Vaccine_Targets_WorkflowTarget_GI00 The GI Number for the target strain. The example below is Bacillus anthracis Ames. 2011-04-01 11:26:57.365 BST 160367075 2011-03-30 20:24:58.462 BST 49176966 2011-03-31 23:56:58.874 BST root_directory00 The directory in which to save the workflow results (FASTA, Blast, and HTML document). 2011-04-01 11:25:46.130 BST D:\Workflows\Ours\Live_Demo\Vaccine\demo 2011-04-01 02:56:16.240 BST D:\Workflows\Ours\Live_Demo\ 2011-04-01 02:56:00.575 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 Source_GI00 225184640 2011-03-31 23:56:32.721 BST The GI number for the source strain. The example below is for Bacillus subtilis 168. 2011-04-01 11:26:33.570 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 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 3 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMicrobase_BlastPsubjectURL0queryURL0BlastReport00net.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.InvokeGet_Source_Fasta_Urlcontents_file0url_string00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true contents_file 0 text/plain 0 url_string 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.InvokeGet_Target_Fasta_Urlcontents_file0url_string00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true contents_file 0 text/plain 0 url_string 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.InvokeString_to_listin10out111net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true in1 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.InvokeFind_Unique_ProteinsblastFile0tfasta0unique_identifiers00net.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.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 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_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 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_uniprotparsed_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.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 1000 5000 0 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 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_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 1000 5000 0 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 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.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 1000 5000 0 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 1000 5000 0 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&gt;luceneQueryString" /><s:basetype optional="true" unbounded="false" typename="string" name="outputFormat" qname="searchCitations&gt;outputFormat" /><s:basetype optional="false" unbounded="false" typename="int" name="offSet" qname="searchCitations&gt;offSet" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="searchCitations&gt;email" /></s:elements></s:complextype></s:extensions> false luceneQueryString 0 'text/plain' false outputFormat 0 'text/plain' false offSet 0 'text/plain' false email 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.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&gt;return"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="hitCount" qname="resultListBean&gt;hitCount" /><s:basetype optional="false" unbounded="false" typename="int" name="offSet" qname="resultListBean&gt;offSet" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="resultBean" name="resultBeanCollection" qname="resultListBean&gt;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&gt;citation"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="abstractText" qname="citation&gt;abstractText" /><s:basetype optional="true" unbounded="false" typename="string" name="affiliation" qname="citation&gt;affiliation" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="author" name="authorCollection" qname="citation&gt;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&gt;citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="collectiveName" qname="author&gt;collectiveName" /><s:basetype optional="true" unbounded="false" typename="string" name="fullName" qname="author&gt;fullName" /><s:basetype optional="true" unbounded="false" typename="string" name="initials" qname="author&gt;initials" /><s:basetype optional="true" unbounded="false" typename="string" name="initialsNonAscii" qname="author&gt;initialsNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="author&gt;lastName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastNameNonAscii" qname="author&gt;lastNameNonAscii" /><s:basetype optional="true" unbounded="false" typename="short" name="orderIn" qname="author&gt;orderIn" /><s:basetype optional="true" unbounded="false" typename="string" name="suffix" qname="author&gt;suffix" /><s:basetype optional="true" unbounded="false" typename="string" name="suffixNonAscii" qname="author&gt;suffixNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="valid" qname="author&gt;valid" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:complextype optional="true" unbounded="false" typename="bookOrReport" name="bookOrReportDetails" qname="citation&gt;bookOrReportDetails"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="bookOrReport&gt;citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="comprisingTitle" qname="bookOrReport&gt;comprisingTitle" /><s:basetype optional="true" unbounded="false" typename="string" name="comprisingTitleNonAscii" qname="bookOrReport&gt;comprisingTitleNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="edition" qname="bookOrReport&gt;edition" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="editor" name="editorCollection" qname="bookOrReport&gt;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&gt;citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="collectiveName" qname="editor&gt;collectiveName" /><s:basetype optional="true" unbounded="false" typename="string" name="initials" qname="editor&gt;initials" /><s:basetype optional="true" unbounded="false" typename="string" name="initialsNonAscii" qname="editor&gt;initialsNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="editor&gt;lastName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastNameNonAscii" qname="editor&gt;lastNameNonAscii" /><s:basetype optional="false" unbounded="false" typename="short" name="orderIn" qname="editor&gt;orderIn" /><s:basetype optional="true" unbounded="false" typename="string" name="suffix" qname="editor&gt;suffix" /><s:basetype optional="true" unbounded="false" typename="string" name="suffixNonAscii" qname="editor&gt;suffixNonAscii" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="extraInformation" qname="bookOrReport&gt;extraInformation" /><s:basetype optional="true" unbounded="false" typename="string" name="isbn10" qname="bookOrReport&gt;isbn10" /><s:basetype optional="true" unbounded="false" typename="string" name="isbn13" qname="bookOrReport&gt;isbn13" /><s:basetype optional="true" unbounded="false" typename="string" name="numberOfPages" qname="bookOrReport&gt;numberOfPages" /><s:basetype optional="true" unbounded="false" typename="byte" name="publicationDay" qname="bookOrReport&gt;publicationDay" /><s:basetype optional="true" unbounded="false" typename="byte" name="publicationMonth" qname="bookOrReport&gt;publicationMonth" /><s:basetype optional="true" unbounded="false" typename="short" name="publicationYear" qname="bookOrReport&gt;publicationYear" /><s:basetype optional="true" unbounded="false" typename="string" name="publisher" qname="bookOrReport&gt;publisher" /><s:basetype optional="true" unbounded="false" typename="string" name="seriesIssn" qname="bookOrReport&gt;seriesIssn" /><s:basetype