Drug_Re_Purposing_WorkflowDrug_Target_Protein_FASTA00
D:\Workflows\Ours\drug_target_proteins.txt
2011-03-30 20:23:16.233 BST
Target_Proteomes_GI11
160367075
2011-03-30 20:24:58.462 BST
root_directory00
D:\Workflows\Ours\Live_Demo\Drug\demo
2011-04-01 02:57:01.501 BST
D:\Workflows\Ours\target_proteins.txt
2011-03-25 18:40:49.587 GMT
D:\Workflows\Ours\target
2011-03-31 16:41:05.518 BST
thresholdIdentity00
90.0
2011-04-01 02:57:35.289 BST
protein_idsNCBIGitoKeggPathways_pathway_descriptionsGO_output_2NCBIGitoKeggPathways_URLInterProPubMed_Results_2outout_2Extract_proteins_using_a_giid1fasta_file_path0file_output11net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
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3
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workflow
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contents_file
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text/plain
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url_string
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1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeString_to_listin10out111net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
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in1
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out1
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeKEGG_ResultsUniprot_ids0pathway_descriptions11URL11net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Uniprot_DataSearchTerm0parsed_data00net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
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0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_identifiers_from_uniprotparsed_uniprot0identifier_name0out111net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
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parsed_uniprot
0
text/plain
java.lang.String
true
identifier_name
0
text/plain
1
out1
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeAC_identifiervalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
AC
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGene_Ontology_Resultsparsed_uniprot0GO_Results00net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeInterPro_Resultsparsed_uniprot0EB_Eye_Results00net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_identifiers_from_uniprot_2_2identifier_name0parsed_uniprot0out111net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
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parsed_uniprot
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text/plain
java.lang.String
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identifier_name
0
text/plain
1
out1
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePubMedvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
PubMed
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesearchCitationsparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.ebi.ac.uk/webservices/citexplore/v1.0/service?wsdl
searchCitations
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesearchCitations_inputluceneQueryString0email0outputFormat0offSet0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="searchCitations" name="parameters" qname="{http://webservice.cdb.ebi.ac.uk/}searchCitations"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="luceneQueryString" qname="searchCitations>luceneQueryString" /><s:basetype optional="true" unbounded="false" typename="string" name="outputFormat" qname="searchCitations>outputFormat" /><s:basetype optional="false" unbounded="false" typename="int" name="offSet" qname="searchCitations>offSet" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="searchCitations>email" /></s:elements></s:complextype></s:extensions>
false
luceneQueryString
0
'text/plain'
false
outputFormat
0
'text/plain'
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offSet
0
'text/plain'
false
email
0
'text/plain'
0
output
0
'text/xml'
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesearchCitations_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="searchCitationsResponse" name="parameters" qname="{http://webservice.cdb.ebi.ac.uk/}searchCitationsResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="resultListBean" name="return" qname="searchCitationsResponse>return"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="hitCount" qname="resultListBean>hitCount" /><s:basetype optional="false" unbounded="false" typename="int" name="offSet" qname="resultListBean>offSet" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="resultBean" name="resultBeanCollection" qname="resultListBean>resultBeanCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="resultBean" name="" qname="{http://webservice.cdb.ebi.ac.uk/}resultBean"><s:elements><s:complextype optional="true" unbounded="false" typename="citation" name="citation" qname="resultBean>citation"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="abstractText" qname="citation>abstractText" /><s:basetype optional="true" unbounded="false" typename="string" name="affiliation" qname="citation>affiliation" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="author" name="authorCollection" qname="citation>authorCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="author" name="" qname="{http://webservice.cdb.ebi.ac.uk/}author"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="author>citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="collectiveName" qname="author>collectiveName" /><s:basetype