Multi-parameter sensitivity analysis (MPSA)

Created: 2011-07-14 08:50:26 Last updated: 2011-07-21 10:08:42

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Exemplary multi-parameter sensitivity analysis (MPSA) experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) WS operations. In this version of MPSA, ODEs simulations are basis of analysis of SBML model parameters space.

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Processors (19)

Name	Type	Description
paramCsv	stringconstant	Value k1.k, k3.k
modelUrl	stringconstant	Value http://bioputer.mimuw.edu.pl/tav4sb/models/enzyme.xml
samplesNr	stringconstant	Value 400
simTime	stringconstant	Value 30
errorVarCsv	stringconstant	Value m4
thresholdMethod	stringconstant	Value median
simTimepointsNr	stringconstant	Value 11
ClassifySamples	workflow
setParamsRange	beanshell	Script source(new URL("http://bioputer.mimuw.edu.pl/tav4sb/workflows/setParamsRange.bsh"));
getModel	localworker	Script BufferedReader getReader (String fileUrl) throws IOException { InputStreamReader reader; try { reader = new FileReader(fileUrl); } catch (FileNotFoundException e) { // try a real URL instead URL url = new URL(fileUrl); reader = new InputStreamReader (url.openStream()); } return new BufferedReader(reader); } StringBuffer sb = new StringBuffer(4000); BufferedReader in = getReader(fileurl); String str; String lineEnding = System.getProperty("line.separator"); while ((str = in.readLine()) != null) { sb.append(str); sb.append(lineEnding); } in.close(); filecontents = sb.toString();
SelectParameters	workflow
CalculateSensitivity	workflow
GenerateSamples	workflow
CalculateSamplesError_OdeSim	workflow
rangeMul	stringconstant	Value 4
ifGeneratePlots	stringconstant	Value true
distribution	stringconstant	Value uniform
samplingMethod	stringconstant	Value LHS
scale	stringconstant	Value LIN

Beanshells (18)

Name	Inputs	Outputs
setParamsRange	paramXmlList multiplier	paramListXml
transpose	list	transposedList
pointListXmlToValuesListList	coordinateNameList pointListXml	coordinateValueListList
pairOfLists	list1 list2	listsPair
sampleXmlList2sampleListXml	sampleXmlList	sampleListXml
toPair	list1 list2	listsPair
fromPair	pair	el1 el2
paramXmlList2selectedParamsXml	paramXmlList	selectedParamsXml
pointListXmlToValuesListList	coordinateNameList pointListXml	coordinateValueListList
transpose	list	transposedList
pairOfLists	list1 list2	listsPair
listsPair	list1 list2	listsPair
setSbmlParams	modelInXml paramListXml	modelOutXml
meanSquaredError	argValList1 argValList2 argValTemplate	error
getSbmlParams	model	paramListXml
buildXPathFilter	attrName attrValList ifQuoteVal	xpath
calculateThreshold	method numbers	threshold
classifySamples	threshold sampleList sampleErrorList	unacceptableSampleList acceptableSampleList

Outputs (6)

Name	Description
paramXmlList
ecdfPlotList
paramRankingXmlList
sampleXmlList
sampleErrorList
sampleErrorThreshold

Datalinks (29)

Source	Sink
thresholdMethod:value	ClassifySamples:method
CalculateSamplesError_OdeSim:sampleErrorList	ClassifySamples:sampleErrorList
GenerateSamples:sampleXmlList	ClassifySamples:sampleList
rangeMul:value	setParamsRange:multiplier
SelectParameters:paramXmlList	setParamsRange:paramXmlList
modelUrl:value	getModel:fileurl
paramCsv:value	SelectParameters:paramNameCsv
getModel:filecontents	SelectParameters:modelXml
ClassifySamples:acceptableSampleList	CalculateSensitivity:acceptableSampleXmlList
ifGeneratePlots:value	CalculateSensitivity:ifGeneratePlots
ClassifySamples:unacceptableSampleList	CalculateSensitivity:unacceptableSampleXmlList
SelectParameters:paramXmlList	CalculateSensitivity:paramXmlList
distribution:value	GenerateSamples:distribution
scale:value	GenerateSamples:scale
samplesNr:value	GenerateSamples:nr
setParamsRange:paramListXml	GenerateSamples:paramListXml
samplingMethod:value	GenerateSamples:method
rangeMul:value	GenerateSamples:rangeMultiplier
errorVarCsv:value	CalculateSamplesError_OdeSim:errVarCsv
GenerateSamples:sampleXmlList	CalculateSamplesError_OdeSim:sampleXmlList
getModel:filecontents	CalculateSamplesError_OdeSim:modelXml
simTimepointsNr:value	CalculateSamplesError_OdeSim:simtp
simTime:value	CalculateSamplesError_OdeSim:simt
SelectParameters:paramXmlList	paramXmlList
CalculateSensitivity:plotList	ecdfPlotList
CalculateSensitivity:paramRankingXmlList	paramRankingXmlList
GenerateSamples:sampleXmlList	sampleXmlList
CalculateSamplesError_OdeSim:sampleErrorList	sampleErrorList
ClassifySamples:errorThreshold	sampleErrorThreshold

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Taverna 2

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trybik

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trybik

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2400 viewings

1553 downloads

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Version History

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Multi-parameter sensitivity analysis (MPSA) of deterministic SBML model

Created by trybik on Thursday 14 July 2011 08:50:26 (UTC)

Last edited by trybik on Thursday 14 July 2011 09:02:21 (UTC)
Multi-parameter sensitivity analysis (MPSA)

Created by trybik on Thursday 21 July 2011 10:06:54 (UTC)

Last edited by trybik on Thursday 21 July 2011 10:08:42 (UTC)

Revision comment:

upgraded parrallel jobs config

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Multi-parameter sensitivity analysis (MPSA)

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