optional="true" unbounded="false" typename="string" name="seriesName" qname="bookOrReport&gt;seriesName" /></s:elements></s:complextype><s:basetype optional="true" unbounded="false" typename="dateTime" name="cachedAt" qname="citation&gt;cachedAt" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="chemical" name="chemicalCollection" qname="citation&gt;chemicalCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="chemical" name="" qname="{http://webservice.cdb.ebi.ac.uk/}chemical"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="id" qname="chemical&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="chemical&gt;name" /><s:basetype optional="true" unbounded="false" typename="string" name="registryNumber" qname="chemical&gt;registryNumber" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="comment" name="commentsAndCorrectionsCollection" qname="citation&gt;commentsAndCorrectionsCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="comment" name="" qname="{http://webservice.cdb.ebi.ac.uk/}comment"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="citationId" qname="comment&gt;citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="externalId" qname="comment&gt;externalId" /><s:basetype optional="true" unbounded="false" typename="string" name="note" qname="comment&gt;note" /><s:basetype optional="false" unbounded="false" typename="byte" name="orderIn" qname="comment&gt;orderIn" /><s:basetype optional="true" unbounded="false" typename="string" name="reference" qname="comment&gt;reference" /><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="comment&gt;source" /><s:basetype optional="true" unbounded="false" typename="string" name="type" qname="comment&gt;type" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="authorsConcatenation" name="concatenatedAuthorsCollection" qname="citation&gt;concatenatedAuthorsCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="authorsConcatenation" name="" qname="{http://webservice.cdb.ebi.ac.uk/}authorsConcatenation"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="authorsConcatenation" qname="authorsConcatenation&gt;authorsConcatenation" /><s:basetype optional="true" unbounded="false" typename="string" name="authorsConcatenation_clob" qname="authorsConcatenation&gt;authorsConcatenation_clob" /><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="authorsConcatenation&gt;citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="hasNonAsciiCharacters" qname="authorsConcatenation&gt;hasNonAsciiCharacters" /><s:basetype optional="true" unbounded="false" typename="string" name="validAuthorsConcatenation" qname="authorsConcatenation&gt;validAuthorsConcatenation" /><s:basetype optional="true" unbounded="false" typename="string" name="validAuthorsConcatenation_clob" qname="authorsConcatenation&gt;validAuthorsConcatenation_clob" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="crossReference" name="crossReferenceAltSpliceFunCollection" qname="citation&gt;crossReferenceAltSpliceFunCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="crossReference" name="" qname="{http://webservice.cdb.ebi.ac.uk/}crossReference"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="dataSource" qname="crossReference&gt;dataSource" /><s:basetype optional="true" unbounded="false" typename="string" name="externalId" qname="crossReference&gt;externalId" /><s:basetype optional="true" unbounded="false" typename="string" name="info1" qname="crossReference&gt;info1" /><s:basetype optional="true" unbounded="false" typename="string" name="info2" qname="crossReference&gt;info2" /><s:basetype optional="true" unbounded="false" typename="string" name="info3" qname="crossReference&gt;info3" /><s:basetype optional="true" unbounded="false" typename="string" name="info4" qname="crossReference&gt;info4" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="crossReference" name="crossReferenceAltSpliceSeqCollection" qname="citation&gt;crossReferenceAltSpliceSeqCollection"><s:elementtype><s:complextype id="{http://webservice.cdb.ebi.ac.uk/}crossReference" optional="false" unbounded="false" typename="crossReference" name="" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="crossReference" name="crossReferenceEMBLCollection" qname="citation&gt;crossReferenceEMBLCollection"><s:elementtype><s:complextype id="{http://webservice.cdb.ebi.ac.uk/}crossReference" optional="false" unbounded="false" typename="crossReference" name="" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="crossReference" name="crossReferenceInterproCollection" qname="citation&gt;crossReferenceInterproCollection"><s:elementtype><s:complextype id="{http://webservice.cdb.ebi.ac.uk/}crossReference" optional="false" unbounded="false" typename="crossReference" name="" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="crossReference" name="crossReferenceUniprotCollection" qname="citation&gt;crossReferenceUniprotCollection"><s:elementtype><s:complextype id="{http://webservice.cdb.ebi.ac.uk/}crossReference" optional="false" unbounded="false" typename="crossReference" name="" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="crossReference" name="crossReferencesChEBICollection" qname="citation&gt;crossReferencesChEBICollection"><s:elementtype><s:complextype id="{http://webservice.cdb.ebi.ac.uk/}crossReference" optional="false" unbounded="false" typename="crossReference" name="" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="crossReference" name="crossReferencesIntactCollection" qname="citation&gt;crossReferencesIntactCollection"><s:elementtype><s:complextype id="{http://webservice.cdb.ebi.ac.uk/}crossReference" optional="false" unbounded="false" typename="crossReference" name="" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="crossReference" name="crossReferencesMSDCollection" qname="citation&gt;crossReferencesMSDCollection"><s:elementtype><s:complextype id="{http://webservice.cdb.ebi.ac.uk/}crossReference" optional="false" unbounded="false" typename="crossReference" name="" /></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="dataSource" qname="citation&gt;dataSource" /><s:basetype optional="true" unbounded="false" typename="dateTime" name="dateOfCompletion" qname="citation&gt;dateOfCompletion" /><s:basetype optional="true" unbounded="false" typename="dateTime" name="dateOfCreation" qname="citation&gt;dateOfCreation" /><s:basetype optional="true" unbounded="false" typename="dateTime" name="dateOfRevision" qname="citation&gt;dateOfRevision" /><s:basetype optional="true" unbounded="false" typename="string" name="externalId" qname="citation&gt;externalId" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="geneOntology" name="geneOntologyCollection" qname="citation&gt;geneOntologyCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="geneOntology" name="" qname="{http://webservice.cdb.ebi.ac.uk/}geneOntology"><s:elements><s:basetype optional="true" unbounded="false" typename="decimal" name="citationId" qname="geneOntology&gt;citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="goId" qname="geneOntology&gt;goId" /><s:basetype optional="true" unbounded="false" typename="string" name="goTerm" qname="geneOntology&gt;goTerm" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="grant" name="grantCollection" qname="citation&gt;grantCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="grant" name="" qname="{http://webservice.cdb.ebi.ac.uk/}grant"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="acronym" qname="grant&gt;acronym" /><s:basetype optional="true" unbounded="false" typename="string" name="agency" qname="grant&gt;agency" /><s:basetype