optional="true" unbounded="false" typename="string" name="fullName" qname="author>fullName" /><s:basetype optional="true" unbounded="false" typename="string" name="initials" qname="author>initials" /><s:basetype optional="true" unbounded="false" typename="string" name="initialsNonAscii" qname="author>initialsNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="author>lastName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastNameNonAscii" qname="author>lastNameNonAscii" /><s:basetype optional="true" unbounded="false" typename="short" name="orderIn" qname="author>orderIn" /><s:basetype optional="true" unbounded="false" typename="string" name="suffix" qname="author>suffix" /><s:basetype optional="true" unbounded="false" typename="string" name="suffixNonAscii" qname="author>suffixNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="valid" qname="author>valid" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:complextype optional="true" unbounded="false" typename="bookOrReport" name="bookOrReportDetails" qname="citation>bookOrReportDetails"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="bookOrReport>citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="comprisingTitle" qname="bookOrReport>comprisingTitle" /><s:basetype optional="true" unbounded="false" typename="string" name="comprisingTitleNonAscii" qname="bookOrReport>comprisingTitleNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="edition" qname="bookOrReport>edition" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="editor" name="editorCollection" qname="bookOrReport>editorCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="editor" name="" qname="{http://webservice.cdb.ebi.ac.uk/}editor"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="editor>citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="collectiveName" qname="editor>collectiveName" /><s:basetype optional="true" unbounded="false" typename="string" name="initials" qname="editor>initials" /><s:basetype optional="true" unbounded="false" typename="string" name="initialsNonAscii" qname="editor>initialsNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="editor>lastName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastNameNonAscii" qname="editor>lastNameNonAscii" /><s:basetype optional="false" unbounded="false" typename="short" name="orderIn" qname="editor>orderIn" /><s:basetype optional="true" unbounded="false" typename="string" name="suffix" qname="editor>suffix" /><s:basetype optional="true" unbounded="false" typename="string" name="suffixNonAscii" qname="editor>suffixNonAscii" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="extraInformation" qname="bookOrReport>extraInformation" /><s:basetype optional="true" unbounded="false" typename="string" name="isbn10" qname="bookOrReport>isbn10" /><s:basetype optional="true" unbounded="false" typename="string" name="isbn13" qname="bookOrReport>isbn13" /><s:basetype optional="true" unbounded="false" typename="string" name="numberOfPages" qname="bookOrReport>numberOfPages" /><s:basetype optional="true" unbounded="false" typename="byte" name="publicationDay" qname="bookOrReport>publicationDay" /><s:basetype optional="true" unbounded="false" typename="byte" name="publicationMonth" qname="bookOrReport>publicationMonth" /><s:basetype optional="true" unbounded="false" typename="short" name="publicationYear" qname="bookOrReport>publicationYear" /><s:basetype optional="true" unbounded="false" typename="string" name="publisher" qname="bookOrReport>publisher" /><s:basetype optional="true" unbounded="false" typename="string" name="seriesIssn" qname="bookOrReport>seriesIssn" /><s:basetype 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The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screened belong to Gram positive bacteria, with special focus on <i>Staphylococcus aureus</i>. We look at a variety of species and strains as the company advised. A mixture of screening targets could potentially identify targets for broad-spectrum antimicrobial development. The drug repurposing workflow shows where in the KEGG pathways the proteins are active and therefore where the action of the drug will be in the biochemical pathways of the bacteria. The workflow will update the Ondex database where new information on Gene Ontology annotations, functional annotation and literature references are available. All information about each unique protein is made available in an HTML document.
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3036 Unique Proteins from Target2Drug
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A-Team: Drug Re-Purposing Analysis
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The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screened belong to Gram positive bacteria, with special focus on <i>Staphylococcus aureus</i>. We look at a variety of species and strains as the company advised. A mixture of screening targets could potentially identify targets for broad-spectrum antimicrobial development. The drug repurposing workflow shows where in the KEGG pathways the proteins are active and therefore where the action of the drug will be in the biochemical pathways of the bacteria. The workflow will update the Ondex database where new information on Gene Ontology annotations, functional annotation and literature references are available. All information about each unique protein is made available in an HTML document.
