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casimir_paper

Workflow Entry: casimir_paper

Created at: 22/01/08 @ 16:22:26 Last updated: 30/05/08 @ 14:40:41

Version 2 (latest) (of 2)

Version created on: 22/01/08 @ 16:22:26 by: Damian | Revision comments Expand

Last edited on: 30/05/08 @ 14:40:41 by: Damian

Title: casimir_paper

Type: Taverna 1

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Workflow Components

Inputs (1)

Name	Description
mgiSymbols

Processors (18)

Name	Type	Description
flattenList1	local
flattenList2	local
mergeStringListToString3	local
removeDupResults	local
flatten_list3	local
flattenList4	local
splitStringByRegularExpression	local
mergeStringListToString1	local
mergeStringListToString2	local
beanshellMergeSnps	beanshell
convBpToMb	beanshell
convBbToMb2	beanshell
beanshellMergePathways	beanshell
beanshellCleanResults	beanshell
mouseEmblBioMart	biomart	Mus musculus genes (NCBIM37)
mouseEnsemblBioMart	biomart	Mus musculus genes (NCBIM37)
pathways	workflow
snpAlleles	workflow

Beanshells (7)

Name	Inputs	Outputs
splitBeanShell	input	output
Beanshell_scripting_host	input	output
beanshellMergeSnps	ensemblGeneID snpID	mergedOutput
convBpToMb	bp	mb
convBbToMb2	bp	mb
beanshellMergePathways	ensemblGeneID keggGeneID	mergedOutput
beanshellCleanResults	input	output

Outputs (4)

Name	Description
pathways
snps
snpAllelePerStrain
pathwayURLs

Links (27)

Source	Sink
beanshellCleanResults:output	splitStringByRegularExpression:string
beanshellMergePathways:mergedOutput	mergeStringListToString3:stringlist
beanshellMergeSnps:mergedOutput	flattenList1:inputlist
convBbToMb2:mb	snpAlleles:toMB
convBpToMb:mb	snpAlleles:fromMB
flatten_list3:outputlist	mergeStringListToString2:stringlist
mergeStringListToString1:concatenated	beanshellMergeSnps:snpID
mergeStringListToString2:concatenated	beanshellMergePathways:keggGeneID
mergeStringListToString3:concatenated	beanshellCleanResults:input
mgiSymbols	mouseEnsemblBioMart:mmusculus_gene_ensembl.mgi_symbol_filter
mouseEmblBioMart:mmusculus_gene_ensembl.embl	pathways:input
mouseEmblBioMart:mmusculus_gene_ensembl.ensembl_gene_id	beanshellMergePathways:ensemblGeneID
mouseEnsemblBioMart:mmusculus_gene_ensembl.chromosome_name	snpAlleles:chr
mouseEnsemblBioMart:mmusculus_gene_ensembl.end_position	convBbToMb2:bp
mouseEnsemblBioMart:mmusculus_gene_ensembl.ensembl_gene_id	beanshellMergeSnps:ensemblGeneID
mouseEnsemblBioMart:mmusculus_gene_ensembl.ensembl_gene_id	mouseEmblBioMart:mmusculus_gene_ensembl.ensembl_gene_id_filter
mouseEnsemblBioMart:mmusculus_gene_ensembl.ensembl_gene_id	snpAlleles:geneInput
mouseEnsemblBioMart:mmusculus_gene_ensembl.start_position	convBpToMb:bp
pathways:id_output	flatten_list3:inputlist
pathways:url_output	flattenList2:inputlist
snpAlleles:snpAllelePerStrain	flattenList4:inputlist
snpAlleles:snps	mergeStringListToString1:stringlist
splitStringByRegularExpression:split	removeDupResults:stringlist
flattenList1:outputlist	snps
flattenList2:outputlist	pathwayURLs
flattenList4:outputlist	snpAllelePerStrain
removeDupResults:strippedlist	pathways

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Damian

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Information Credits (1)

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Damian

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Information Tags (1)

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casimir

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Private item

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Information Statistics

1152 viewings

881 downloads

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Version History

Earliest Version:
[1] - Case example for CASIMIR paper on solutions to databse interoperability

Created on: Tuesday 22 January 2008 @ 16:22:26 (GMT)

Created by: Damian

Last edited on: Tuesday 22 April 2008 @ 11:21:21 (GMT)

Last edited by: Damian

Revision comments:

None

Latest Version:
[2] - casimir_paper

Created on: Tuesday 22 January 2008 @ 16:22:26 (GMT)

Created by: Damian

Last edited on: Friday 30 May 2008 @ 14:40:41 (GMT)

Last edited by: Damian

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Comments (1)

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Morris Swertz	Monday 21 April 2008 @ 14:10:58 (GMT)
	See http://www.myexperiment.org/files/31 for MOLGENIS definition of mouse phenome database.

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Viewed: 40 times | Downloaded: 16 times

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