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    JSim Modeling System

    Category  Cross-Omics>Agent-Based Modeling/Simulation/Tools

    Abstract  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 ordinary differential equations (ODEs),
    partial differential equations (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 the Systems Biology Markup Language (SBML) and
    CellML model archival formats (see G6G Product Number 20293) and
    (see G6G Product Number 20294).

    JSim model calculations are specified in JSim's own Mathematical
    Modeling Language (MML) an easy-to-read text-based language.

    MML models are most often expressed in terms of mathematical
    equations (for example, ordinary and partial differential equations,
    implicit equations), but formulation via discrete events and function calls
    to Java, C and FORTRAN are also available.

    MML is constructed so that model writers may intermix mathematics,
    events and procedural code as needed.

    JSim supports multiple "domains" or independent variables (e.g. time,
    space).

    MML variables may vary over any combination of the declared domains.

    JSim's MML compiler does extensive cross-checks to insure that
    models are neither over-specified nor under-specified and that a
    variable's declared domains are consistent with its usage.

    MML models are aware of physical units, and the model compiler
    contains a ‘unit balancer’ that automatically adjusts run-time
    calculations with appropriate conversion factors, while rejecting
    nonsensical equations (such as kg = kg/sec).

    JSim's extensive cross-checking catches many common mistakes and
    so facilitates creation of valid models more quickly and easily than with
    standard procedural languages.

    The JSim graphical user interface (GUI) allows modelers to edit and
    compile multiple MML models, manipulate model parameters, run
    models and graph results.

    Experimental data and/or built-in function generators may be used to
    drive model inputs.

    Numeric data may be fed into and retrieved from JSim in a variety of
    formats allowing interconnection with other programs.

    JSim's built-in model analysis tools include loops (multiple model runs
    with varying parameters), sensitivity analysis and automated parameter
    optimization.

    JSim project files encapsulate the complete state of a JSim GUI
    window, potentially including multiple models, data sets, parameter
    sets, notes, and plot pages.

    Project files are self-contained, facilitating sharing of results between
    researchers and restoration of state in later JSim sessions.

    JSim uses a variety of public and proprietary numeric solvers for solving
    ODEs, PDEs, linear and non-linear implicit equations and parameter
    optimization.

    Default settings are provided automatically for these solvers so that
    beginning modelers normally do Not need to worry about the settings.

    However, the settings are controllable in high-performance settings for
    more sophisticated users.

    Other features/capabilities of JSim include:

    1) JSim's Run Time Markup Language (RTML) which allows model
    writers to develop more sophisticated run-time interfaces for their
    model incorporating multiple pages, diagrams and hyperlinks.

    2) jsbatch, a command-line tool that provides access to the JSim
    computational engine in a form convenient for batch processing.

    3) jsfim, a tool for constructing functional (parametric) images using
    region-of-interest (ROI) data and the JSim computational engine.

    4) JSim remote server which allows model computations to be done on
    a more advanced server computer rather than the user's desktop;
    The server is also used to power JSim enabled web sites.

    5) JSim plug-ins allows programmers to extend JSim base functionality,
    such as customized graphics, data formats, and GUI-based model
    builders.

    6) JSim supports import of models in the CellML and SBML archival
    formats.

    7) JSim 1.6.67 and above support multiprocessing, the ability to utilize
    'multiple system' processors for faster calculation.

    System Requirements  

    JSim downloads are available as precompiled binaries (Linux, Mac,
    Windows) or source code.

    JSim can also run as a Java applet within your web browser.

    Manufacturer   

    JSim is developed by the National Simulation Resource at the
    University of Washington, Department of Bioengineering.

    Manufacturer's Web Site   

    http://nsr.bioeng.washington.edu/jsim/

    Price   Contact manufacturer

    G6G Product Number  20473

    G6G Manufacturer Number 104098
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