The Physiome.org website, host of the National Simulation Resource for Circulatory Mass Transport and Exchange (NSR Physiome Project), has changed its location and its sponsor: having been supported by multiple institutes at the National Institutes of Health (NIH) for the past four decades at the University of Washington, UW, in Seattle WA, it is now hosted in Washington DC at the NIH/National Institute for Bioimaging and Bioengineering managed by the Interagency Modeling and Analysis Group (IMAG) under the leadership of Grace Peng, PhD, Director.
A special thanks to Anuj Sharma for the translation of the Physiome.org website to this IMAG wiki site. The new Physiome site should be very similar to the original one with all the same models and information. The JSim simulation software, physiological modelling tips, best reproducible modeling practices, and all of the JSim models are available for download. Also included for download are many SBML (SBML.org) translations of these models as well as models written in Matlab and fortran. Please browse.
As this site is active and not just an archive, please send us new models as well as any corrections to models on this site. New models can be sent to one of the contacts listed in the Physiome Contacts/Feedback page. Please see https://www.imagwiki.nibib.nih.gov/physiome/models/modelinginfo for useful information if submitting a new model.
Thank you very much for your time and support,
James B. Bassingthwaighte, MD, PhD
Prof. Bioengineering, Radiology
University of Washington
July 12, 2021
The Physiome Project is the worldwide effort of several loosely connected research groups to define the physiome via databasing and the development of integrated quantitative and descriptive modeling. This work will help determine the future of medicine, change the way we think about human physiology, and strengthen the fabric of international scientific collaboration across political allegiances. The physiome.org website is now on the IMAG wiki. The physiomeproject.org website is primarily sponsored by the International Union of Physiological Sciences (IUPS) and is led by Peter Hunter of the University of Auckland, NZ. Both sites offers simulation software and models published in refereed journals that further the aim of integrating every level of human biology into a whole.
The NSR Physiome Project Provides
NSR, the National Simulation Resource at the University of Washington Department of Bioengineering, provides the following tools in support of the Physiome Project:
The JSim Modeling System
- Home Page (Getting started with JSim)
- JSim on GitHub
- JSim Modular Program Constructor (MPC). A tool to assist in building modular JSim MML models.
Physiological Model and Tutorial Repository
- NSR Physiome Models and Information
- Models related to current research (Analyzing the Cardiac Power Grid).
- Tutorials list
- Reproducible modeling and model standards
Collaborative modeling and software efforts
- The Virtual Physiological Rat Project: Understanding the systems biology of cardiovascular disease. UM
- The Cardiac Mechanics Research Group: Investigating the mechanics and electrical dynamics of the normal and diseased heart from molecular to organ scales. UCSD
- Heart and Muscle Mechanics (HAMM) Lab: Researchers in the HAMM Lab use interdisciplinary, multiscale approaches to study contraction in healthy and diseased muscles and develop myofilament-based therapies. UW
- SemGen: SemGen is an experimental software tool for automating the modular composition and decomposition of biosimulation models
- Biological Control Systems, Modeling, and Software: Sauro Lab, Modeling tools for systems and synthetic biologists. UW
Courses in Physiological Systems Modeling
- No courses currently scheduled.
- Archived course materials are available via the NSR Course Archives.
The Physiome Commission of the International Union of Physiological Sciences, IUPS, provides leadership to the Physiome Project through its satellite and central meetings and through the University of Auckland's IUPS Physiome Website. Please take advantage of the information provided by the IUPS and this website to learn more about the project.
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.