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| <!DOCTYPE PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> | ||
| <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> | ||
| <head> | ||
| <title>Simulation Core Library: Documentation</title> | ||
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| <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> | ||
| <meta name="page-type" content="documentation"> | ||
| <meta name="Author" content="Andreas Dräger, Roland Keller, Alexander Dörr"> | ||
| <meta name="keywords" content="Simulation Core Library; Java; JSBML; source code; example; introduction; documentation"> | ||
| <meta name="description" content="A brief overview of the Simulation Core Library including source code examples."> | ||
| <meta name="allow-search" content="yes"> | ||
| <meta name="page-topic" content="Simulation Core Library"> | ||
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| </head> | ||
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| <body> | ||
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| <h2>Simulation Core Library: Documentation</h2> | ||
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| <h3>About Simulation Core Library</h3> | ||
| <p> | ||
| The Java™ API Simulation Core Library comprises a collection of | ||
| integrators for differential equation systems combined with an interpreter | ||
| for the Systems Biology Markup Language | ||
| (<a href="http://sbml.org" target="_blank">SBML</a>). | ||
| It is the first simulation library that is based on | ||
| <a href="http://sbml.org/Software/JSBML/" target="_blank">JSBML</a>. | ||
| The user can read an SBML model and simulate it with one of the provided | ||
| numerical integration routines. All SBML levels and versions are | ||
| supported. | ||
| The library can easily be integrated into customized software, such as | ||
| parameter estimation tools. | ||
| </p> | ||
| <p style="border-style:solid; border-color:#A51E37; padding: 10px;"> | ||
| <b>When using the Simulation Core Library, please cite</b>:<br/> | ||
| Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael | ||
| J. Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Le Novère, | ||
| Noriko Hiroi, Hannes Planatscher, Andreas Zell, and Andreas Dräger. | ||
| The systems biology simulation core algorithm. BMC Systems Biology, 7:55, | ||
| July 2013. [ <a href="http://dx.doi.org/10.1186/1752-0509-7-55">DOI</a> | | ||
| <a href="http://www.biomedcentral.com/1752-0509/7/55">link</a> | | ||
| <a href="http://www.biomedcentral.com/content/pdf/1752-0509-7-55.pdf">pdf</a> ] | ||
| </p> | ||
|
|
||
| <h3>How to integrate Simulation Core Library into your software?</h3> | ||
| <p> | ||
| You just have to add the provided jar-file simulation-core-library.jar to the class path of your Java project. | ||
| Then you have access to all classes of the library. | ||
| This library depends on the following third-party libraries: | ||
| <ul> | ||
| <li><a href="http://commons.apache.org/math/" target="_blank">Commons-math-2.2.jar</a></li> | ||
| <li><a href="http://www.junit.org/" target="_blank">JUnit-4.8.jar</a></li> | ||
| <li><a href="http://sbml.org/Software/JSBML" target="_blank">JSBML</a></li> | ||
| </ul> | ||
| For <a href="http://sed-ml.org/" target="_blank">SED-ML</a> support, the following | ||
| additional libraries are required: | ||
| <ul> | ||
| <li><a href="http://commons.apache.org/proper/commons-io/" target="_blank">commons-io-1.4.jar</a></li> | ||
| <li><a href="http://jaxen.codehaus.org/apidocs/" target="_blank">jaxen-1.1.1.jar</a></li> | ||
| <li><a href="http://www.jdom.org/docs/apidocs.1.1/" target="_blank">jdom-contrib.jar</a></li> | ||
| <li><a href="http://www.jdom.org/docs/apidocs.1.1/" target="_blank">jdom.jar</a></li> | ||
