JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim's model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports and exports model archive formats SBML and CellML.

JSim downloads are available as precompiled binaries (Linux, MacIntosh, Windows) or source code. JSim is provided free for non-commercial use as a public service by the National Simulation Resource at the University of Washington.

JSim 2.20 released (25 jun 2020): release notes / download

Getting oriented:

• JSim overview : what JSim does and how it is structured.
• JSim article, published 2014.
• Introduction to the JSim GUI : an step-by-step introduction to using the JSim graphic user interface.
• Introductory Survey of MML : writing models with JSim's Mathematical Modeling Language.
• JSim's GitHub repository.

Related software:

• J4: Java-based quantitative medical imaging system.
• I4: J4's predecessor imaging system.
• XSIM: JSim's predecessor simulation
• SemGen: Software for automating the modular composition and decomposition of biosimulation models.
• More ...

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.