Websites:

Physiome Projects
Physiome Sites with Models Displayed or Available for Download
Physiome Markup Languages
Simulation Software and Modeling Environments

Ontologies

Enzyme-Genome-Proteome Databases

Other Related Links

Physiome Projects

Asia

Computational Bioengineering Laboratory: National University, Singapore

Institute for Advanced Biosciences E-cell Project: Keio University, Tokyo, Japan

Kitano Symbiotic Systems Project: Tokyo, Japan

Center for Advanced Medical Engineering and Informatics: Osaka University, Osaka, Japan

Australasia

IUPS Physiome Project: University of Auckland, Auckland, New Zealand

Kidney Physiome Project: Information Systems and Physiology at Melbourne University and the Bioengineering Institute at Auckland University

Europe

BIOMED Town : Biomedical Research & Technology, Biomedical Industry and Clinical Practice

Computational Biology Group: University of Leeds, Leeds, UK

Oxford Cardiac Electrophysiology Group: Dr. Denis Noble, Oxford University, Oxford, UK

COR (Cellular Open Source): Dr. Alan Garny, Cardiac Electrophysiology Group

European Bioinformatics Institute : Cambridge, United Kingdom

Quantitative Kidney Database (QKDB): Necker Hospital, Paris, France

International

The Living Human Project: International

Giome.com: Asia, Europe, North America

Harvey Project: International

North America

Biological Network Modeling Center: California Institute of Technology, Pasedena, California, USA

Cardiac Bioelectricity Research and Training Center: Washington University, St. Louis, MO, USA

Cardiac Mechanics Research Group: University of California, San Diego, San Diego, CA, USA

The Center for Cardiovascular Bioinformatics and Modeling: Dr. Raimond Winslow, School of Medicine, The Johns Hopkins University, Baltimore, MD, USA

Center for Cell Analysis and Modeling: Dr. Les Loew, University of Connecticut, Farmington, CT, USA

The Hamner Institute for Health Sciences: Research Triangle Park, NC, USA

Interagency Modeling and Analysis Group (IMAG): Interagency: NIH, NSF, NASA, DOE, DOD, USDA, USDVA

IMAG and MSM Working Group Wiki: IMAG and Multi-scale Modeling Consortium (MSM)

MRC Group on Functional Regulation of Ion Channels and Transporters: University of Calgary, Faculty of Medicine, Calgary, Alberta, Candada

National Center for Cell Analysis and Modeling: Center for Biomedical Imaging Technology, University of Connecticut Health Center, Farmington, CT, USA

National Simulation Resource for Circulatory Transport: Dr. James Bassingthwaighte, University of Washington, Seattle, WA, USA

NIH Center for Bioelectric Field Modeling, Simulation and Visulization: University of Utah, Salt Lake City, UT, USA

PathCase: Pathways Database System: Case Western Reserve University, Cleveland, OH, USA

PhysioNet: Free access via the web to large collections of recorded physiologic signals and related open-source software. : Cambridge, Massachusetts, USA

Respiratory Tract 3D: Imaging and Modeling: Dr. Melissa Kreuger, Pulmonary Critical Care, University of Washington, Seattle WA, USA

RHN Québec: The Respiratory Health Network, Montréal, Québec, Canada

San Diego Supercomputer Center: University of California, San Diego, USA

Sys-Bio: Sauro Lab, University of Washington, Seattle, USA

Physiome Sites with Models Displayed or Available for Download

European Bioinformatics Institute:Cambridge, United Kingdom

EBI BioModels Database: Cambridge, United Kingdom

The Center for Cardiovascular Bioinformatics and Modeling: Dr. Raimond Winslow, School of Medicine, The Johns Hopkins University, Baltimore, MD, USA

