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Multi-parameter sensitivity analysis (MPSA) with PMC

Workflow Entry: Multi-parameter sensitivity analysis (MPSA) with PMC

Created at: 14/07/11 @ 08:59:23 Last updated: 21/07/11 @ 10:08:07

Version 2 (latest) (of 2)

Version created on: 21/07/11 @ 10:07:16 by: trybik | Revision comments Expand

Last edited on: 21/07/11 @ 10:08:07 by: trybik

Title: Multi-parameter sensitivity analysis (MPSA) with PMC

Type: Taverna 2

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Description

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

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Workflow Components

Authors (1)

Titles (2)

Descriptions (1)

Inputs (0)

Processors (18)

Name	Type	Description
samplesNr	stringconstant
paramCsv	stringconstant
model	stringconstant
thresholdMethod	stringconstant
setParamsRange	beanshell
ClassifySamples	workflow
SelectParameters	workflow
CalculateSensitivity	workflow
GenerateSamples	workflow
CalculateSamplesError_PMC	workflow
rangeMul	stringconstant
ifGeneratePlots	stringconstant
samplingMethod	stringconstant
scale	stringconstant
distribution	stringconstant
properties_value	stringconstant
getRewards	localworker
rewardsUrl	stringconstant

Beanshells (15)

Name	Inputs	Outputs
setParamsRange	paramXmlList multiplier	paramListXml
fromPair	pair	el1 el2
paramXmlList2selectedParamsXml	paramXmlList	selectedParamsXml
sampleXmlList2sampleListXml	sampleXmlList	sampleListXml
toPair	list1 list2	listsPair
buildXPathFilter	attrName attrValList ifQuoteVal	xpath
getSbmlParams	model	paramListXml
calculateThreshold	method numbers	threshold
classifySamples	threshold sampleList sampleErrorList	unacceptableSampleList acceptableSampleList
setSbmlParams	modelInXml paramListXml	modelOutXml
meanAbsDiff	valList1 valList2	error
pointListXmlToValuesListList	pointListXml coordinateNameList	coordinateValueListList
refPointListXmlToValuesListList	pointListXml coordinateNameList	coordinateValueListList
setConstantCompactXmlList	input	output
wrapWithResultsTag	str name	wrapped

Outputs (6)

Name	Description
paramXmlList
ecdfPlotList
paramRankingXmlList
sampleErrorList
sampleXmlList
sampleErrorThreshold

Datalinks (28)

Source	Sink
SelectParameters:paramXmlList	setParamsRange:paramXmlList
rangeMul:value	setParamsRange:multiplier
GenerateSamples:sampleXmlList	ClassifySamples:sampleList
CalculateSamplesError_PMC:sampleErrorList	ClassifySamples:sampleErrorList
thresholdMethod:value	ClassifySamples:method
paramCsv:value	SelectParameters:paramNameCsv
model:value	SelectParameters:modelXml
ClassifySamples:unacceptableSampleList	CalculateSensitivity:unacceptableSampleXmlList
SelectParameters:paramXmlList	CalculateSensitivity:paramXmlList
ClassifySamples:acceptableSampleList	CalculateSensitivity:acceptableSampleXmlList
ifGeneratePlots:value	CalculateSensitivity:ifGeneratePlots
scale:value	GenerateSamples:scale
samplesNr:value	GenerateSamples:nr
setParamsRange:paramListXml	GenerateSamples:paramListXml
samplingMethod:value	GenerateSamples:method
distribution:value	GenerateSamples:distribution
rangeMul:value	GenerateSamples:rangeMultiplier
GenerateSamples:sampleXmlList	CalculateSamplesError_PMC:sampleXmlList
properties_value:value	CalculateSamplesError_PMC:properties
model:value	CalculateSamplesError_PMC:modelXml
getRewards:filecontents	CalculateSamplesError_PMC:rewards
rewardsUrl:value	getRewards:fileurl
SelectParameters:paramXmlList	paramXmlList
CalculateSensitivity:plotList	ecdfPlotList
CalculateSensitivity:paramRankingXmlList	paramRankingXmlList
CalculateSamplesError_PMC:sampleErrorList	sampleErrorList
GenerateSamples:sampleXmlList	sampleXmlList
ClassifySamples:errorThreshold	sampleErrorThreshold

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

trybik

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trybik

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Information Tags (9)

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Information Statistics

81 viewings

186 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - Multi-parameter sensitivity analysis (MPSA) of a stochastic SBML model

Created on: Thursday 14 July 2011 @ 08:59:23 (GMT)

Created by: trybik

Last edited on: Thursday 14 July 2011 @ 09:01:31 (GMT)

Last edited by: trybik

Revision comments:

None

Latest Version:
[2] - Multi-parameter sensitivity analysis (MPSA) with PMC

Created on: Thursday 21 July 2011 @ 10:07:16 (GMT)

Created by: trybik

Last edited on: Thursday 21 July 2011 @ 10:08:07 (GMT)

Last edited by: trybik

Revision comments:

upgraded parrallel jobs config

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Other workflows that use similar services (10)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 2

Original Uploader

trybik

Plot error surface (v1)

Created: 14/07/11 @ 09:03:42 | Last updated: 14/07/11 @ 09:06:16

Credits: trybik

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Exemplary workflow for plotting error surface using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) mahtPlot WS operation. Data input format is compatibile with Tav4SB MPSA workflows.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 3 times | Downloaded: 3 times

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