Tutorials are works in progress. Each tutorial will provide an overview of the topic and a beginning guide to a set of models which can be run on the website or downloaded for running on one's own computer under JSim (under Windows, Macintosh or Linux). The intention of the tutorials is to provide elementary material on a given topic, and by way of example, to use the primitive modules as components within a modest number of increasingly complex forms. Any suggestions will be gratefully received. Each tutorial links to a set of model Wiki pages. Each model page gives a name, a description, model equations, a diagram (usually), and RUN MODEL links to a model archive to bring up a JSim standard window and allow one to run a model, change parameters, edit the program, and save it on your own computer. One can develop one's own interface to replace the standard JSim window if so desired.
Models in tutorials are usually available for download. Models written in JSim MML unless otherwise noted.
Tutorials available at this time:
- Lung Models.
- Compartmental Models.
- Modeling of transport and metabolism in whole organs according to Goresky.
- Enzyme Model of the NaKATPase or Sodium pump according to Chapman.
- Transporters.
- Neural Modeling (Non-JSim) Using Genesis 2 simulation software. Genesis Simulator
Additional tutorials are under construction:
- Diffusion.
- Hemoglobin and Oxygen: binding and transport.
- Optimization: fitting model to data.
- Multiscale modeling with Modular Program Constructor (MPC).
Modeling Information and Standards
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.