optional="false" unbounded="false" typename="int" name="citationId" qname="grant&gt;citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="grantId" qname="grant&gt;grantId" /><s:basetype optional="false" unbounded="false" typename="short" name="orderIn" qname="grant&gt;orderIn" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="int" name="id" qname="citation&gt;id" /><s:complextype optional="true" unbounded="false" typename="journalIssue" name="journalIssue" qname="citation&gt;journalIssue"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="dateOfPublication" qname="journalIssue&gt;dateOfPublication" /><s:basetype optional="true" unbounded="false" typename="int" name="id" qname="journalIssue&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="issue" qname="journalIssue&gt;issue" /><s:complextype optional="true" unbounded="false" typename="journal" name="journal" qname="journalIssue&gt;journal"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="ESSN" qname="journal&gt;ESSN" /><s:basetype optional="true" unbounded="false" typename="string" name="ISOAbbreviation" qname="journal&gt;ISOAbbreviation" /><s:basetype optional="true" unbounded="false" typename="string" name="ISSN" qname="journal&gt;ISSN" /><s:basetype optional="true" unbounded="false" typename="int" name="id" qname="journal&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="medlineAbbreviation" qname="journal&gt;medlineAbbreviation" /><s:basetype optional="true" unbounded="false" typename="string" name="NLMid" qname="journal&gt;NLMid" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="journal&gt;title" /></s:elements></s:complextype><s:basetype optional="true" unbounded="false" typename="byte" name="monthOfPublication" qname="journalIssue&gt;monthOfPublication" /><s:basetype optional="true" unbounded="false" typename="string" name="volume" qname="journalIssue&gt;volume" /><s:basetype optional="true" unbounded="false" typename="short" name="yearOfPublication" qname="journalIssue&gt;yearOfPublication" /></s:elements></s:complextype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="keyword" name="keywordCollection" qname="citation&gt;keywordCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="keyword" name="" qname="{http://webservice.cdb.ebi.ac.uk/}keyword"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="eurofirCode" qname="keyword&gt;eurofirCode" /><s:basetype optional="true" unbounded="false" typename="int" name="id" qname="keyword&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="keyword" qname="keyword&gt;keyword" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="language" qname="citation&gt;language" /><s:complextype optional="true" unbounded="false" typename="medlineXml" name="medlineXML" qname="citation&gt;medlineXML"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="dataSource" qname="medlineXml&gt;dataSource" /><s:basetype optional="true" unbounded="false" typename="string" name="pubmedID" qname="medlineXml&gt;pubmedID" /><s:basetype optional="true" unbounded="false" typename="string" name="XML" qname="medlineXml&gt;XML" /></s:elements></s:complextype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="meshHeading" name="meshCollection" qname="citation&gt;meshCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="meshHeading" name="" qname="{http://webservice.cdb.ebi.ac.uk/}meshHeading"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="meshHeading&gt;citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="majorTopic_YN" qname="meshHeading&gt;majorTopic_YN" /><s:complextype optional="true" unbounded="false" typename="meshHeadingType" name="meshHeadingType" qname="meshHeading&gt;meshHeadingType"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="descriptor" qname="meshHeadingType&gt;descriptor" /><s:basetype optional="true" unbounded="false" typename="int" name="id" qname="meshHeadingType&gt;id" /></s:elements></s:complextype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="meshQualifier" name="meshQualifierCollection" qname="meshHeading&gt;meshQualifierCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="meshQualifier" name="" qname="{http://webservice.cdb.ebi.ac.uk/}meshQualifier"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="majorTopic_YN" qname="meshQualifier&gt;majorTopic_YN" /><s:complextype optional="true" unbounded="false" typename="meshQualifierType" name="meshQualifierType" qname="meshQualifier&gt;meshQualifierType"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="abbreviation" qname="meshQualifierType&gt;abbreviation" /><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="meshQualifierType&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="qualifier" qname="meshQualifierType&gt;qualifier" /></s:elements></s:complextype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="originalTitle" qname="citation&gt;originalTitle" /><s:basetype optional="true" unbounded="false" typename="string" name="pageInfo" qname="citation&gt;pageInfo" /><s:complextype optional="true" unbounded="false" typename="patentAbstractXml" name="patentAbstractXML" qname="citation&gt;patentAbstractXML"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="dataSource" qname="patentAbstractXml&gt;dataSource" /><s:basetype optional="true" unbounded="false" typename="string" name="patentNumber" qname="patentAbstractXml&gt;patentNumber" /><s:basetype optional="true" unbounded="false" typename="string" name="XML" qname="patentAbstractXml&gt;XML" /></s:elements></s:complextype><s:complextype optional="true" unbounded="false" typename="patentDetails" name="patentDetails" qname="citation&gt;patentDetails"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="patentDetails&gt;citationId" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="patentClassifier" name="classifierCollection" qname="patentDetails&gt;classifierCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="patentClassifier" name="" qname="{http://webservice.cdb.ebi.ac.uk/}patentClassifier"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="classification" qname="patentClassifier&gt;classification" /><s:basetype optional="true" unbounded="false" typename="string" name="classificationType" qname="patentClassifier&gt;classificationType" /><s:basetype optional="true" unbounded="false" typename="string" name="hyperlink" qname="patentClassifier&gt;hyperlink" /><s:basetype optional="true" unbounded="false" typename="int" name="patentDetailId" qname="patentClassifier&gt;patentDetailId" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="country" qname="patentDetails&gt;country" /><s:basetype optional="true" unbounded="false" typename="string" name="countryCode" qname="patentDetails&gt;countryCode" /><s:basetype optional="true" unbounded="false" typename="int" name="patentDetailId" qname="patentDetails&gt;patentDetailId" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="secondaryNumber" name="secondaryNumberCollection" qname="patentDetails&gt;secondaryNumberCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="secondaryNumber" name="" qname="{http://webservice.cdb.ebi.ac.uk/}secondaryNumber"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="dataType" qname="secondaryNumber&gt;dataType" /><s:basetype optional="true" unbounded="false" typename="short" name="orderIn" qname="secondaryNumber&gt;orderIn" /><s:basetype optional="true" unbounded="false" typename="int" name="patentDetailId" qname="secondaryNumber&gt;patentDetailId" /><s:basetype optional="true" unbounded="false" typename="string" name="value" qname="secondaryNumber&gt;value" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="typeCode" qname="patentDetails&gt;typeCode" /><s:basetype