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Drug Re-Purposing Workflow
2011-03-31 22:53:13.693 BST
Untitledworkflow14parsed_uniprot00EB_Eye_ResultsInterPro_ResultsEntry_Id0Domain0getEntry_output_entryValues11net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_identifiers_from_uniprot_2_2parsed_uniprot0identifier_name0out111net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
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parsed_uniprot
0
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identifier_name
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text/plain
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketo_Lower_Case_2in10out100net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
in1
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text/plain
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out1
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_String_List_to_a_Stringgo_ids1go_defs1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.StringListMerge
workflow
java.lang.String
true
go_defs
1
l('text/plain')
java.lang.String
true
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java.lang.String
true
go_ids
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concatenated
0
UserNameHere
2011-03-30 16:25:55.280 BST
UserNameHere
2011-03-30 16:27:49.467 BST
UserNameHere
2011-03-30 16:29:15.546 BST
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_String_List_to_a_String_2stringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.StringListMerge
workflow
java.lang.String
true
stringlist
1
l('text/plain')
java.lang.String
true
seperator
0
'text/plain'
0
concatenated
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeInterProvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
InterPro
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeInterPro_ResultsEntry_IdInterPro_ResultsDomainget_identifiers_from_uniprot_2_2parsed_uniprotget_identifiers_from_uniprot_2_2identifier_nameto_Lower_Case_2in1Merge_String_List_to_a_Stringgo_idsMerge_String_List_to_a_Stringgo_defsMerge_String_List_to_a_String_2stringlistEB_Eye_Results
2011-03-28 16:28:59.317 BST
c88315af-4ce4-43fb-b48d-45cc0e9424b2
2011-03-28 18:57:59.270 BST
d7ce24f5-f65b-4b2b-8500-6d35cf027d1c
2011-03-28 19:02:12.80 BST
f5b50570-afa2-4768-a298-a7bd35e90e11
2011-03-28 19:28:47.180 BST
fda20a14-917b-454a-a88e-4d4cf58e24c6
2011-03-28 18:34:50.789 BST
33afbd5c-d9a6-4e58-a255-ac744742875a
2011-03-28 18:38:03.893 BST
2011-03-28 16:28:59.317 BST
ff900e9f-7b8d-43fc-be47-cc638b4266d4
2011-03-28 19:00:51.178 BST
4ed40fd8-b13c-4aa2-8977-329988763674
2011-03-28 17:56:58.784 BST
fb843096-2675-4579-9a51-05f43e15ba79
2011-03-28 17:54:29.330 BST
5f08104a-de65-423f-b532-dc7eb89c28ce
2011-03-28 16:39:56.913 BST
f5c68892-7c8c-4bba-96cf-6e4094272de2
2011-03-28 18:51:46.105 BST
Untitled workflow #14
2011-03-28 16:28:59.317 BST
11d4d655-87f9-4a31-88f1-eef56a3a03ee
2011-03-28 16:58:53.309 BST
5bc429c4-927b-4d7e-b4c8-9f8cd17838b7
2011-03-30 17:22:18.272 BST
427f85e8-da08-4e29-800f-8479992b79e5
2011-03-30 16:48:37.456 BST
3117ba0d-f09f-4956-ad74-7761dbf998d9
2011-03-28 19:18:13.311 BST
acd0a40b-a688-473f-8618-1bdbd2046096
2011-03-28 16:33:17.871 BST
416a5592-70f9-4c5f-af15-397bd21af3cb
2011-03-28 19:15:54.482 BST
1752f7dd-badb-4e4a-a2f1-d50327f80d60
2011-03-30 16:46:50.149 BST
7ae7f0a1-1f28-48e1-8c41-7c6da1587e3d
2011-03-28 16:34:34.815 BST
ef9de97c-ca76-479e-b933-d396f043e138
2011-03-28 16:39:02.585 BST
eccaf02b-b85b-4894-9974-c4c49a168673
2011-03-30 16:40:30.44 BST
7f7920cf-259e-4947-8a28-bbd0bf0d5de4
2011-03-28 18:59:44.143 BST
2c33a9b5-8e1e-449a-9bf3-07b1ad48beab
2011-03-30 16:41:33.953 BST
7b3873e1-cd30-4e5c-ab3a-4e0178648eb6
2011-03-30 16:43:19.253 BST
9fedbdd2-dde5-4b08-ab50-80991ea7c41c
2011-03-28 18:55:56.909 BST
Extract_proteins_using_a_gi___output_as_fasta_file_fasta_file_path00
This is where the workflow will save the fasta file
2010-03-18 23:57:05.740 GMT
id11
The workflow uses the gi no to retrieve the xml genbank entry
2010-03-18 23:58:02.898 GMT
file_output
protein output for specified gi in fasta format
2010-03-18 23:58:47.780 GMT
Extraction_of_infoxml_result0fastas_out00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
xml_result
0
text/plain
0
fastas_out
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWrite_Text_FileoutputFile0filecontents0outputFile00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
net.sourceforge.taverna.scuflworkers.io.TextFileWriter
workflow
java.lang.String
true
outputFile
0
'text/plain'
java.lang.String
true
filecontents
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0
outputFile
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Nucleotide_GBSeq_XMLid0outputText00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker
workflow
java.lang.String
true
id
0
'text/plain'
0
outputText
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtraction_of_infoxml_resultWrite_Text_FileoutputFileWrite_Text_FilefilecontentsGet_Nucleotide_GBSeq_XMLidfile_output
6beeaaf5-900a-438a-8791-76184cbcb463
2011-03-24 19:03:54.809 GMT
The workflow uses the gi id to retrieve a xml format of the genbank entry. Using a beanscript, the workflow then parses the required data for the creation of the protein fasta file.
