Physiome Models
NSR Physiome Model Repository
- Indexed NSR Model list and search.
- Browse NSR Models.
- Tutorials.
- JSim Model Standards and General Modeling Guidlines.
- Biomodels, JWS, Kegg Pathway, and CellML converted to JSim MML.
This is a collection of biophysical and physiological models covering mainly physiological transport, cellular biophysics, and biophysics, biomechanics and biochemistry of cardiovascular and respiratory physiology and pathophysiology. A growing number of renal, hepatic, and neural models are being installed. Models have been contributed by a large variety of investigators.
This model repository also includes separate access to four other model databases (Biomodels, JWS, Kegg Pathway, and CellML) and contains JSim MML translations as well as links to the original sources.
The NSR Physiome models are mainly in JSim, which uses declarative code allowing ODEs, DAEs, PDEs, and a variety of other constructs but does not allow (yet) iterative procedures or subroutines except in Java. JSim is open source, and innovations are welcomed. Some models are provided in Matlab, C++ or Fortran. Contribution of models is invited, given that the source code is open; author recognition is provided on the site.
All of the models are open source licensed and available for download.
Models include those that have been published. Many include data sets providing validation tests of the models. Analytical solutions are used in some models as verification of the numerical methods.
Models in JSim can currently be run over the web, allowing parameter exploration, modifying the graphical output, revising the source code and recompiling, adding models, etc., on this host server, that is, operating as if on your own computer BUT without the ability to save a revised project file. To preserve one's work, you can download the revised model and the simulation system itself, JSim, to one's own computer to explore at your convenience.
The JSim PROJECT FILE (model name.proj) provides packaging for REPRODUCIBLE RESEARCH to accompany published papers. (See JSim project file information ).
Models available for running through your web browser as a JAVA applet or for download. Models written in JSim MML unless otherwise noted.
- (beta) Search Consolidated Model database. Search for models in the Biomodels, JWS, Kegg Pathway, CellML and NSR model databases.
- JSim Modular Program Constructor (MPC). Tool to assist in building modular JSim MML models.
Other Physiology models (models from other sources that either run stand-alone, converted to JSim, or on different simulation platforms).
- Models converted to run in JSim:
- Event-Tracking Model of Adhesion (external site). La Jolla Institute for Allergy and Immunology Division of Inflammation Biology.
Event-Tracking Model of Adhesion (ETMA) is a direct, 3D, stochastic, pi-calculus driven model of leukocyte rolling, progressing by varying time steps and tracking consecutive bond formation and dissociation events. - Physiome sites with models.
NSR Physiome legacy models (models and documentation for XSim and older fortran models).
Model development and archiving support at https://www.imagwiki.nibib.nih.gov/physiome provided by the following grants: NIH U01HL122199 Analyzing the Cardiac Power Grid, 09/15/2015 - 05/31/2020, NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; 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.