optional="true" unbounded="false" typename="string" name="typeDescription" qname="patentDetails&gt;typeDescription" /></s:elements></s:complextype><s:basetype optional="true" unbounded="false" typename="string" name="pubModel" qname="citation&gt;pubModel" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="publicationType" name="pubTypeCollection" qname="citation&gt;pubTypeCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="publicationType" name="" qname="{http://webservice.cdb.ebi.ac.uk/}publicationType"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="description" qname="publicationType&gt;description" /><s:basetype optional="true" unbounded="false" typename="int" name="id" qname="publicationType&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="publicationType&gt;name" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="reference" name="referenceCollection" qname="citation&gt;referenceCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="reference" name="" qname="{http://webservice.cdb.ebi.ac.uk/}reference"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="authors" qname="reference&gt;authors" /><s:basetype optional="true" unbounded="false" typename="string" name="citationType" qname="reference&gt;citationType" /><s:basetype optional="false" unbounded="false" typename="int" name="citedOrder" qname="reference&gt;citedOrder" /><s:basetype optional="true" unbounded="false" typename="string" name="comments" qname="reference&gt;comments" /><s:basetype optional="true" unbounded="false" typename="string" name="doi" qname="reference&gt;doi" /><s:basetype optional="true" unbounded="false" typename="string" name="edition" qname="reference&gt;edition" /><s:basetype optional="true" unbounded="false" typename="string" name="editors" qname="reference&gt;editors" /><s:basetype optional="true" unbounded="false" typename="string" name="essn" qname="reference&gt;essn" /><s:basetype optional="true" unbounded="false" typename="string" name="externalId" qname="reference&gt;externalId" /><s:basetype optional="true" unbounded="false" typename="string" name="externalLink" qname="reference&gt;externalLink" /><s:basetype optional="true" unbounded="false" typename="decimal" name="id" qname="reference&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="isbn" qname="reference&gt;isbn" /><s:basetype optional="true" unbounded="false" typename="string" name="issn" qname="reference&gt;issn" /><s:basetype optional="true" unbounded="false" typename="string" name="issue" qname="reference&gt;issue" /><s:basetype optional="true" unbounded="false" typename="string" name="journalAbbr" qname="reference&gt;journalAbbr" /><s:basetype optional="true" unbounded="false" typename="string" name="match" qname="reference&gt;match" /><s:basetype optional="true" unbounded="false" typename="string" name="pageInfo" qname="reference&gt;pageInfo" /><s:basetype optional="false" unbounded="false" typename="int" name="parentId" qname="reference&gt;parentId" /><s:basetype optional="false" unbounded="false" typename="int" name="pubYear" qname="reference&gt;pubYear" /><s:basetype optional="true" unbounded="false" typename="string" name="publisherLoc" qname="reference&gt;publisherLoc" /><s:basetype optional="true" unbounded="false" typename="string" name="publisherName" qname="reference&gt;publisherName" /><s:basetype optional="true" unbounded="false" typename="string" name="refId" qname="reference&gt;refId" /><s:basetype optional="true" unbounded="false" typename="string" name="seriesName" qname="reference&gt;seriesName" /><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="reference&gt;source" /><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="reference&gt;title" /><s:basetype optional="true" unbounded="false" typename="string" name="unstructuredInformation" qname="reference&gt;unstructuredInformation" /><s:basetype optional="true" unbounded="false" typename="string" name="volume" qname="reference&gt;volume" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="textFragment" name="refererCollection" qname="citation&gt;refererCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="textFragment" name="" qname="{http://webservice.cdb.ebi.ac.uk/}textFragment"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="citationId" qname="textFragment&gt;citationId" /><s:basetype optional="false" unbounded="false" typename="int" name="lineNum" qname="textFragment&gt;lineNum" /><s:basetype optional="false" unbounded="false" typename="int" name="orderInReference" qname="textFragment&gt;orderInReference" /><s:basetype optional="true" unbounded="false" typename="string" name="referencedBy_ExternalId" qname="textFragment&gt;referencedBy_ExternalId" /><s:basetype optional="true" unbounded="false" typename="string" name="referencedBy_Source" qname="textFragment&gt;referencedBy_Source" /><s:basetype optional="true" unbounded="false" typename="string" name="text" qname="textFragment&gt;text" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="subSet" name="subsetCollection" qname="citation&gt;subsetCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="subSet" name="" qname="{http://webservice.cdb.ebi.ac.uk/}subSet"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="code" qname="subSet&gt;code" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="subSet&gt;name" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="citation&gt;title" /><s:basetype optional="true" unbounded="false" typename="string" name="titleNonAscii" qname="citation&gt;titleNonAscii" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="fullTextURL" name="urlCollection" qname="citation&gt;urlCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="fullTextURL" name="" qname="{http://webservice.cdb.ebi.ac.uk/}fullTextURL"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="availability" qname="fullTextURL&gt;availability" /><s:basetype optional="true" unbounded="false" typename="string" name="availabilityCode" qname="fullTextURL&gt;availabilityCode" /><s:basetype optional="true" unbounded="false" typename="string" name="documentStyle" qname="fullTextURL&gt;documentStyle" /><s:basetype optional="true" unbounded="false" typename="string" name="externalId" qname="fullTextURL&gt;externalId" /><s:basetype optional="true" unbounded="false" typename="string" name="id" qname="fullTextURL&gt;id" /><s:basetype optional="true" unbounded="false" typename="string" name="site" qname="fullTextURL&gt;site" /><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="fullTextURL&gt;source" /><s:basetype optional="true" unbounded="false" typename="string" name="url" qname="fullTextURL&gt;url" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype><s:basetype optional="false" unbounded="false" typename="float" name="score" qname="resultBean&gt;score" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> java.lang.String false input 0 'text/xml' 0 return 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.Invokeemailvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity m.l.taschuk@ncl.ac.uk 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.Invokecorevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity core 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.Invokezerovalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 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.InvokedeXMLerin10out100net.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.InvokeMerge_String_List_to_a_Stringdata1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringListMerge workflow java.lang.String true seperator 0 'text/plain' java.lang.String true data 1 text/plain 0 concatenated 0 UserNameHere 2011-03-30 16:29:15.546 BST UserNameHere 2011-03-30 16:27:49.467 BST UserNameHere 2011-03-30 16:25:55.280 BST UserNameHere 2011-03-30 16:51:40.964 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.