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  4. The JSim Fortran Package

The JSim Fortran Package

This page is for the current JSim version 2.0 and higher. Click here for the earlier JSim 1.6 version.

This document gives overall information about the JSim Fortran package (fpack), a set of classic XSim Fortran models ported to run under JSim. Contents:

 

Available models

The following models are currently available:

  • body: a whole-body recirculation model with multiple organs;
  • btex20: a two-region, distributed blood-tissue exchange model;
  • btex40: a four-region, distributed blood-tissue exchange model;
  • demo: a demonstration model showing decaying sine, cosine, and tangent functions;
  • gentex: a multi-path, multi-species, five region organ model with nonlinear transmembrane transport, nonlinear reactions and time-varying blood flow and volume;
  • gentex2: a version of the gentex model with restricted capability for users who do not require the full capability of gentex.
  • mhed: a carbon11--meta-hydroxyephedrine transport model (based on gentex);
  • mmid4: a multi-path, multi-indicator, four-region organ model;
  • msid4: a multi-path, multi-indicator, multi-species, four-region organ model.

Using the fpack models

Example project files for the fpack models may be found in the doc/examples/fpack directory of your JSim distribution. The models are stored in project files (rather than simple .mod files) because they contain run-time layout customizations (RTML) as well as MML model code. Copy an example project file to your working directory and work there. Alternatively, you may incorporate an example model into an existing project by opening it in a separate project window and using the "Project" tab copy/paste mechanisms. Do not do your work inside the distributed example files or your work will be lost next time you upgrade JSim.

Important: be sure to read the caveats below before trying them out.

Some caveats

Fpack is currently available only under Linux and MacOS. Fpack for Windows is still in development. All of the models except btex20, btex40 and demo currently require GLIBC_2.3.

Customized graphic front-ends for the fpack models are are still a bit rough. They were created via an automated conversion program from the original XSim .cf files, and will require some hand-tuning to look just right. This hand-tuning will be done as time allows.

Comments or Questions?

 

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.