2010-03-18 23:56:41.809 GMT
Extract proteins using a gi - output as fasta file
2010-03-18 23:55:22.983 GMT
nclteamc
2010-03-18 23:54:52.375 GMT
Untitledworkflow4SearchTerm00
2011-03-28 17:43:19.351 BST
uniprot_recordparsed_dataEmbl_Acc
text/plain
2011-03-28 17:43:19.351 BST
fieldNamevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
Alltext
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeparse_uniprotfile_direct_data0report00output00net.sf.taverna.t2.activitiessoaplab-activity1.2net.sf.taverna.t2.activities.soaplab.SoaplabActivity
http://phoebus.cs.man.ac.uk:1977/axis/services/seq_analysis.parse_uniprot
0
1.0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeUniprot_searchfieldname0searchterm0result00report00net.sf.taverna.t2.activitiessoaplab-activity1.2net.sf.taverna.t2.activities.soaplab.SoaplabActivity
http://phoebus.cs.man.ac.uk:1977/axis/services/uniprotsequence.uniprot
0
1.0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeparse_embl_idinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
input
0
'text/plain'
0
output
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeparse_uniprotfile_direct_dataUniprot_searchfieldnameUniprot_searchsearchtermparse_embl_idinputuniprot_recordparsed_dataEmbl_Acc
2011-03-28 17:43:19.515 BST
2011-03-28 17:43:19.515 BST
733461a4-348d-4198-b6ba-899bbf28ba64
2011-03-28 17:43:19.611 BST
Untitled workflow #4
2011-03-28 17:43:19.515 BST
Workflow3JobID00StatusgetJobStateparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdl
getJobState
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobState_inputjobId0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getJobState" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getJobState"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="jobId" qname="getJobState>jobId" /></s:elements></s:complextype></s:extensions>
false
jobId
0
'text/plain'
0
output
0
'text/xml'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
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net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobState_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getJobStateResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getJobStateResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="getJobStateResponse>return" /></s:elements></s:complextype></s:extensions>
java.lang.String
false
input
0
'text/xml'
0
return
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobStateparametersgetJobState_inputjobIdgetJobState_outputinputStatus
d5767d0c-5a85-4f35-a4fc-8ef5e5bbf60c
2011-03-18 12:22:47.500 GMT
4e01e2d8-674e-4af5-8df0-317b9ecaa9f2
2011-03-16 19:37:52.588 GMT
c73c43fa-0789-480d-99c8-8207a12fdbaf
2011-03-16 17:37:44.858 GMT
EBI_OLS_TermInfoOntology_Id00
text/plain
2011-03-30 10:54:12.634 BST
Ontology term identifier to retrive information about. For example: GO:0008150.
2011-03-30 10:54:12.634 BST
Ontology_term
text/xml
2011-03-30 10:54:12.634 BST
text/plain
2011-03-30 10:54:12.634 BST
getTermMetadataparameters0attachmentList11parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.ebi.ac.uk/ontology-lookup/OntologyQuery.wsdl
getTermMetadata
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeInput_parameterstermId0ontologyName0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getTermMetadata" name="parameters" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}getTermMetadata"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="termId" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}>getTermMetadata>termId" /><s:basetype optional="false" unbounded="false" typename="string" name="ontologyName" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}>getTermMetadata>ontologyName" /></s:elements></s:complextype></s:extensions>
java.lang.String
true
termId
0
'text/plain'
java.lang.String
true
ontologyName
0
'text/plain'
0
output
0
'text/xml'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeUnwrap_resultinput0getTermMetadataReturn00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getTermMetadataResponse" name="parameters" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}getTermMetadataResponse"><s:elements><s:arraytype optional="false" unbounded="false" wrapped="false" typename="Map" name="getTermMetadataReturn" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}>getTermMetadataResponse>getTermMetadataReturn"><s:elementtype><s:complextype optional="false" unbounded="false" typename="mapItem" name="" qname="{http://xml.apache.org/xml-soap}mapItem"><s:elements><s:basetype optional="false" unbounded="false" typename="anyType" name="key" qname="{http://xml.apache.org/xml-soap}mapItem>key" /><s:basetype optional="false" unbounded="false" typename="anyType" name="value" qname="{http://xml.apache.org/xml-soap}mapItem>value" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
java.lang.String
true
input
0
'text/xml'
0
getTermMetadataReturn
0
'text/xml'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGOvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
GO
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetTermMetadataparametersInput_parameterstermIdInput_parametersontologyNameUnwrap_resultinputOntology_term
4eaf1d8b-b3dc-478f-8337-bc4213714abb
2011-03-30 10:54:12.741 BST
Hamish McWilliam
2011-03-30 10:54:12.659 BST
EBI_OLS_TermInfo
2011-03-30 10:54:12.659 BST
Get details of an ontology term given its identifer.
This workflow uses the EBI's Ontology Lookup Service (OLS) to get the details of the ontology term. The OLS suports a wide range of biological and bioinformatic ontologies. See http://www.ebi.ac.uk/ontology-lookup/ for more information.
