoretical Biologists and Bioinformaticians

• Academic Sites
  • National Resource for Cell Analysis and Modeling - home of the Virtual Cell - great for PDEs - lacks strong optimizer/statistics
  • Institute for Systems Biology - Seattle
  • Alliance for Cellular Signaling
  • Center for Computational Medicine and Biology - Johns Hopkins
  • Institute for Computational Biomedicine - Mt. Sinai School of Mecicine - home of SigPath
  • Penn Bimathematics Unit - home of the WinSAAM software - the pioneer for optimization
  • Penn Computational Biology and Informatics Lab
  • Metabolic Control Analysis Web - University of Wales Aberystwyth
  • Department of Engineering Science - University of Auckland - home of CellML and other XML-based biological markup languages
  • Bioinformatics and Biocomputing Server, National University of Singapore
  • Bioinformatics Links at George Mason University - a fabulous resource - no longer updated - still useful
  • The Godess Project - interested in very large systems of ODEs? - visit this site
  • Laboratory of Experimental and Computational Biology - NCI, NIH
  • Marseilles group in Enzyme Kinetics and Control Analysis - Centre National de la Recherche Scientifique
  • Mathematical Research Branch - NIDDK, NIH
  • Metabolic Control Analysis Research Group - Oxford Brookes University
  • Alliance for Cellular Signaling - An NIGMS GLUE grant with a clear integrative vision
  • Gepasi - a superb biochemical and cell biological simulation tool with deep roots in enzyme kinetics
  • BioPathways Consortium
  • Systems Biology Software at Caltech - home of Jarnac, JDesigner, and the venerable Scamp
  • Abacuss - an open modeling environment and simulator from MIT

• Corporate Sites
  • The SAAM Institute, Inc. - home of the SAAM II software - perhaps the best optimizer in the world - lacks GUI for nonlinear systems
  • Berkeley Madonna - a wonderful simulation tool - lacks documentation of its numerics
  • BioKin - home of Petr Kuzmic's DYNAFIT - a widely used biochemical kinetics tool, free to academic users
  • Physiome Sciences, Inc. - great team, keen insights, a glimpse of the future
  • MGA Software - home of the ACSL family of simulation software packages
  • Mathworks - home of the MATLAB software
  • Simulation Resources, Inc. - home of the SCoP software package
  • InnaPhase - home of the Kinetica software suite
  • Cherwell Scientific Publishing - home of the ModelMaker software package
  • Gene Network Sciences - a totally awesome model of a cancer cell and an impressive selection of network analysis tools
  • Entelos - Virtual patients and the PhysioLab software
  • Integrative BioInformatics, Inc. - home of ProcessDB (I think this is very cool, but I'm also very biased)

• Bioinformatics Databases
  • The National Center for Biotechnology Information
  • AfCS/Nature Molecule Pages
  • Science's STKE - Signal transduction knowledge environment
  • Hopkins Bio-Informatics Home Page
  • TransFac - the transcription factor database
  • Metabolism, Enzyme, Protein, Alignment, Phylogeny Database at ANL
  • GenomeNet - home of the KEGG database
  • Library of Kinetic Models of Biological Systems at Georgetown University
  • PROWL - The Enzyme Commission Classification Site
  • GenoBase Database Gateway - CIT (nee DCRT), NIH
  • The Institute for Genomic Research
  • National Center for Genome Resources
  • SYQUA Bioinformatics Site
  • CS ChemFinder - Quick! What's the structural formula for NADPH and what's its molecular weight?
  • KEGG - Kyoto Encyclopedia of Genes and Genomes - great databases hidden behind a clean-but-cryptic user interface
  • DBGET - A cute, powerful one stop shopping location for empirical public bioinformatics databases

   

• Bioinformatics and Computational Biology Tools and Tutorials
  • Integrative Bioinformatics: Practical Kinetic Modeling of Biological Systems
  • PathDB - from NCGR
  • BCD BioComputing Tutorial
  • AG BIODV Software Development for Molecular Biology - home of the FastM software
  • TESS - Transcription Element Search Software
  • Pedro's BioMolecular Research Tools
  • Biologist's Control Panel - Baylor College of Medicine

   

• Literature Searching
  • Internet Grateful Med
  • Pubmed Medline Query
  • BioMedNet Evaluated Medline (this one requires a membership, but it's free)

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