| <li><a href="http://jlibsedml.sourceforge.net" target="_blank">jlibsedml.jar</a></li> | ||
| <li><a href="http://sourceforge.net/projects/jmathml/" target="_blank">jmathml.jar</a></li> | ||
| <li><a href="http://www.xom.nu/" target="_blank">xom-1.2.1.jar</a></li> | ||
| </ul> | ||
| Please make sure to include the correct third-party libraries into your | ||
| class path before working with this library. | ||
| </p> | ||
|
|
||
| <h3>The provided integration methods</h3> | ||
| <p> | ||
| The {@link org.simulator.math.odes.RosenbrockSolver} is best suitable for integrating stiff differential | ||
| equation systems and also has a precise timing of SBML events. It is taken | ||
| and adapted from | ||
| <a href="http://www.math.hmc.edu/clinic/projects/2010/" target="_blank">Kotcon <i>et al.</i> (2011)</a> | ||
| </p><p> | ||
| Several further solvers have been taken from the | ||
| <a href="http://commons.apache.org/math/" target="_blank">Apache Commons | ||
| Math Library</a> and wrapped into our library: | ||
| <ul> | ||
| <li>{@link org.simulator.math.odes.AdamsBashforthSolver}</li> | ||
| <li>{@link org.simulator.math.odes.AdamsMoultonSolver}</li> | ||
| <li>{@link org.simulator.math.odes.DormandPrince54Solver}</li> | ||
| <li>{@link org.simulator.math.odes.DormandPrince853Solver}</li> | ||
| <li>{@link org.simulator.math.odes.GraggBulirschStoerSolver}</li> | ||
| <li>{@link org.simulator.math.odes.HighamHall54Solver}</li> | ||
| </ul> | ||
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| The following solvers have been implemented additionally and are fast, but | ||
| not suitable for all differential equation systems: | ||
| <ul> | ||
| <li>{@link org.simulator.math.odes.EulerMethod}</li> | ||
| <li>{@link org.simulator.math.odes.RungeKutta_EventSolver}</li> | ||
| </ul> | ||
| </p><p> | ||
| For a full list of available solvers, see {@link org.simulator.math.odes}. | ||
| </p> | ||
|
|
||
| <h3>Reading an SBML model and creating the respective differential equation | ||
| system</h3> | ||
| <p> | ||
| A model can be read in by using the {@link org.sbml.jsbml.SBMLReader} | ||
| class from <a href="http://sbml.org/Software/JSBML" target="_blank">JSBML</a>. | ||
| With the model in memory the {@link org.simulator.sbml.SBMLinterpreter} | ||
| can create the differential equation system that provides the basis for | ||
| simulation: | ||
| </p> | ||
| <pre><code class="spoiled"> | ||
| <span class="class">Model</span> model = (<span class="keyword">new</span> <span class="class">SBMLReader</span>()).<span class="method">readSBML</span>(sbmlfile).<span class="method">getModel()</span>;<br/> | ||
| <span class="class">SBMLinterpreter</span> interpreter = <span class="keyword">new</span> <span class="class">SBMLinterpreter</span>(model); | ||
| </code></pre> | ||
| <p> | ||
| For more documentation about working with SBML models in simulations see | ||
| {@link org.simulator.sbml}. | ||
| </p> | ||
|
|
||
| <h3>Simulation of a differential equation system</h3> | ||
| <p> | ||
| The created differential equation system can then be simulated with a | ||
| chosen solver and given time points. | ||
| The result is stored in a data structure called | ||
| {@link org.simulator.math.odes.MultiTable}. | ||
| </p> | ||
| <pre><code class="spoiled"> | ||
| <span class="class">AbstractDESSolver</span> solver = <span class="keyword">new</span> <span class="class">RosenbrockSolver</span>();<br/> | ||
| <span class="keyword">double</span>[] timePoints = {0.0, 0.1, 0.2, 0.3, 0.4, 0.5};<br/> | ||
| <span class="class">MultiTable</span> solution = solver.<span class="method">solve</span>(interpreter, interpreter.<span class="method">getInitialValues</span>(), timePoints); | ||
