odeSolver Web service
Created: 2011-01-26 22:01:53
Last updated: 2011-01-26 22:01:56
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Workflow Components
Inputs (6)
| Name |
Description |
| model |
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> |
| simt |
Simulation end time in abstract time units (whatever time scale model is using).
Example value:
30 |
| simtp |
Time points to print in simulation. By default each integer time point (value of the 'simt' parameter).
Example value:
10 |
| atol |
Absolute error tolerance used during ODEs integration. By default 1e-12.
Example value:
1e-12 |
| rtol |
Relative error tolerance used during ODEs integration. By default 1e-6.
Example value:
1e-6 |
| sensitivityAnalysis |
Currently not used. Flag indicating whether to activate sensitivity analysis. By default false.
Example value:
false |
Processors (6)
| Name |
Type |
Description |
| odeSolver |
arbitrarywsdl |
|
| odeSolverResultXML |
local |
|
| odeSolverParamsXML |
local |
|
| trajectoriesXML |
local |
|
| getVariablesNames |
local |
|
| variablesNamesXPath |
stringconstant |
|
Outputs (3)
| Name |
Description |
| error |
OdeSolver error message; mutually exclusive with other outputs. |
| timepointsXml |
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> |
| variablesList |
|
Links (14)
| Source |
Sink |
| atol |
odeSolverParamsXML:atol |
| model |
odeSolverParamsXML:model |
| odeSolver:odeSolverResult |
odeSolverResultXML:input |
| odeSolverParamsXML:output |
odeSolver:odeSolverParams |
| rtol |
odeSolverParamsXML:rtol |
| sensitivityAnalysis |
odeSolverParamsXML:sensitivityAnalysis |
| simt |
odeSolverParamsXML:simt |
| simtp |
odeSolverParamsXML:simtp |
| getVariablesNames:nodelist |
variablesList |
| odeSolverResultXML:trajectories |
trajectoriesXML:input |
| trajectoriesXML:variables |
getVariablesNames:xml-text |
| variablesNamesXPath:value |
getVariablesNames:xpath |
| odeSolverResultXML:error |
error |
| trajectoriesXML:timepoints |
timepointsXml |
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