2011-03-30 10:54:12.659 BST
672f9ccb-befa-40ea-ad98-ed1905681a36
2011-03-30 10:59:32.867 BST
95e54190-f04b-4903-b7b1-11f40bb672de
2011-03-30 11:01:12.1 BST
5991ef38-c361-422d-82ab-5c100a76112c
2011-03-30 10:55:35.943 BST
GO_Data_from_GO_IDparsed_uniprot00
File location of the parsed Uniprot results
2011-03-30 16:11:49.141 BST
File location of the parsed Uniprot results. To generate this file, see http://www.myexperiment.org/workflows/26.html
2011-03-30 16:14:06.340 BST
GO_Resultsget_identifiers_from_uniprot_2_2parsed_uniprot0identifier_name0out111net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
parsed_uniprot
0
text/plain
java.lang.String
true
identifier_name
0
text/plain
1
out1
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeEBI_OLS_TermInfoOntology_Id0Ontology_term00net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGO_deXMLerin10out100net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
in1
0
text/plain
0
out1
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGOvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
GO
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_String_List_to_a_Stringgo_defs1go_ids1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.StringListMerge
workflow
java.lang.String
true
go_defs
1
l('text/plain')
java.lang.String
true
seperator
0
'text/plain'
java.lang.String
true
go_ids
1
text/plain
0
concatenated
0
UserNameHere
2011-03-30 16:27:49.467 BST
UserNameHere
2011-03-30 16:25:55.280 BST
UserNameHere
2011-03-30 16:29:15.546 BST
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_identifiers_from_uniprot_2_2parsed_uniprotget_identifiers_from_uniprot_2_2identifier_nameEBI_OLS_TermInfoOntology_IdGO_deXMLerin1Merge_String_List_to_a_Stringgo_defsMerge_String_List_to_a_Stringgo_idsGO_Results
416a5592-70f9-4c5f-af15-397bd21af3cb
2011-03-28 19:15:54.482 BST
a129e83f-4d68-4d84-bb21-b7b2c29cdab9
2011-03-30 12:01:49.842 BST
7ae7f0a1-1f28-48e1-8c41-7c6da1587e3d
2011-03-28 16:34:34.815 BST
a7da9321-f578-410e-93b3-2115c326a8d4
2011-03-30 16:15:18.613 BST
c88315af-4ce4-43fb-b48d-45cc0e9424b2
2011-03-28 18:57:59.270 BST
fb843096-2675-4579-9a51-05f43e15ba79
2011-03-28 17:54:29.330 BST
f5c68892-7c8c-4bba-96cf-6e4094272de2
2011-03-28 18:51:46.105 BST
33afbd5c-d9a6-4e58-a255-ac744742875a
2011-03-28 18:38:03.893 BST
4ed40fd8-b13c-4aa2-8977-329988763674
2011-03-28 17:56:58.784 BST
6ad18fe7-29cc-4cd2-ad50-6b2b62c7be8c
2011-03-30 16:23:46.939 BST
b4078147-9bbb-45c3-a045-dc6090bf95bb
2011-03-30 11:01:16.668 BST
11d4d655-87f9-4a31-88f1-eef56a3a03ee
2011-03-28 16:58:53.309 BST
2011-03-28 16:28:59.317 BST
2011-03-28 16:28:59.317 BST
fda20a14-917b-454a-a88e-4d4cf58e24c6
2011-03-28 18:34:50.789 BST
GO Data from GO ID
2011-03-30 16:15:03.966 BST
21781546-1ad8-4dea-81d0-6780a7ec9e66
2011-03-30 16:35:51.793 BST
73ae7c45-6300-40e1-86c2-5da602996ff8
2011-03-30 10:59:35.473 BST
acd0a40b-a688-473f-8618-1bdbd2046096
2011-03-28 16:33:17.871 BST
Untitled workflow #14
2011-03-28 16:28:59.317 BST
d7ce24f5-f65b-4b2b-8500-6d35cf027d1c
2011-03-28 19:02:12.80 BST
e276142b-824b-4fca-94b4-5a7402085b73
2011-03-30 10:59:54.93 BST
9e103ba0-8dce-4f23-a7f4-165bd80a8f93
2011-03-30 10:56:21.121 BST
9fedbdd2-dde5-4b08-ab50-80991ea7c41c
2011-03-28 18:55:56.909 BST
ff900e9f-7b8d-43fc-be47-cc638b4266d4
2011-03-28 19:00:51.178 BST
2011-03-30 16:14:48.557 BST
2011-03-30 16:15:18.518 BST
473b328e-5f9a-4db9-b31a-c868afc8da4c
2011-03-30 10:55:52.642 BST
5f08104a-de65-423f-b532-dc7eb89c28ce
2011-03-28 16:39:56.913 BST
0523fd65-210c-421c-a12d-86216a61de19
2011-03-30 16:14:43.704 BST
7f7920cf-259e-4947-8a28-bbd0bf0d5de4
2011-03-28 18:59:44.143 BST
3117ba0d-f09f-4956-ad74-7761dbf998d9
2011-03-28 19:18:13.311 BST
19dbb793-e604-4c3c-82a6-e2fe1be4d084
2011-03-29 11:06:03.489 BST
ef9de97c-ca76-479e-b933-d396f043e138
2011-03-28 16:39:02.585 BST
Threshold_BLAST_resultsblast_file00
File : D:\Workflows\Ours\blast_results.txt
2011-03-28 11:41:26.692 BST
Add file location of tab-delimited BLAST results to be thresholded
2011-03-28 11:41:06.278 BST
File : D:\Workflows\Ours\blast_results
2011-03-28 11:41:21.424 BST
thresholdIdentity00
90.00
2011-03-28 11:42:20.533 BST
The amount of identity that two proteins must have to be included in the thresholded results
2011-03-28 11:41:50.694 BST
thresholdedBlastResultsthreshold_BLAST_resultsblast_file0thresholdIdentity0out100net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
blast_file
0
text/plain
java.lang.String
true
thresholdIdentity
0
text/plain
0
out1
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokethreshold_BLAST_resultsblast_filethreshold_BLAST_resultsthresholdIdentitythresholdedBlastResults
59b138d5-5cb4-4a34-a8cb-f4dfd035ef8b
2011-03-28 11:42:41.787 BST
Thresholds tab-delimited BLAST results to a certain percent identity.
