This page defines basic JSim terminology, with pointers to additional information.

API

For "Application Programmer Interface", is a specification for how to write computer code to work properly with a given software system. JSim provides several API's for interaction. More info.

BCL

For "Biological Component Library", a set of JSim templates designed for component-wise building of biological models. The only BCL currently distributed with JSim is MFAX. More info.

data set

A JSim accessible collection of numeric data. Data sets may be imported/exported to and from JSim via a variety of supported data file formats. More info.

event

An MML construct for describing discrete state changes, such as gate openings and closings. More info.

functions & procedures

MML constructs for the embedding of procedural code (e.g. Java, C, Fortran) in MML models. Also called F&P. More info .

MFAX

For "Metabolite Flow And eXchange", this BCL allow component-wise modeling of compartments, chemical reactions, flow and membrane transport. More info.

MML

For "Mathematical Modeling Language", MML is the language JSim uses to specify models. More info.

jsbatch

A command-line program, distributed with the JSim suite, accessing the JSim computational engine in a batch-oriented environment. More info.

jsfim

A command-line program, distributed with the JSim suite, for generating functional images. More info.

JSim

Spelled "JSim" refers to the entire JSim software project, including its distributed programs (jsim, jsbatch, jsfim, jsserver), and file format (MML, RTML, project, various data files).

jsim

Spelled "jsim" refers to the JSim graphical user interface(GUI) which is the most commonly used program in the JSim suite. Also known as the JSim GUI. More info.

jsserver

A program, distributed with the JSim suite, that creates a network-accessible JSim computational engine for use by JSim user programs (jsim, jsbatch, jsfim) or WWW applets. More info.

NSR

For "National Simulation Resource", the National Simulation Resource for Transport, Metabolism and Reaction creates, collects and disseminates material of interest to biological modelers, including JSim. More info.

plug-in

A code module (JAR format) that is loaded into JSim at run-time to enhance functionality. More info.

project file

An XML-based file encapsulating a set of JSim models, datasets, parameters sets, plot pages and notes. Project files are the normal means for sharing a fully configured JSim analysis. More info.

RTML

For "Run-Time Markup Language", RTML is an XML specification for graphic model markup for use within the JSim GUI, allowing model authors to customize the run-time appearance of their models. More info.

template

An MML construct for creating structured code and reusable model components. More info.

XSIM

An X-windows based simulation system, developed and distributed by NSR, that was JSim's predecessor. The XSIM application is no longer supported, however many popular XSIM models have been adapted to run under JSim. More info.

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.