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.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.InvokeGet_Target_Filenamegi_num0root0path00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true root 0 text/plain java.lang.String true gi_num 0 text/plain 0 path 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.InvokeHeader_OutputIntro0Sim_M0outPutFile0Title0Sid0Tid0TotalID_d0outputFile00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true Title 0 text/plain java.lang.String true Intro 0 text/plain java.lang.String true Tid 0 text/plain java.lang.String true Sid 0 text/plain java.lang.String true Sim_M 0 text/plain java.lang.String true TotalID_d 0 text/plain java.lang.String true outPutFile 0 text/plain 0 outputFile 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.InvokeGet_HTML_Filenameroot0path00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true root 0 text/plain java.lang.String true gi_num 0 text/plain 0 path 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.InvokeIntro_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Comparison of the genome of <i>Bacillus anthracis</i> to closely related strains will allow the discovery of proteins which may be involved in pathogenicity. Based on the biochemical pathways where the protein interacts, vaccines can be designed for these unique proteins. By gaining insight into the biochemical pathways that the unique proteins are involved in, the proteins can also be assessed for potential quality as vaccines. The key components of the vaccine finding system are the following: The vaccine finding system reads in at least two annotated whole genome sequences in EMBL or GenBank format; the source (non-pathogen) and the target (<i>Bacillus anthracis</i>). At this point, the workflow runs a BlastP search to compare the two strains of bacteria. Assessment of the evolutionary relationship between the two genomes ascertains whether they are closely related enough to derive meaningful comparisons. The vaccine finding system then parses the proteins from the data set that are only coded for in the target genome <i>Bacillus anthracis</i>, giving a new data set of unique proteins which can then be assessed in the KEGG PATHWAY database. The position of the unique proteins in the pathways will give a good indication of the enzymatic role of the proteins in <i>Bacillus anthracis</i>. The vaccine finding system then records its findings in an HTML file, as well as additional information such as annotations from Gene Ontology, functional annotations and literature references. 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.InvokeSim_Measure_Statementthreshold0out100net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true threshold 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.InvokeTitle_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivity A-Team: Vaccine Targets Analysis 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.InvokeWrite_Protein_HTMLGO0InterPro0PubMed0KPI0KDiagram0Title0input0Tid0output100net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true Tid 0 text/plain java.lang.String true TSpecies 0 text/plain java.lang.String true Sid 0 text/plain java.lang.String true SSpecies 0 text/plain java.lang.String true KPI 0 text/plain java.lang.String true input 0 text/plain java.lang.String true KDiagram 0 text/plain java.lang.String true GO 0 text/plain java.lang.String true InterPro 0 text/plain java.lang.String true PubMed 0 text/plain java.lang.String true OC_R 0 text/plain java.lang.String true Title 0 text/plain java.lang.String true OS 0 text/plain 0 output1 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.InvokeMerge_String_List_to_a_String_5stringlist1concatenated00net.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.InvokeFilename_SHIMfilename0uniprot1uniprot_ids11filenames11net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true filename 0 text/plain java.lang.String true uniprot 1 text/plain 1 filenames 1 1 uniprot_ids 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.InvokeExtract_proteins_using_a_gi_2id1fasta_file_path0net.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 3 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Source_Filenamegi_num0root0path00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true root 0 text/plain java.lang.String true gi_num 0 text/plain 0 path 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.InvokeWrite_Text_Filefilecontents0outputFile0net.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 0 'text/plain' 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_Blast_Filenameroot0source_gi_num0target_gi_num0path00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true root 0 text/plain java.lang.String true source_gi_num 0 text/plain java.lang.String true target_gi_num 0 text/plain 0 path 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.InvokeGet_EMBL_IDsthresholded_blast0embl_ids00net.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.InvokeWorkflow27blast_file0overallSimilarity00net.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.InvokeMerge_String_List_to_a_String_3stringlist1concatenated00net.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.InvokeExtract_proteins_using_a_giidTarget_GIExtract_proteins_using_a_gifasta_file_pathGet_Target_FilenamepathMicrobase_BlastPsubjectURLGet_Source_Fasta_Urlurl_stringMicrobase_BlastPqueryURLGet_Target_Fasta_Urlurl_stringGet_Source_Fasta_Urlcontents_fileGet_Source_FilenamepathGet_Target_Fasta_Urlcontents_fileGet_Target_FilenamepathString_to_listin1Get_EMBL_IDsembl_idsFind_Unique_ProteinsblastFileGet_Blast_FilenamepathFind_Unique_ProteinstfastaExtract_proteins_using_a_gifile_outputKEGG_ResultsUniprot_idsFlatten_ListoutputlistGet_Uniprot_DataSearchTermString_to_listout1get_identifiers_from_uniprotparsed_uniprotGet_Uniprot_Dataparsed_dataget_identifiers_from_uniprotidentifier_nameAC_identifiervalueGene_Ontology_Resultsparsed_uniprotGet_Uniprot_Dataparsed_dataInterPro_Resultsparsed_uniprotGet_Uniprot_Dataparsed_dataget_identifiers_from_uniprot_2_2identifier_namePubMedvalueget_identifiers_from_uniprot_2_2parsed_uniprotGet_Uniprot_Dataparsed_datasearchCitationsparameterssearchCitations_inputoutputsearchCitations_inputluceneQueryStringget_identifiers_from_uniprot_2_2out1searchCitations_inputemailemailvaluesearchCitations_inputoutputFormatcorevaluesearchCitations_inputoffSetzerovaluesearchCitations_outputinputsearchCitationsparametersdeXMLerin1searchCitations_outputreturnMerge_String_List_to_a_StringdatadeXMLerout1Flatten_Listinputlistget_identifiers_from_uniprotout1Merge_String_List_to_a_String_2stringlistKEGG_Resultspathway_descriptionsGet_Target_Filenamegi_numTarget_GIGet_Target_Filenamerootroot_directoryHeader_OutputIntroIntro_valuevalueHeader_OutputSim_MSim_Measure_Statementout1Header_OutputoutPutFileGet_HTML_FilenamepathHeader_OutputTitleTitle_valuevalueHeader_OutputSidSource_GIHeader_OutputTidTarget_GIHeader_OutputTotalID_dMerge_String_List_to_a_String_3concatenatedGet_HTML_Filenamerootroot_directorySim_Measure_StatementthresholdWorkflow27overallSimilarityWrite_Protein_HTMLGOGene_Ontology_ResultsGO_ResultsWrite_Protein_HTMLInterProInterPro_ResultsEB_Eye_ResultsWrite_Protein_HTMLPubMedMerge_String_List_to_a_StringconcatenatedWrite_Protein_HTMLKPIMerge_String_List_to_a_String_2concatenatedWrite_Protein_HTMLKDiagramMerge_String_List_to_a_String_5concatenatedWrite_Protein_HTMLTitleFilename_SHIMuniprot_idsWrite_Protein_HTMLinputFilename_SHIMfilenamesWrite_Protein_HTMLTidGet_Uniprot_Dataparsed_dataMerge_String_List_to_a_String_5stringlistKEGG_ResultsURLFilename_SHIMfilenameGet_HTML_FilenamepathFilename_SHIMuniprotFlatten_ListoutputlistExtract_proteins_using_a_gi_2idSource_GIExtract_proteins_using_a_gi_2fasta_file_pathGet_Source_FilenamepathGet_Source_Filenamegi_numSource_GIGet_Source_Filenamerootroot_directoryWrite_Text_FilefilecontentsMicrobase_BlastPBlastReportWrite_Text_FileoutputFileGet_Blast_FilenamepathGet_Blast_Filenamerootroot_directoryGet_Blast_Filenamesource_gi_numSource_GIGet_Blast_Filenametarget_gi_numTarget_GIGet_EMBL_IDsthresholded_blastFind_Unique_Proteinsunique_identifiersWorkflow27blast_fileMicrobase_BlastPBlastReportMerge_String_List_to_a_String_3stringlistFind_Unique_Proteinsunique_identifiersprotein_idsGet_Uniprot_Dataparsed_dataNCBIGitoKeggPathways_pathway_descriptionsMerge_String_List_to_a_String_2concatenatedGO_output_2Gene_Ontology_ResultsGO_ResultsNCBIGitoKeggPathways_URLKEGG_ResultsURLInterProInterPro_ResultsEB_Eye_ResultsPubMed_Results_2Merge_String_List_to_a_StringconcatenatedoutHeader_OutputoutputFileout_2Write_Protein_HTMLoutput1 531a8205-e72e-4a14-b99e-d72154909b92 2011-03-31 20:50:26.494 BST 4a513a74-4ff9-43e4-b869-e48ac1ac8ac5 2011-04-01 11:57:24.815 BST 627bcf2b-9512-4e79-9f6b-470f3910b765 2011-03-31 22:53:29.457 BST b485a670-0c3e-4b3b-b0e8-9c969011217f 2011-03-30 20:05:24.997 BST b7314f4a-d93a-4582-b782-a1aef5b386f2 2011-03-25 15:22:44.991 GMT 5c7ab668-f89d-4da0-a35a-8f08cf5348a6 2011-03-30 20:28:06.400 BST b44d1586-4b9f-46e8-84e1-8bc9f901faa3 2011-03-31 23:45:25.780 BST 2c17cf54-dbb3-42e5-8e1e-ee7d0360b768 2011-03-31 17:38:23.5 BST faee7798-f653-4d07-b6bb-1c4e71e4222e 2011-04-01 11:27:03.849 BST 781051a8-81d5-4b14-9e4c-09c95ad8c9f8 2011-04-01 00:21:45.475 BST c8ffe6bc-0577-4a7a-8f5a-5a29d311f809 2011-03-30 20:25:19.255 BST fc0f8722-ba6e-43bb-b1dd-0c2444028c30 2011-04-01 10:36:43.985 BST 6353f76e-d241-4b18-910a-d4d19ec2ed71 2011-03-31 21:25:39.593 BST 806afaae-4232-4141-97af-5dbd5a437fa3 2011-04-01 02:57:41.919 BST 882b7448-8cd8-4abc-9474-168d797ade7e 2011-04-01 01:54:29.114 BST d009369e-c283-403f-9b0e-f0554631e1da 2011-03-31 23:47:20.574 BST 50b9c052-1ee1-423b-bc8c-05eeb82d39f2 2011-03-30 10:42:56.949 BST a149bb84-02f1-4295-a75b-ed7282796efd 2011-03-31 17:32:24.433 BST 40ee0320-dc68-48e4-9ff8-2a8be39a3308 2011-03-31 21:48:34.121 BST efe69d39-5ebc-4cd6-9102-ef61d7a3913e 2011-03-30 10:47:51.219 BST 08be2a06-ae0a-47c6-a0ec-306b17161c36 2011-03-31 15:42:08.915 BST f93a61d2-330c-4418-a4bf-31434b3298b3 2011-03-31 23:55:41.429 BST 8f8386df-6385-453c-9550-9c24583c9249 2011-03-28 13:56:08.131 BST f6558964-cc08-45b1-8ead-2700014d51df 2011-03-25 19:11:46.295 GMT 595cc410-b061-4ba6-967d-9fe586132561 2011-03-31 23:51:38.227 BST 299440f3-f6cb-4917-90a8-f9e27b4f9792 2011-03-30 20:34:33.670 BST daf61cd4-8796-4f36-bc20-e765960d9f4b 2011-03-31 19:23:55.564 BST c50df741-8cbb-402a-a3aa-ce106a8a622b 2011-04-01 01:54:00.923 BST 71f23402-77b6-4c3e-bbea-d07686d36de9 2011-03-31 20:25:08.531 BST 7cd5bdbd-66f3-4c98-9367-7126756d2f54 2011-04-01 00:51:28.171 BST dc46f972-c7a8-409d-993a-7c3edb1e504c 2011-04-01 11:54:48.474 BST ff808d5b-0681-427f-b2a3-90f89b5b9128 2011-03-31 22:49:45.469 BST 5c4c34f7-7cea-4ace-9973-4051ecb08c85 2011-03-31 23:18:50.41 BST 63826d21-9052-48ee-9725-0f828b9c6875 2011-03-31 23:57:29.611 BST 1d3a29d6-0fa8-43ab-b83a-fcad500c3a34 2011-03-31 20:40:24.959 BST b45c784f-e7d7-41e2-a19f-84365ccc64e5 2011-04-01 00:56:47.15 BST 40329737-b8f1-41ed-839c-27d919202a35 2011-03-31 20:05:43.488 BST Comparison of the genome of <i>Bacillus anthracis</i> to closely related strains will allow the discovery of proteins which may be involved in pathogenicity. Based on the biochemical pathways where the protein interacts, vaccines can be designed for these unique proteins. By gaining insight into the biochemical pathways that the unique proteins are involved in, the proteins can also be assessed for potential quality as vaccines. The key components of the vaccine finding system are the following: The vaccine finding system reads in at least two annotated whole genome sequences in EMBL or GenBank format; the source (non-pathogen) and the target (<i>Bacillus anthracis</i>). At this point, the workflow runs a BlastP search to compare the two strains of bacteria. Assessment of the evolutionary relationship between the two genomes ascertains whether they are closely related enough to derive meaningful comparisons. The vaccine finding system then parses the proteins from the data set that are only coded for in the target genome <i>Bacillus anthracis</i>, giving a new data set of unique proteins which can then be assessed in the KEGG PATHWAY database. The position of the unique proteins in the pathways will give a good indication of the enzymatic role of the proteins in <i>Bacillus anthracis</i>. The vaccine finding system then records its findings in an HTML file, as well as additional information such as annotations from Gene Ontology, functional annotations and literature references. 2011-03-31 23:46:02.101 BST 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. 2011-03-31 22:53:28.880 BST 2b36819c-4f4a-45f2-996c-e02cda810018 2011-03-31 16:41:25.315 BST Vaccine Targets Workflow 2011-03-31 23:46:11.901 BST Drug Re-Purposing Workflow 2011-03-31 22:53:13.693 BST UniProt_ID_to_Kegg_PathwaysUniprot_ids00 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 215422388 2011-03-25 18:07:46.275 GMT text/plain 2010-03-15 17:26:56.908 GMT A8YYV3 2011-04-01 11:48:34.917 BST The UniProt identifier of the gene of interest. 2011-04-01 11:46:15.448 BST 2010-03-15 17:26:56.908 GMT imports gi numbers to be used by the workflow to create the pathways 2010-03-19 03:48:31.724 GMT KEGGID text/plain 2010-03-15 17:26:56.908 GMT kegg ids 2010-03-19 03:50:43.170 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 pathway ids and corresponding pathways descriptions 2010-03-19 03:51:25.813 GMT text/plain 2010-03-15 17:26:56.908 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_pathwaysstringlistget_pathways_by_genesreturnmerge_pathways_2stringlistRemove_duplicate_pathwaysstrippedlistmerge_descriptionsstringlistbtitreturnRemove_duplicate_pathwaysstringlistmerge_pathwaysconcatenatedbtitstringextract_gene_idsoutputbtit1stringmerge_pathwaysconcatenatedbconvstringadd_uniprot_to_stringoutputremove_Nullsinputmerge_descriptionsconcatenatedextract_gene_idsinputFlatten_Listoutputlistremove_nulls_2inputmerge_pathways_2concatenatedadd_uniprot_to_stringinputUniprot_idsGet_image_from_URLurlcolor_pathway_by_objects_2returncolor_pathway_by_objects_2pathway_idsplit_by_regex_2splitcolor_pathway_by_objects_2bg_color_listpinkvaluecolor_pathway_by_objects_2fg_color_listpurplevaluecolor_pathway_by_objects_2object_id_listFlatten_List_3outputlistsplit_by_regex_2regexregex_2valuesplit_by_regex_2stringremove_nulls_2outputsplit_by_regexregexregexvaluesplit_by_regexstringextract_gene_idsoutputget_pathways_by_genesgenes_id_listsplit_by_regexsplitFlatten_ListinputlistbconvreturnFlatten_List_3inputlistsplit_by_regexsplitKEGGIDextract_gene_idsoutputpathway_by_genesremove_nulls_2outputpathway_descriptionsbtit1returnkegg_descriptionsremove_NullsoutputURLcolor_pathway_by_objects_2returnimageGet_image_from_URLimage 446598ae-de47-4e9a-af0a-e192c2cb3b26 2011-04-01 11:48:37.376 BST a110afdb-d845-4164-8b6a-49f76cfb514d 2011-03-31 11:19:46.601 BST 1495f977-2aeb-4ca7-a79d-e9aa9472af27 2011-03-25 18:08:37.965 GMT f38c6560-baaa-400e-be8a-b02171e13db0 2011-03-31 15:02:01.586 BST 31e58e2c-47a8-4ed4-a7ab-c6b8d1d67149 2011-03-31 