2011-04-01 12:04:20.645 BST
90be7e33-afc5-4ecb-82bf-712e2a39bc8d
2011-03-28 11:45:51.374 BST
Threshold BLAST results
2011-04-01 12:03:56.350 BST
770542e1-6648-4a17-9d31-b4db57f8e21f
2011-04-01 12:04:30.841 BST
bd3db62e-7772-4c70-b67b-4a264023adbf
2011-03-28 11:44:34.517 BST
Workflow40Entry_Id00Domain00getEntry_output_entryValuesgetEntryparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.ebi.ac.uk/ebisearch/service.ebi?wsdl
getEntry
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetEntry_inputentry0fields1domain0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getEntry" name="parameters" qname="{http://www.ebi.ac.uk/EBISearchService}getEntry"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="domain" qname="{http://www.ebi.ac.uk/EBISearchService}>getEntry>domain" /><s:basetype optional="false" unbounded="false" typename="string" name="entry" qname="{http://www.ebi.ac.uk/EBISearchService}>getEntry>entry" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="fields" qname="{http://www.ebi.ac.uk/EBISearchService}>getEntry>fields"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
false
domain
0
'text/plain'
false
entry
0
'text/plain'
false
fields
1
l('text/plain')
0
output
0
'text/xml'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetEntry_outputinput0entryValues11net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getEntryResponse" name="parameters" qname="{http://www.ebi.ac.uk/EBISearchService}getEntryResponse"><s:elements><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="entryValues" qname="{http://www.ebi.ac.uk/EBISearchService}>getEntryResponse>entryValues"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
java.lang.String
false
input
0
'text/xml'
1
entryValues
1
l('text/plain')
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokelistFieldsparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.ebi.ac.uk/ebisearch/service.ebi?wsdl
listFields
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokelistFields_inputdomain0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="listFields" name="parameters" qname="{http://www.ebi.ac.uk/EBISearchService}listFields"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="domain" qname="{http://www.ebi.ac.uk/EBISearchService}>listFields>domain" /></s:elements></s:complextype></s:extensions>
false
domain
0
'text/plain'
0
output
0
'text/xml'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokelistFields_outputinput0arrayOfFieldNames11net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="listFieldsResponse" name="parameters" qname="{http://www.ebi.ac.uk/EBISearchService}listFieldsResponse"><s:elements><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="arrayOfFieldNames" qname="{http://www.ebi.ac.uk/EBISearchService}>listFieldsResponse>arrayOfFieldNames"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>
java.lang.String
false
input
0
'text/xml'
1
arrayOfFieldNames
1
l('text/plain')
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConcatenate_two_stringsstring10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.StringConcat
workflow
java.lang.String
true
string1
0
'text/plain'
java.lang.String
true
string2
0
'text/plain'
0
output
0
UserNameHere
2011-03-30 16:39:34.159 BST
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetEntryparametersgetEntry_inputentrygetEntry_inputfieldsgetEntry_inputdomaingetEntry_outputinputlistFieldsparameterslistFields_inputdomainlistFields_outputinputConcatenate_two_stringsstring1Concatenate_two_stringsstring2getEntry_output_entryValues
28d4438b-5326-4ec1-9c46-1ee3b08cb23b
2011-03-28 19:08:29.809 BST
5d320077-d00d-48c4-ad88-009a51fd10a1
2011-03-28 18:25:30.628 BST
a8e6c66a-2319-47dd-9b2b-cf4642a180be
2011-03-28 19:07:07.123 BST
fac4bed3-abac-4864-8df7-8c97c5d9faba
2011-03-28 18:22:17.369 BST
4db4c4e5-4f28-448c-8ab8-ab579454d6ee
2011-03-28 18:27:54.841 BST
4cc17549-3f52-4a93-adb4-52746c2e31a3
2011-03-28 19:12:01.629 BST
3cc20f68-58e9-4f62-ac8b-4f78e3814906
2011-03-28 18:55:42.38 BST
0ff56878-b4d2-4b72-b768-ecfa14497393
2011-03-28 18:57:50.617 BST
6dc968df-61ce-43fe-b497-5701fa930ff4
2011-03-30 16:39:39.780 BST
6d71ee52-0f98-499a-b48d-ea6586d334b9
2011-03-28 19:11:45.502 BST
NCBIGitoKeggPathwaysUniprot_ids00
215422388
2011-03-25 18:07:46.275 GMT
imports gi numbers to be used by the workflow to create the pathways
2010-03-19 03:48:31.724 GMT
text/plain
2010-03-15 17:26:56.908 GMT
2010-03-15 17:26:56.908 GMT
imports gi numbers to be used by the workflow to create the pathways
Tried this one and it worked
2011-03-25 18:07:56.507 GMT
KEGGID
kegg ids
2010-03-19 03:50:43.170 GMT
text/plain
2010-03-15 17:26:56.908 GMT
pathway_by_genes
pathway ids
2010-03-19 03:51:34.611 GMT
text/plain
2010-03-15 17:26:56.908 GMT
pathway_descriptions
text/plain
2010-03-15 17:26:56.908 GMT
pathway ids and corresponding pathways descriptions
2010-03-19 03:51:25.813 GMT
kegg_descriptions
Kegg Ids and corresponding Kegg descriptions
2010-03-19 03:50:34.309 GMT
URL
corresponding url to the pathway id
2010-03-19 03:52:02.52 GMT
image
corresponding image to the pathway id
2010-03-19 03:52:25.108 GMT
merge_pathwaysstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.StringListMerge
workflow
java.lang.String
true
stringlist
1
l('text/plain')
java.lang.String
true
seperator
0
'text/plain'
0
concatenated
