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
University of Auckland, Auckland, New Zealand
Information Systems and Physiology at Melbourne University and the Bioengineering Institute at Auckland University
Europe
Biomedical Research & Technology, Biomedical Industry and Clinical Practice
University of Leeds, Leeds, UK
Oxford Cardiac Electrophysiology Group
Dr. Denis Noble, Oxford University, Oxford, UK
Dr. Alan Garny, Cardiac Electrophysiology Group
European Bioinformatics Institute
Cambridge, United Kingdom
Quantitative Kidney Database (QKDB)
Necker Hospital, Paris, France
International
International
Asia, Europe, North America
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
Cambridge, Massachusetts, USA
Respiratory Tract 3D: Imaging and Modeling
Dr. Melissa Kreuger, Pulmonary Critical Care, University of Washington, Seattle WA, USA
The Respiratory Health Network, Montréal, Québec, Canada
San Diego Supercomputer Center
University of California, San Diego, USA
Sauro Lab, University of Washington, Seattle, USA
Physiome Sites with Models Displayed or Available for Download
European Bioinformatics Institute
Cambridge, United Kingdom
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
Dr. Alan Garny, Cardiac Electrophysiology Group
Institute for Advanced Biosciences E-cell Project
Keio University, Tokyo, Japan
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
CellML, (Cell Markup Language)
The Bioengineering Research Group at the University of Auckland
The Bioengineering Research Group at the University of Auckland
FieldML, (Field Markup Language)
The Bioengineering Research Group at the University of Auckland
SBML (Systems Biology Markup Language)
The SBML Team, North America, Europe, Asia
MathML (Math Markup Language)
W3C
Simulation Software and Modeling Environments
University of Washington, Seattle, WA, USA
Systems Biology Workbench (SBW)
Sauro Lab, University of Washington, Seattle, USA
University of California, Berkeley, CA, USA
Lawrence Berkeley National Laboratory, University of California, Berkeley, USA
BISEN: The Biochemical Simulation Environment
BioTech Center, Medical College of Wisconsin, Milwaukee, WI, USA
University of California, San Diego, CA, USA
BIONT: Modeling Program for the Complex Biochemical Systems
University of Auckland, Auckland, NZ
Keio University, Tokyo, Japan
NCRR Center for Integrative Biomedical Computing, University of Utah, USA
List of Simulation Software that Supports SBML
Resources for physics-based simulation of biomedical structures.
Ontologies
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
Standards and Ontologies for Functional Genomics
Edinburgh, Scotland, UK
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
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
Research Collaboratory for Structural Bioinformatics (RCSB)
Protein Knowledgebase
The Biomolecular Networks Initiative (BNI)
Pacific Northwest National Laboratory
Proteometrics
Other Related Links
Grant Sources
National Institute of General Medical Studies (NIGMS)
Find NIGMS-NIH Grant opportunities.
National Science Foundation (NSF)
National Center for Research Resources (NIH/NCRR)
National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)
Relevant Links
National Heart Lung and Blood Institute Computational Modeling
Medical Physiology Course Directors Website
National Center for Biotechnology Information
Biotechnolgy and Bioengineering Center: Medical College of Wisconsin, Milwaukee, WI, USA
PMaC: Performance Modeling and Characterization San Diego Supercomputer Center
Dr. Stephen Schwartz's Web Page
Bruce Shapiro's Cell Simulation Project
[This page was last modified 16Nov09, 11:14 am.]
Model development and archiving support at physiome.org provided by the following grants: NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.