14:42:16.155 BST 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 17596066-d978-42f2-a5a1-3082300be8ea 2011-03-31 11:14:43.208 BST c2ab2676-5a31-4889-9913-0601a8f0e238 2011-03-31 13:58:25.963 BST Retrieves pathway information, pathway images (with genes highlighted in pink) and URLs, the KEGG ID and descriptions using UniProt Identifiers. Runs faster than previous versions with larger input sets by flattening the list several time. 2011-04-01 11:45:54.518 BST 94c3b907-cb48-438b-bb8e-c64463e1303c 2011-04-01 11:46:39.891 BST 3542735a-febb-4b90-af1d-7571fa36d73e 2011-03-28 12:03:17.584 BST Paul Fisher 2010-03-15 17:26:56.962 GMT NCBI Gi to Kegg Pathways 2010-03-15 17:26:56.962 GMT 2011-04-01 11:44:03.421 BST b9b894bb-350e-47f2-81ba-e076e9f50608 2011-03-31 13:57:42.749 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 d5d0df3b-2ac7-4a8d-85ce-223e0ff17132 2011-03-25 17:57:31.266 GMT UniProt ID to Kegg Pathways 2011-04-01 11:43:57.585 BST d456be95-e8be-419b-a86e-fa54751ae1b0 2011-03-31 14:50:44.6 BST Retrieves pathway information, pathway images (with genes highlighted in pink) and URLs, the KEGG ID and descriptions using UniProt Identifiers. Runs faster than previous versions with larger input sets by flattening the list several times. 2011-04-01 11:45:58.44 BST aeba0128-e6e4-4246-8da0-b816c51b62cc 2011-03-31 11:57:51.849 BST nclteamc and Paul Fisher 2010-03-19 03:46:54.347 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 Extract_EMBL_Ids_from_BLASTthresholded_blast00 Tab-delimited BLAST results. 2011-04-01 11:38:49.491 BST File : C:\myblast.blast 2011-04-01 11:39:11.736 BST Tab-delimited BLAST results. Add as file location. 2011-04-01 11:38:57.38 BST embl_idsextract_embl_from_blastunique_identifiers0out100net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true unique_identifiers 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.Invokeextract_embl_from_blastunique_identifiersthresholded_blastembl_idsextract_embl_from_blastout1 df44d724-29e3-4388-9ad7-c91b3c155448 2011-03-28 14:23:43.718 BST 9da54ff9-666e-4b37-9b51-4253ce2aa4e3 2011-03-28 14:15:58.425 BST d59fa6cd-cf4d-4c4e-969b-2aaa6e715cb0 2011-03-28 14:17:58.13 BST 7ecb3fae-7fa0-4a8e-9be2-0249d0d93c85 2011-03-28 14:06:16.349 BST Extract EMBL Ids from BLAST 2011-04-01 11:35:52.859 BST Returns the EMBL ids from a tab-delimited FASTA file (retrieved from the GenBank file). 2011-04-01 11:36:42.612 BST 2ee1bf16-50b0-43d9-a017-33d197bdced9 2011-03-28 16:48:23.946 BST 8d2027c6-c223-4e1c-a388-a9a76d1fe9a1 2011-03-28 16:47:49.242 BST 685f9123-2cda-440d-bddc-56c89ff31a2a 2011-03-28 14:19:20.984 BST 61754d49-84e4-465f-bb1b-14932249c169 2011-03-28 16:43:03.711 BST fc421123-fbb0-4793-9d33-6144808b1a63 2011-03-28 16:46:55.748 BST fed9062a-2a7d-4f65-bd56-6192178619f4 2011-03-28 14:21:28.705 BST b0f93f0d-7821-4056-a53f-07961afb4264 2011-03-28 16:56:29.848 BST c2d1d84b-5fe7-44f7-8623-be156fdb7022 2011-03-28 14:24:09.153 BST bdc2723f-dc2c-48e1-ac6c-8cacd3da705d 2011-03-28 14:17:17.190 BST 97ca9486-2650-4c74-8fed-55434ecfcb5f 2011-03-28 14:22:49.653 BST c149a342-53fe-4a09-ad40-fbb63a4a525a 2011-03-29 18:44:24.857 BST 7fc42d35-5cce-471c-97da-98bbef355bc5 2011-03-28 14:11:24.932 BST 947351f6-7bd1-4045-a085-20ac5321adb9 2011-03-28 16:45:50.692 BST 98909241-55c4-432e-b98c-88852aad7c02 2011-03-31 23:18:42.548 BST 17305750-742e-4a5e-8e90-5c2428445012 2011-03-28 16:57:30.14 BST ab1440e1-4318-4124-adc4-2288c3bc6101 2011-03-28 14:14:35.23 BST 84eb7e30-96bb-4aaf-bf80-449579424f0b 2011-03-28 14:13:10.264 BST 3aab4589-ed9a-47f1-9bd1-286581af7f22 2011-03-28 14:12:25.862 BST cf58c3d7-d887-4d76-ae34-88c1c8db722e 2011-03-28 14:20:09.898 BST a02d4f7b-c8cf-4d4b-928c-ba1a261b55d2 2011-03-28 16:44:55.235 BST e07c0f89-8abe-4fba-9c4b-09969b7c5e8c 2011-03-28 14:08:00.146 BST c58ba6c6-bca5-4037-a14c-227dd20ef335 2011-04-01 11:36:42.674 BST 031fa9b7-183c-499a-b269-f3b8faf12752 2011-03-28 14:06:55.834 BST 19c5e68c-d782-48bb-9e23-c1231a2d1b4e 2011-04-01 11:39:11.814 BST 1ae5ea65-68cb-47b1-9f19-dd02451f0981 2011-03-28 14:10:13.533 BST Extract_unique_proteins_from_blast_resultsblastFile00 The URL or file path location of the tab-delimited format of the Blast results. Type the path as a string (not a file location). 2011-03-24 15:20:55.164 GMT inputs the xml format of the blast results 2010-03-19 03:21:20.950 GMT C:\Users\You 2011-03-24 15:20:32.41 GMT The URL or file path location of the tab-delimited format of the Blast results. Type the path as a string (not 2011-03-24 15:20:42.61 GMT C:\Users\You\Documents\my_blast_results.tab 2011-03-24 15:21:18.503 GMT The URL or file path location of the tab-delimited format of the Blast results. 2011-03-24 15:20:06.729 GMT tfasta00 Fasta file of the target proteins to extract the sequences. Add as file location. 2011-03-24 15:21:53.195 GMT Fasta file of the target proteins to extract the sequences. 2011-03-24 15:21:32.450 GMT File : C:\Users\You\Documents\target_fasta.faa 2011-03-24 15:22:34.14 GMT fasta file of the target proteins to extract the sequences 2010-03-19 03:19:27.444 GMT File 2011-03-24 15:21:59.270 GMT unique_identifiers Unique identifiers that appear in the FASTA file but not in the BLAST file. Identifiers are separated by new lines. 2011-03-24 15:28:07.208 GMT gi|321313668|ref|YP_004205955.1| gi|321312432|ref|YP_004204719.1| gi|321314996|ref|YP_004207283.1| 2011-03-24 15:28:18.998 GMT blasted_identifiers Identifiers of the target genome from the BLAST results. These identifiers are those that are similar to the source proteome. 2011-03-24 15:26:18.245 GMT gi|321313668|ref|YP_004205955.1| gi|321312432|ref|YP_004204719.1| gi|321314996|ref|YP_004207283.1| 2011-03-24 15:27:27.684 GMT Read_Text_Filefileurl0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.TextFileReader workflow java.lang.String true fileurl 0 'text/plain' 0 filecontents 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.Invokeextract_blast_idsxml_result0gi_lines_val00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true xml_result 0 text/plain 0 gi_lines_val 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.Invokefind_unique_proteinsgi_val0tfasta_in0cfasta_out00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true gi_val 0 text/plain java.lang.String true tfasta_in 0 text/plain 0 cfasta_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 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_FilefileurlblastFileextract_blast_idsxml_resultRead_Text_Filefilecontentsfind_unique_proteinsgi_valextract_blast_idsgi_lines_valfind_unique_proteinstfasta_intfastaunique_identifiersfind_unique_proteinscfasta_outblasted_identifiersextract_blast_idsgi_lines_val 737d3624-b4d2-4a08-b274-cc14742bce4c 2011-03-29 17:38:42.291 BST fetchEnsemblSeqsAndBlast 2010-03-15 11:30:59.109 GMT cc480ca8-ff58-4ff6-9949-17d47f4449ac 2011-03-29 17:40:41.746 BST nclteamc 2010-03-19 03:15:57.858 GMT 93e32a3d-4e18-465b-8d3f-d2705d281a24 2011-03-29 17:44:59.100 BST Bela Tiwari 2010-03-15 11:30:59.109 GMT Workflow outputs a list of proteins encoded by the target genomes that do not have sequences similarity to those encoded by the source genome 2010-03-19 03:18:26.823 GMT c39cf70b-850d-4f5a-a83e-d6570a9c468c 2011-03-28 11:10:21.821 BST 8dd7abc2-2a03-403f-b241-90fe56b28a30 2011-04-01 11:33:12.635 BST 9adf3d21-e3ce-44cb-b1d1-f58b89a7045d 2011-03-29 18:02:43.52 BST 782c8659-5afb-4518-a8c3-0376a0884816 2011-03-24 13:52:32.878 GMT 7045bed3-10bd-4d68-9c66-0135b0ed2dde 2011-03-24 15:28:27.232 GMT 63e1f905-8094-472f-9564-694024af6d41 2011-03-29 17:51:04.462 BST This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you. Shortcomings: The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created. All files created in the working directory are not yet coded to be deleted via the workflow. Ideally there would be an option that a user could choose that would set the files to be kept or deleted after use. 2010-03-15 11:30:59.109 GMT af914252-ebc4-432f-992e-e2b0d39017f9 2011-03-29 17:39:30.204 BST 60c8aba2-6a4b-4c8c-b66a-bbbf02104f94 2011-03-29 17:56:11.11 BST 4626edc0-7e50-4e5d-8b94-7a2dfcd25175 2011-03-29 17:43:35.769 BST 133c1ed5-3710-4e6a-956e-265beacfa6c4 2011-03-28 11:06:19.156 BST 498004e2-20fa-4e68-beb8-c37363ed1d7c 2011-03-29 19:06:48.198 BST The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created. 