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_pathways_2stringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.StringListMerge
workflow
java.lang.String
true
stringlist
1
l('text/plain')
java.lang.String
true
seperator
0
'text/plain'
0
concatenated
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_descriptionsstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.StringListMerge
workflow
java.lang.String
true
stringlist
1
l('text/plain')
java.lang.String
true
seperator
0
'text/plain'
0
concatenated
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRemove_duplicate_pathwaysstringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
workflow
java.lang.String
true
stringlist
1
l('text/plain')
1
strippedlist
1
l('text/plain')
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokebtitstring0return00attachmentList11net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://soap.genome.jp/KEGG.wsdl
btit
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokebtit1string0return00attachmentList11net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://soap.genome.jp/KEGG.wsdl
btit
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokebconvstring0return00attachmentList11net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://soap.genome.jp/KEGG.wsdl
bconv
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_Nullsinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
input
0
'text/plain'
0
output
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_gene_idsinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
input
0
'text/plain'
0
output
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeremove_nulls_2input0output00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
input
0
'text/plain'
0
output
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeadd_uniprot_to_stringinput0output00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
input
0
'text/plain'
0
output
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_image_from_URLurl0image00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.WebImageFetcher
workflow
java.lang.String
true
url
0
'text/x-taverna-web-url'
java.lang.String
true
base
0
'text/x-taverna-web-url'
0
image
0
'image/*'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecolor_pathway_by_objects_2pathway_id0bg_color_list1fg_color_list1object_id_list1attachmentList11return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://soap.genome.jp/KEGG.wsdl
color_pathway_by_objects
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_by_regex_2regex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
workflow
java.lang.String
true
string
0
'text/plain'
java.lang.String
true
regex
0
'text/plain'
1
split
1
l('text/plain')
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
\n
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_by_regexregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
workflow
java.lang.String
true
string
0
'text/plain'
java.lang.String
true
regex
0
'text/plain'
1
split
1
l('text/plain')
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregexvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
\n
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_pathways_by_genesgenes_id_list1attachmentList11return11net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://soap.genome.jp/KEGG.wsdl
get_pathways_by_genes
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
0
0
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokepinkvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
pink
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokepurplevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
purple
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.FlattenList
workflow
[B
true
inputlist
2
l(l(''))
1
outputlist
1
l('')
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_3inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity
org.embl.ebi.escience.scuflworkers.java.FlattenList
workflow
[B
true
inputlist
2
l(l(''))
1
outputlist
1
l('')
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_pathwaysstringlistmerge_pathways_2stringlistmerge_descriptionsstringlistRemove_duplicate_pathwaysstringlistbtitstringbtit1stringbconvstringremove_Nullsinputextract_gene_idsinputremove_nulls_2inputadd_uniprot_to_stringinputGet_image_from_URLurlcolor_pathway_by_objects_2pathway_idcolor_pathway_by_objects_2bg_color_listcolor_pathway_by_objects_2fg_color_listcolor_pathway_by_objects_2object_id_listsplit_by_regex_2regexsplit_by_regex_2stringsplit_by_regexregexsplit_by_regexstringget_pathways_by_genesgenes_id_listFlatten_ListinputlistFlatten_List_3inputlistKEGGIDpathway_by_genespathway_descriptionskegg_descriptionsURLimage
1495f977-2aeb-4ca7-a79d-e9aa9472af27
2011-03-25 18:08:37.965 GMT
b9b894bb-350e-47f2-81ba-e076e9f50608
2011-03-31 13:57:42.749 BST
d456be95-e8be-419b-a86e-fa54751ae1b0
2011-03-31 14:50:44.6 BST
a110afdb-d845-4164-8b6a-49f76cfb514d
2011-03-31 11:19:46.601 BST
17596066-d978-42f2-a5a1-3082300be8ea
2011-03-31 11:14:43.208 BST
aeba0128-e6e4-4246-8da0-b816c51b62cc
2011-03-31 11:57:51.849 BST
c2ab2676-5a31-4889-9913-0601a8f0e238
2011-03-31 13:58:25.963 BST
NCBI Gi to Kegg Pathways
2010-03-15 17:26:56.962 GMT
f38c6560-baaa-400e-be8a-b02171e13db0
2011-03-31 15:02:01.586 BST
This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.