| </code></pre> | ||
|
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| <h3>Using SED-ML for simulation</h3> | ||
| <p> | ||
| The following example shows how to read in a {@link java.io.File} f (in | ||
| <a href="http://sed-ml.org/" target="_blank">SED-ML</a> format) and how to run a simulation | ||
| described in this file afterwards. The simulation results are stored in a | ||
| {@link org.simulator.math.odes.MultiTable}: | ||
| </p> | ||
|
|
||
| <pre><code class="spoiled"> | ||
| <span class="class">SEDMLDocument</span> doc = <span class="class">Libsedml</span>.<span class="method">readDocument</span>(f);<br/> | ||
| <span class="class">SedML</span> sedml = doc.<span class="method">getSBMLModel</span>();<br/> | ||
| <span class="class">Output</span> wanted = sedml.<span class="method">getOutputs</span>().<span class="method">get</span>(0);<br/> | ||
| <span class="class">SedMLSBMLSimulatorExecutor</span> exe = <span class="keyword">new</span> <span class="class">SedMLSBMLSimulatorExecutor</span>(sedml, wanted);<br/> | ||
| <span class="class">Map<Task, IRawSedmlSimulationResults></span> res = exe.<span class="method">runSimulations</span>();<br/> | ||
| <span class="class">MultiTable</span> solution = exe.<span class="method">processSimulationResults</span>(wanted, res);<br/> | ||
| </code></pre> | ||
|
|
||
| <p> | ||
| For more information about how to use SED-ML to execute your simulation | ||
| experiments, see {@link org.simulator.sedml}. | ||
| </p> | ||
|
|
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| <h3>Simulation of the models in the SBML Test Suite</h3> | ||
| <p> | ||
| You can run the simulation of the models in the | ||
| <a href="http://sbml.org/Facilities/Online_SBML_Test_Suite" target="_blank">SBML Test | ||
| Suite</a> by using the command below. <i>TestSuiteDirectory</i> denotes | ||
| the directory containing your copy of the (entire) SBML test suite. | ||
| Here we assume that the actual test cases are located in the sub-folder | ||
| <i>cases/semantic/</i> within the <i>TestSuiteDirectory</i> on your | ||
| computer. | ||
| The simulation is conducted for the models with numbers from <i>first</i> | ||
| to <i>last</i> (these numbers are the indices of the models in the test | ||
| suite, without leading zeros). | ||
| </p> | ||
| <pre><code class="spoiled"> | ||
| java -cp SimulationCoreLibrary_vX.Y_incl-libs.jar org.simulator.SBMLTestSuiteRunner TestSuiteDirectory/cases/semantic/ first last | ||
| </code></pre> | ||
| Please note that, you have to replace <i>_vX.Y_</i> within the library's | ||
| name by the current release number, e.g., 1.2. | ||
| <p> | ||
| For example, if you like to simulate all test suite models ranging from | ||
| <i>00259</i> to <i>00326</i>, simply call the algorithm with | ||
| <i>first = 259</i> and <i>last = 326</i>. | ||
| </p> | ||
|
|
||
| <p> | ||
| Note that for the sake of a simple configuration, the simulation is | ||
| started using default settings for the selection of the | ||
| integration routine, step size etc. | ||
| </p> | ||
|
|
||
| <p> | ||
| The | ||
| <a href="http://sbml.org/Facilities/Database/Simulator">SBML Test Suite Database</a> | ||
| provides an up-to-date overview about the | ||
| capabilities of various SBML-compliant solver implementations. | ||
| </p> | ||
|
|
||
| <h3>Simulation of the models from BioModels database</h3> | ||
| <p> | ||
| In a similar way, you can also download and simulate all models from | ||
| <a href="http://www.ebi.ac.uk/biomodels-main/" target="_blank">BioModels database</a>: | ||
| <pre><code class="spoiled"> | ||
| java -cp SimulationCoreLibrary_vX.Y_incl-libs.jar org.simulator.TestBiomodels BioModelsDirectory/ first last | ||
| </code></pre> | ||
