Links Physiome

About IMAG

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

Europe

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
EBI BioModels Database: Cambridge, United Kingdom
Quantitative Kidney Database (QKDB): Randy Thomas, France

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 Institute for Computational Medicine: 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
Genomic Science Program, Systems Biology for Energy and Environment: US Department of Energy
The Hamner Institute for Health Sciences: Research Triangle Park, NC, USA
Center for Reproducible Biomedical Modeling: The center aims to enable larger and more accurate systems biology models, as well as their applications to science, bioengineering, and medicine, by enhancing their understandability, reusability, and reproducibility.
Interagency Modeling and Analysis Group (IMAG): Interagency: NIH, NSF, NASA, DOE, DOD, USDA, USDVA
National Center for Cell Analysis and Modeling (VCELL): 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 Integrative Biomedical Computing: 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
The Virtual Physiological Rat Project: Medical College of Wisconsin, Milwaukee, USA

Physiome Sites with Models Displayed or Available for Download

EBI BioModels Database: Cambridge, United Kingdom
COR (Cellular Open Source): Dr. Alan Garny, Cardiac Electrophysiology Group
GENESIS (GEneral NEural SImulation System) is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models.
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
Virtual Cell modeling and Analysis Software: National Resource Center for Cell Analysis and Modeling, Center for Biomedical Imaging Technology, University of Connecticut Health Center, Farmington, CT, USA
NIH/NIGMS Center for Integrative Biomedical Computing: University of Utah, Salt Lake City, UT, USA
NSR Physiome Project Model Database: University of Washington, Seattle,WA, USA
Shepherd lab Model Database: Computational neuroscience models, Yale University, MA, USA

Physiome Markup Languages

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
NuML The Numerical Markup Language (NuML) aims to standardize the exchange and archiving of numerical results.
SBML (Systems Biology Markup Language): The SBML Team, North America, Europe, Asia
SEDML (Simulation Experiment Markup Language)

Simulation Software and Modeling Environments

JSim: University of Washington, Seattle, WA, USA
Systems Biology software : Sauro Lab, University of Washington, Seattle, USA
Berkeley Madonna: University of California, Berkeley, CA, USA
BioSpice : Lawrence Berkeley National Laboratory, University of California, Berkeley, USA
BISEN: The Biochemical Simulation Environment : BioTech Center, Medical College of Wisconsin, Milwaukee, WI, USA
BIONT: Modeling Program for the Complex Biochemical Systems
Continuity 6: University of California, San Diego, CA, USA
CMISS:University of Auckland, Auckland, NZ
E-Cell System: Keio University, Tokyo, Japan
GENESIS (GEneral NEural SImulation System) is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models.
Copasi: Biochemical system simulator, a software application for simulation and analysis of biochemical networks and their dynamics.
CIBC Software: Problem solving software 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
SimTK simulation and modeling resources: Simtk.org is the home of the software framework initiated and developed by Simbios, the National NIH Center for Biomedical Computing focusing on Physics-based Simulation of Biological 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
KiSAO (Kinetic Simulation Algorithm Ontology)
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

Genome Databases

European Molecular Biology Laboratory: Heidelberg, Germany
Insitute for Genomics and System Biology. Argonne National Laboratory, IL
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
Integrative omics at Pacific Northwest National Laboratory (BNI): Pacific Northwest National Laboratory
PROWL for Intranet: Proteometrics