The Hamner Institute for Health Sciences: Research Triangle Park, NC, USA

COR (Cellular Open Source): Dr. Alan Garny, Cardiac Electrophysiology Group

Institute for Advanced Biosciences E-cell Project: Keio University, Tokyo, Japan

IUPS Physiome Project: University of Auckland, Auckland, New Zealand

JWS Online Cellular Systems Modeling: South Africa

National Center for Cell Analysis and Modeling: Center for Biomedical Imaging Technology, University of Connecticut Health Center, Farmington, CT, USA

NIH Center for Bioelectric Field Modeling, Simulation and Visulization: University of Utah, Salt Lake City, UT, USA

Quantitative Kidney Database (QKDB): Necker Hospital, Paris, France

NSR Physiome Project Models Database: University of Washington, Seattle,WA, USA

Physiome Markup Languages

AnatML Viewer, (Anatomical Markup Language): The Bioengineering Research Group at the University of Auckland

CellML, (Cell Markup Language): The Bioengineering Research Group at the University of Auckland

FieldML, (Field Markup Language): The Bioengineering Research Group at the University of Auckland

MathML (Math Markup Language): W3C

NeuroML (Computational Neuroscience Markup Language): Neuro ML Team, England, Scotland, USA

SBML (Systems Biology Markup Language): The SBML Team, North America, Europe, Asia

Simulation Software and Modeling Environments

JSim: University of Washington, Seattle, WA, USA

Systems Biology Workbench (SBW): Sauro Lab, University of Washington, Seattle, USA

Berkeley Madonna: University of California, Berkeley, CA, USA

BioSpice - Arkin Lab: Lawrence Berkeley National Laboratory, University of California, Berkeley, USA

BISEN: The Biochemical Simulation Environment : BioTech Center, Medical College of Wisconsin, Milwaukee, WI, USA

Continuity 6: University of California, San Diego, CA, USA

BIONT: Modeling Program for the Complex Biochemical Systems

CMISS:University of Auckland, Auckland, NZ

E-Cell System: Keio University, Tokyo, Japan

Gepasi: computer simulation of biochemistry

SCIRun: Problem solving environment for modeling, simulation and visualization of scientific problems.: NCRR Center for Integrative Biomedical Computing, University of Utah, USA

List of Simulation Software that Supports SBML

Simbiome simulation resources: Resources for physics-based simulation of biomedical structures.

Virtual Cell Modeling and Analysis Software: Developed by the National Resource for Cell Analysis and Modeling (NRCAM) University of Connecticut Health Center

Ontologies

Foundational Model of Anatomy: University of Washington, Seattle, Washington, USA

National Center for Biomedical Ontology: Stanford University, Palo Alto, California, USA

National Center for Ontological Research: Stanford University, Palo Alto, California; University of Buffalo, New York; USA

Open Biomedical Ontologies

Standards and Ontologies for Functional Genomics: Edinburgh, Scotland, UK

Visible Human Project: National Library of Medicine, NIH, USA

Enzyme Databases

REBASE -- The Restriction Enzyme Database: Dr. Richard J. Roberts, New England Biolabs

MetaCyc Database Enzyme Database: Menlo Park, CA

Computational Biology Group. High throughput comparative and evolutionary analysis of Genomes and metabolic networks with Grid computational backend. Argonne National Laboratory.

Genome Databases

European Molecular Biology Laboratory: Heidelberg, Germany

Sequence Retrieval System at EMBL-EBI, Hinxton, UK: Network Browser for Databanks in Molecular Biology European Bioinformatics Institute

Genome and Metabolic Pathways Database: Bioinformatics Research Group, SRI International, Menlo Park, CA

KEGG: Kyoto Encyclopedia of Genes and Genomes Database: Kanehisa Laboratory, Kyoto University and University of Tokyo, Japan

Proteome Databases

Protein Data Bank (PDB): Research Collaboratory for Structural Bioinformatics (RCSB)

SWISS-PROT: Protein Knowledgebase

The Biomolecular Networks Initiative (BNI): Pacific Northwest National Laboratory

PROWL for Intranet: Proteometrics