| Again, you have to replace <i>_vX.Y_</i> within the library's | ||
| name by the current release number, e.g., 1.2. Please use the variables | ||
| <i>first</i> and <i>last</i> without leading zeros as in the previous | ||
| case. The variable <i>BioModelsDirectory</i> gives the path to your local | ||
| copy of | ||
| <a href="http://www.ebi.ac.uk/biomodels-main/" target="_blank">BioModels database</a>. | ||
| </p> | ||
| <p> | ||
| As in the previous case, the simulation is conducted using default | ||
| settings. | ||
| </p> | ||
|
|
||
| <h3>Listening to SBML constraint violation</h3> | ||
| <p> | ||
| In version 1.3 a new listener interface has been added to | ||
| this library, which can be used to perform user-defined actions upon violation | ||
| of a {@link org.sbml.jsbml.Constraint}'s math expression during a simulation. | ||
| A simple implementation is already included in this package, | ||
| which logs violation at the | ||
| {@link java.util.logging.Level#WARNING} using standard Java™ | ||
| logging (see {@link java.util.logging.Logger}). | ||
| By default the | ||
| {@link org.simulator.sbml.SBMLinterpreter} adds this | ||
| {@link org.simulator.sbml.SimpleConstraintListener} to its internal list of | ||
| {@link org.simulator.sbml.ConstraintListener}s. | ||
| </p> | ||
|
|
||
| <p> | ||
| You can remove this listener by calling the method | ||
| {@link org.simulator.sbml.SBMLinterpreter#removeConstraintListener(int)}, | ||
| with the argument 0 for the first listener in the list, | ||
| and add your own listener implementation with the help of method | ||
| {@link org.simulator.sbml.SBMLinterpreter#addConstraintListener(ConstraintListener)}. | ||
| </p> | ||
| <p>The following example demonstrates how you can easily define your customized | ||
| {@link org.simulator.sbml.ConstraintListener}: | ||
| <pre><code class="spoiled"> | ||
| <span class="keyword">double</span> timeEnd = 5d;<br/> | ||
| <span class="class">SBMLDocument</span> doc = <span class="class">SBMLReader</span>.<span class="method">read</span>(<span class="keyword">new</span> <span class="class">File</span>(<span class="stringliteral">"path/to/file.xml"</span>));<br/> | ||
| <span class="class">SBMLinterpreter</span> interpreter = <span class="keyword">new</span> <span class="class">SBMLinterpreter</span>(doc.<span class="method">getModel</span>());<br/> | ||
| interpreter.<span class="method">addConstraintListener</span>(<span class="keyword">new</span> <span class="class">ConstraintListener</span>() {<br/> | ||
|   <span class="comment-single">/* (non-Javadoc)<br/> | ||
|    * @see org.simulator.sbml.ConstraintListener#processViolation(org.simulator.sbml.ConstraintEvent)<br/> | ||
|    */</span><br/> | ||
|   public <span class="keyword">void</span> <span class="method">processViolation</span>(<span class="class">ConstraintEvent</span> evt) {<br/> | ||
|     <span class="class">System</span>.err.<span class="method">println</span>(<span class="stringliteral">"Constraint violated at time "</span> + evt.<span class="method">getTime</span>() + <span class="stringliteral">": "</span> + evt.<span class="method">getSource</span>().<span class="method">getMath</span>().<span class="method">toFormula</span>());<br/> | ||
|   }<br/> | ||
| });<br/> | ||
| solver.<span class="method">solve</span>(interpreter, interpreter.<span class="method">getInitialValues()</span>, 0d, timeEnd); | ||
| </code></pre> | ||
| </p> | ||
| <p> | ||
| You can find more details about this topic in the description of package | ||
| {@link org.simulator.sbml}. | ||
| </p> | ||
|
|
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| </body> | ||
|
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| </html> |
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