SBML ODE Solver Library (http://www.tbi.univie.ac.at/~raim/odeSolver/) Web service.
http://bioputer.mimuw.edu.pl/tav4sb/services/wsdl
odeSolver
org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
org.embl.ebi.escience.scuflworkers.java.XMLOutputSplitter
net.sourceforge.taverna.scuflworkers.xml.XPathTextWorker
//variable/@name
SBML model file content.
Example value:
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model id="Reaction" name="Single reaction">
<listOfUnitDefinitions>
<unitDefinition id="substance" name="moles">
<listOfUnits>
<unit kind="mole" scale="1" multiplier="1" offset="0"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="M" name="M">
<listOfUnits>
<unit kind="mole" scale="1" multiplier="1" offset="0"/>
<unit kind="litre" exponent="-1" multiplier="1" offset="0"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="M_per_second" name="M/s">
<listOfUnits>
<unit kind="mole" scale="1" multiplier="1" offset="0"/>
<unit kind="litre" exponent="-1" multiplier="1" offset="0"/>
<unit kind="second" exponent="-1" multiplier="1" offset="0"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="sec_inv" name="1/s">
<listOfUnits>
<unit kind="second" exponent="-1" multiplier="1" offset="0"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="s" name="solution" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="S" name="Substrate" compartment="s" initialConcentration="10"/>
<species id="P" name="Product" compartment="s" initialConcentration="0"/>
</listOfSpecies>
<listOfReactions>
<reaction id="r1" name="Substrate conversion" reversible="false">
<listOfReactants>
<speciesReference species="S"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="P"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k </ci>
<ci> S </ci>
</apply>
</math>
<listOfParameters>
<parameter id="k" value="0.1"/>
</listOfParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
Simulation end time in abstract time units (whatever time scale model is using).
Example value:
30
Time points to print in simulation. By default each integer time point (value of the 'simt' parameter).
Example value:
10
Absolute error tolerance used during ODEs integration. By default 1e-12.
Example value:
1e-12
Relative error tolerance used during ODEs integration. By default 1e-6.
Example value:
1e-6
Currently not used. Flag indicating whether to activate sensitivity analysis. By default false.
Example value:
false
OdeSolver error message; mutually exclusive with other outputs.
text/xml
XML with timepoints list, each containing time value and list variables values. Mutually exclusive with the 'error' output.
Example value:
<timepoints>
<timepoint>
<time name="time">0</time>
<variable name="S">10</variable>
<variable name="P">0</variable>
<variable name="s">1</variable>
</timepoint>
<timepoint>
<time name="time">3</time>
<variable name="S">7.40818</variable>
<variable name="P">2.59182</variable>
<variable name="s">1</variable>
</timepoint>
...
<timepoint>
<time name="time">30</time>
<variable name="S">0.497877</variable>
<variable name="P">9.50212</variable>
<variable name="s">1</variable>
</timepoint>
</timepoints>