BioXSD example workflow

Created: 2010-10-12 09:19:17 Last updated: 2010-10-12 09:21:55

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An attempt to implement in the BioXSD workflow described by Kalas et al., (2010) Bioinformatics 26:i540-6. The workflow only calls one BioXSD web service (BLAST) since the second service (ClustalW) in the example workflow is currently down :(

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Workflow Components

Authors (1)

Titles (1)

Descriptions (3)

Dependencies (0)

Inputs (1)

Name	Description
querySequence	A query protein sequence in BioXSD format

Processors (11)

Name	Type	Description
getStatus	workflow
getResult	workflow
runBlastp	workflow
alignmentNumber	stringconstant	Value 5
databaseURI	stringconstant	Value Swiss-Prot
expectValue	stringconstant	Value 10
gapOpenPenalty	stringconstant	Value -1
matrix_value	stringconstant	Value BLOSUM62
wordsize	stringconstant	Value 0
gapExtensionPenalty	stringconstant	Value -1
getAccessionIds	xpath	Xpath Expression /BlastOutput/ns2:BlastOutput_iterations/ns2:Iteration/ns2:Iteration_hits/ns2:Hit/ns2:Hit_accession

Beanshells (0)

Outputs (4)

Name	Description
GetResult_output_BlastOutput
GetResult_output_DbStatus
getStatus_status
getAccessionIds_nodelist

Datalinks (15)

Source	Sink
runBlastp:jobId	getStatus:jobId
runBlastp:jobId	getResult:jobId
querySequence	runBlastp:querySequence
alignmentNumber:value	runBlastp:alignmentNumber
databaseURI:value	runBlastp:databaseURI
expectValue:value	runBlastp:expectValue
gapOpenPenalty:value	runBlastp:gapOpenPenalty
matrix_value:value	runBlastp:matrix
wordsize:value	runBlastp:wordsize
gapExtensionPenalty:value	runBlastp:gapExtensionPenalty
getResult:blastOutput	getAccessionIds:xml_text
getResult:blastOutput	GetResult_output_BlastOutput
getResult:dbStatus	GetResult_output_DbStatus
getStatus:status	getStatus_status
getAccessionIds:nodelist	getAccessionIds_nodelist

Coordinations (1)

Controller	Target
getStatus	getResult

Information Workflow Type

Taverna 2

Information Uploader

Peter Li

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Peter Li

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Information Statistics

897 viewings

1086 downloads

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BioXSD example workflow

Created by Peter Li on Tuesday 12 October 2010 09:19:17 (UTC)

Last edited by Peter Li on Tuesday 12 October 2010 09:21:55 (UTC)