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index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<title>JSim home</title>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.5.0/css/bootstrap.min.css">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.16.0/umd/popper.min.js"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.5.0/js/bootstrap.min.js"></script>
<script src="scripts/acknowledgements.js"></script>
<link rel="stylesheet" href="css/jsim.css">
<link rel="stylesheet" href="css/small.css">
</head>
<body>
<nav class="navbar navbar-expand-sm bg-dark navbar-dark">
<a class="navbar-brand" href="index.html">Home</a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#collapsibleNavbar">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="collapsibleNavbar">
<ul class="navbar-nav">
<!-- <li class="nav-item">
<a class="nav-link" href="">JSim home</a>
</li> -->
</ul>
</div>
</nav>
<div class="jsimleft100">
<div class="jsimleft30">
<div class="jslogo">
<img src="pics/jsimlogo_doc.gif">
</div>
<div class="jstoc">
<dl class="toc">
<dt><a href="docs/news.html"><img src="pics/news.gif"></a>
</dt>
<dd><a href="docs/news.html">What's new?</a>
</dd>
<dt><a href="download/index.html"><img src="pics/download.gif"></a>
</dt>
<dd><a href="download/index.html">Download and installation</a>
</dd>
<dt><a href="docs/User.html"><img src="pics/running.gif"></a>
</dt>
<dd><a href="docs/User.html">Running JSim</a>
</dd>
<dt><a href="docs/MML.html"><img src="pics/write.gif"></a>
</dt>
<dd><a href="docs/MML.html">Writing JSim models</a>
</dd>
<dt><a href="docs/MML.html"><img src="pics/tick.png" height="32" width="32"></a>
</dt>
<dd><a href="docs/cite.html">Citing JSim</a>
</dd>
<dt><a href="https://www.physiome.org/Models/modeling_info.html"><img src="pics/lightbulb.png" height="32" width="32"></a>
<dd><a href="https://www.physiome.org/Models/modeling_info.html">JSim Model Standards</a></dd>
<dt><a href="models/index.html"><img src="pics/model.gif"></a>
</dt>
<dd><a href="https://www.physiome.org/Models/index.html">Model Repository</a>
</dd>
<!-- <dt><a href="movies/index.html"><img src="pics/movie.gif"></a>
</dt>
<dd><a href="movies/index.html">Instructional videos</a>
</dd> -->
<dt><a href="https://github.com/NSR-Physiome/JSim/wiki/JSim-Glossary"><img src="pics/glossary.gif"></a>
</dt>
<dd><a href="https://github.com/NSR-Physiome/JSim/wiki/JSim-Glossary">Glossary</a>
</dd>
<dt><a href="https://github.com/NSR-Physiome/JSim/wiki/JSim-Development"><img src="pics/developer.png"></a>
</dt>
<dd><a href="https://github.com/NSR-Physiome/JSim/wiki/JSim-Development">JSim Development</a>
</dd>
<dt><a href="docs/JSim_Refs.html"><img src="pics/biblio.gif"></a>
</dt>
<dd><a href="https://www.physiome.org/Links/publications.html">Biblio of JSim related work</a>
</dd>
<dt><a href="docs/JSim_Acknow.html"><img src="pics/acknow.gif"></a>
</dt>
<dd><a href="docs/JSim_Acknow.html">Acknowledgements</a>
</dd>
<!-- <dt><a href="#team"><img src="pics/problem.gif"></a>
</dt> -->
<!-- <dd><a href="/Contact">Confused? Contact us.</a>
</dd> -->
</dl>
</div> <!-- end jstoc -->
</div> <!-- end jsimleft35 -->
<div class="jsimright30">
<h1>JSim Home Page</h1>
<p>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.</p>
<p>JSim downloads are available as <a
href="download/index.html">precompiled binaries</a> (Linux, Apple MacIntosh,
Windows) or <a href="https://github.com/NSR-Physiome/JSim">source code</a>. JSim
can also <a href="docs/User_WWW.html">run as a Java Web Start App</a> downloaded through your web
browser. JSim is provided free for non-commercial use as a public service
by the <a href="http://nsr.bioeng.washington.edu">National Simulation
Resource</a> at the University of Washington.</p>
<!-- <p><img src="/jsim/pics/new.png" />The <a href="/jsim/db/">JSim -->
<!-- Consolidated Model Database</a> is now available.</p> -->
<p> <!-- <img src="/jsim/pics/new.png" /> --> JSim 2.20 released (25 jun 2020): <a href="docs/news.html">release notes</a> / <a
href="download/index.html">download</a> </p>
<p><strong>Getting oriented:</strong></p>
<ul>
<li><a href="docs/overview.html">JSim overview</a> : what JSim does and
how it is structured.</li>
<li><a href="https://f1000research.com/articles/2-288/v3">JSim article,</a> published 2014.
<li><a href="docs/User_Intro.html">Introduction to the JSim GUI</a> : an
step-by-step
introduction to using the JSim graphic user interface.</li>
<li><a href="docs/MML_Intro.html">Introductory Survey of MML</a> :
writing models with JSim's Mathematical Modeling Language.</li>
</ul>
<p>Related software:</p>
<ul>
<li><a href="https://www.physiome.org/software/j4/">J4</a>: Java-based quantitative medical
imaging system.</li>
<li><a href="https://www.physiome.org/software/i4/">I4</a>: J4's predecessor imaging system.</li>
<li><a href="https://www.physiome.org/software/xsim/">XSIM</a>: JSim's predecessor simulation </li>
<li><a
href="https://sites.google.com/site/semanticsofbiologicalprocesses/projects/semgen">
SemGen</a>: Software for automating the modular composition and decomposition of
biosimulation models.</li>
</ul>
</div> <!-- end jsimright30 -->
</div> <!-- end jsimleft100 -->
<br />
<p id="acknowledge"></p>
<script>
document.getElementById("acknowledge").innerHTML = getAcknowledge();
</script>
</body>
</html>