2010-03-15 17:26:56.962 GMT
"This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings."
2010-03-19 03:47:03.582 GMT
89621269-d95c-45f4-b969-0bce9cccd125
2011-03-31 11:19:29.823 BST
358042ee-ccdc-43f4-8301-5e7448bfbd53
2011-03-25 11:49:22.194 GMT
31e58e2c-47a8-4ed4-a7ab-c6b8d1d67149
2011-03-31 14:42:16.155 BST
3542735a-febb-4b90-af1d-7571fa36d73e
2011-03-28 12:03:17.584 BST
Paul Fisher
2010-03-15 17:26:56.962 GMT
nclteamc
and
Paul Fisher
2010-03-19 03:46:54.347 GMT
d5d0df3b-2ac7-4a8d-85ce-223e0ff17132
2011-03-25 17:57:31.266 GMT
Workflow8subjectURL00queryURL00JobIDOutputBlastReportFinalStatusaquireSubjectFileparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdl
aquireInputFile
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSubjectUrlInputurl0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFile" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="url" qname="aquireInputFile>url" /></s:elements></s:complextype></s:extensions>
false
url
0
'text/plain'
0
output
0
'text/xml'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubjectFileIDinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFileResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFileResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="aquireInputFileResponse>return" /></s:elements></s:complextype></s:extensions>
java.lang.String
false
input
0
'text/xml'
0
return
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaquireQueryFileparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdl
aquireInputFile
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeQueryUrlInputurl0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFile" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="url" qname="aquireInputFile>url" /></s:elements></s:complextype></s:extensions>
false
url
0
'text/plain'
0
output
0
'text/xml'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokequeryFileIDinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFileResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFileResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="aquireInputFileResponse>return" /></s:elements></s:complextype></s:extensions>
java.lang.String
false
input
0
'text/xml'
0
return
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubmitBlastPJobparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdl
submitBlastPJob
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubmitBlastPJob_inputsubjectFileId0queryFileId0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="submitBlastPJob" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}submitBlastPJob"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="subjectFileId" qname="submitBlastPJob>subjectFileId" /><s:basetype optional="true" unbounded="false" typename="string" name="queryFileId" qname="submitBlastPJob>queryFileId" /></s:elements></s:complextype></s:extensions>
false
subjectFileId
0
'text/plain'
false
queryFileId
0
'text/plain'
0
output
0
'text/xml'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJobIDinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="submitBlastPJobResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}submitBlastPJobResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="submitBlastPJobResponse>return" /></s:elements></s:complextype></s:extensions>
java.lang.String
false
input
0
'text/xml'
0
return
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeAwaitJobCompletionJobID0Status00net.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop
<activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
<script>loop = "" + ! Status.equals("COMPLETED");
if ("true".matches(loop)) {
Thread.sleep(10000);
}</script>
<dependencies />
<classLoaderSharing>workflow</classLoaderSharing>
<localDependencies />
<artifactDependencies />
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
<name>Status</name>
<depth>0</depth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<granularDepth>0</granularDepth>
<name>loop</name>
<depth>0</depth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity>
true
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetBlastReportparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdl
getBlastReport
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetBlastReport_inputjobId0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getBlastReport" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getBlastReport"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="jobId" qname="getBlastReport>jobId" /></s:elements></s:complextype></s:extensions>
false
jobId
0
'text/plain'
0
output
0
'text/xml'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetBlastReport_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getBlastReportResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getBlastReportResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="getBlastReportResponse>return" /></s:elements></s:complextype></s:extensions>
java.lang.String
false
input
0
'text/xml'
0
return
0
'text/plain'
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
1
net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry
1.0
1000
5000
0
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