1. Welcome to the NSR Physiome Project!
  2. Physiome JSim
  3. JSim Developer and Support Acknowledgements

JSim Developer and Support Acknowledgements

This page is for the older JSim version 1.6. Click here for the latest JSim 2.0 version.

JSim software is developed at the University of Washington by the National Simulation Resource, James B. Bassingthwaighte, director, and is supported by NIH/NIBIB grant EB01973-22.

JSim software was designed and written primarily by Erik Butterworth. Other NSR staff contributing code to the project include Andy Matuszkiewicz, Eric Lawson, Gary Raymond, Lucian Smith, Zheng Li, Mike Kellen and Asa Packer.

Andreas Schwab has contributed additional code relating to the MacIntosh port of JSim.

The JSim logo was designed by Tania Butterworth.

JSim makes extensive use of the Java computer language designed and distributed by Sun Microsystems .

JSim language processing makes use of the following toolkits:

  • The CUP parser generator by Scott Hudson, Frank Flannery, C. Scott Ananian;
  • The JLex lexical analyzer generator.

JSim plots and graphs are produced using the Scientific Graphics Toolkit , by Donald Denbo. Thanks and credit are also due to his sponsors NOAA and the PMEL/EPIC group .

JSim XML processing makes use of the Xerces2 Java Parser distributed by The Apache Software Foundation

JSim SBML processing makes use of the JigCell SBML Parser created at Virginia Tech .

The JSim computational engine makes use of the following:

  • The Radau and Dopri5 solvers for ordinary differential equations, written by E. Hairer and G. Wanner;
  • The CVODE solver for ordinary differential equations was written by Scott D. Cohen, Alan C. Hindmarsh, Radu Serban,and Dan Shumaker at Lawrence Livermore National Laboratory and is copyrighted by The Regents of the University of California.
  • The Tom690 and Toms731 solvers for partial differential equations written by Martin Berzins. These are available from netlib.org ;
  • The ggopt optimization algorithm is based on work by T. Glad, A. A. Goldstein, J. B. Bassingthwaighte, I. S. Chan, and I. B. Russak. Our implementation utilizes the blas and linpackd math packages available from netlib.org ;
  • The NL2SOL optimization algorithm was written by John E. Dennis, Jr., David M. Gay, and Roy E. Welsh, and our implementation is a modification of their source code.
  • The Sensop optimzation algorithm was originally written by Joseph Chan, and later improved by Rick King, Asa Packer and Gary Raymond.
  • The JAMA Java Matrix package.
  • JSim's NelderMead optimizer, originally developed by J.A. Nelder and R. Mead (Computer Journal, 1965, vol 7, pp 308-313), is based on an implementation by Dr Michael Thomas Flanagan .
  • Simulated annealing was originally developed by S. Kirkpatrick and C. D. Gelatt and M. P. Vecchi. JSim's multiprocessing implementation was written by Gary Raymond.
  • JSim's Bessel functions (besseli0, besseli1, besseljn, besselkn, besselyn) and error functions (erf, erfc) are from the Colt Project, copyrighted 1999 by CERN - European Organization for Nuclear Research.

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.