2010-03-19 03:23:47.653 GMT The workflow parses uses the tab-delimited BLAST results to determine the unique proteins found in the target genome that have no similarity to the source genome. 2011-04-01 11:32:55.135 BST A-Team 2011-04-01 11:32:13.835 BST 1b646021-1281-4a60-87d2-30ff347c440e 2011-03-29 17:32:31.887 BST b2579890-b32e-4be4-975b-28659feea68f 2011-03-24 13:12:29.54 GMT 4de394ba-bb1d-40bb-9091-6814ed44a022 2011-03-29 18:03:07.210 BST Extract unique proteins from blast results 2010-03-19 03:16:29.89 GMT c1f4908c-1669-4b80-bba1-13a2024ef9f4 2011-03-25 19:44:27.821 GMT 150d4e84-1ab0-445e-a68f-59c9520fcb13 2011-03-29 18:00:45.354 BST a3deee76-a760-4d32-a267-c6b198eafc6f 2011-03-29 17:31:59.467 BST 8192e733-05b6-4855-9246-997adf9d9da8 2011-03-25 20:01:56.11 GMT 0bf98650-2884-406a-98a0-557f9de13e1c 2011-03-29 17:35:46.991 BST 4d837fd7-5124-4e7c-964b-17de794236cc 2011-03-24 15:25:33.719 GMT 2010-03-19 03:14:00.733 GMT 6d6d19ae-76d8-4e21-a247-3a200324d0be 2011-03-29 18:05:10.408 BST 3bf00d4e-1435-4e32-b252-cd4db7d34aa4 2011-03-29 17:30:29.191 BST 407de167-b803-49a3-8d88-330ea6dad2cd 2011-03-29 17:53:15.739 BST 07a797c2-caa6-48b9-bbde-148dfc94b6bd 2011-03-29 17:51:41.951 BST b066272d-8732-4505-a7b1-aa424a011c42 2011-03-29 17:37:52.118 BST EBI_OLS_TermInfoOntology_Id00 Ontology term identifier to retrive information about. For example: GO:0008150. 2011-03-30 10:54:12.634 BST text/plain 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}&gt;getTermMetadata&gt;termId" /><s:basetype optional="false" unbounded="false" typename="string" name="ontologyName" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}&gt;getTermMetadata&gt;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}&gt;getTermMetadataResponse&gt;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&gt;key" /><s:basetype optional="false" unbounded="false" typename="anyType" name="value" qname="{http://xml.apache.org/xml-soap}mapItem&gt;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_parametersoutputInput_parameterstermIdOntology_IdInput_parametersontologyNameGOvalueUnwrap_resultinputgetTermMetadataparametersOntology_termUnwrap_resultgetTermMetadataReturn 4eaf1d8b-b3dc-478f-8337-bc4213714abb 2011-03-30 10:54:12.741 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 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 Hamish McWilliam 2011-03-30 10:54:12.659 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}&gt;getEntry&gt;domain" /><s:basetype optional="false" unbounded="false" typename="string" name="entry" qname="{http://www.ebi.ac.uk/EBISearchService}&gt;getEntry&gt;entry" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="fields" qname="{http://www.ebi.ac.uk/EBISearchService}&gt;getEntry&gt;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}&gt;getEntryResponse&gt;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}&gt;listFields&gt;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}&gt;listFieldsResponse&gt;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_inputoutputgetEntry_inputentryEntry_IdgetEntry_inputfieldslistFields_outputarrayOfFieldNamesgetEntry_inputdomainDomaingetEntry_outputinputgetEntryparameterslistFieldsparameterslistFields_inputoutputlistFields_inputdomainDomainlistFields_outputinputlistFieldsparametersConcatenate_two_stringsstring1listFields_outputarrayOfFieldNamesConcatenate_two_stringsstring2getEntry_outputentryValuesgetEntry_output_entryValuesConcatenate_two_stringsoutput fac4bed3-abac-4864-8df7-8c97c5d9faba 2011-03-28 18:22:17.369 BST 28d4438b-5326-4ec1-9c46-1ee3b08cb23b 2011-03-28 19:08:29.809 BST 4cc17549-3f52-4a93-adb4-52746c2e31a3 2011-03-28 19:12:01.629 BST 4db4c4e5-4f28-448c-8ab8-ab579454d6ee 2011-03-28 18:27:54.841 BST 5d320077-d00d-48c4-ad88-009a51fd10a1 2011-03-28 18:25:30.628 BST 6dc968df-61ce-43fe-b497-5701fa930ff4 2011-03-30 16:39:39.780 BST 3cc20f68-58e9-4f62-ac8b-4f78e3814906 2011-03-28 18:55:42.38 BST 6d71ee52-0f98-499a-b48d-ea6586d334b9 2011-03-28 19:11:45.502 BST 0ff56878-b4d2-4b72-b768-ecfa14497393 2011-03-28 18:57:50.617 BST a8e6c66a-2319-47dd-9b2b-cf4642a180be 2011-03-28 19:07:07.123 BST Use_UniProt_to_retrieve_InterPro_dataparsed_uniprot00 The file location of the parsed Uniprot file (see http://www.myexperiment.org/workflows/26.html). 2011-04-01 11:53:45.625 BST EB_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 1000 5000 0 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 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.Invoketo_Lower_Case_2in10out100net.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.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 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 16:29:15.546 BST UserNameHere 2011-03-30 16:25:55.280 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_Idget_identifiers_from_uniprot_2_2out1InterPro_ResultsDomainto_Lower_Case_2out1get_identifiers_from_uniprot_2_2parsed_uniprotparsed_uniprotget_identifiers_from_uniprot_2_2identifier_nameInterProvalueto_Lower_Case_2in1InterProvalueMerge_String_List_to_a_Stringgo_idsget_identifiers_from_uniprot_2_2out1Merge_String_List_to_a_Stringgo_defsMerge_String_List_to_a_String_2concatenatedMerge_String_List_to_a_String_2stringlistInterPro_ResultsgetEntry_output_entryValuesEB_Eye_ResultsMerge_String_List_to_a_Stringconcatenated ef9de97c-ca76-479e-b933-d396f043e138 2011-03-28 16:39:02.585 BST 4ed40fd8-b13c-4aa2-8977-329988763674 2011-03-28 17:56:58.784 BST f5c68892-7c8c-4bba-96cf-6e4094272de2 2011-03-28 18:51:46.105 BST 427f85e8-da08-4e29-800f-8479992b79e5 2011-03-30 16:48:37.456 BST fda20a14-917b-454a-a88e-4d4cf58e24c6 2011-03-28 18:34:50.789 BST 2c33a9b5-8e1e-449a-9bf3-07b1ad48beab 2011-03-30 16:41:33.953 BST 2a76c6a1-b3d1-4ca2-9459-ddf394593250 2011-04-01 11:53:46.891 BST 2011-04-01 11:51:41.635 BST Untitled workflow #14 2011-03-28 16:28:59.317 BST eccaf02b-b85b-4894-9974-c4c49a168673 2011-03-30 16:40:30.44 BST 3117ba0d-f09f-4956-ad74-7761dbf998d9 2011-03-28 19:18:13.311 BST Use UniProt to retrieve InterPro data 2011-04-01 11:51:41.323 BST 9fedbdd2-dde5-4b08-ab50-80991ea7c41c 2011-03-28 18:55:56.909 BST Used parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from InterPro. 2011-04-01 11:53:15.420 BST f5b50570-afa2-4768-a298-a7bd35e90e11 2011-03-28 19:28:47.180 BST 5bc429c4-927b-4d7e-b4c8-9f8cd17838b7 2011-03-30 17:22:18.272 BST 416a5592-70f9-4c5f-af15-397bd21af3cb 2011-03-28 19:15:54.482 BST Used parsed Uniprot results (see workflow 2011-04-01 11:52:07.242 BST 33afbd5c-d9a6-4e58-a255-ac744742875a 2011-03-28 18:38:03.893 BST 5f08104a-de65-423f-b532-dc7eb89c28ce 2011-03-28 16:39:56.913 BST 2011-03-28 16:28:59.317 BST 7b3873e1-cd30-4e5c-ab3a-4e0178648eb6 2011-03-30 16:43:19.253 BST 2011-03-28 16:28:59.317 BST ff900e9f-7b8d-43fc-be47-cc638b4266d4 2011-03-28 19:00:51.178 BST 7f7920cf-259e-4947-8a28-bbd0bf0d5de4 2011-03-28 18:59:44.143 BST 11d4d655-87f9-4a31-88f1-eef56a3a03ee 2011-03-28 16:58:53.309 BST acd0a40b-a688-473f-8618-1bdbd2046096 2011-03-28 16:33:17.871 BST 7ae7f0a1-1f28-48e1-8c41-7c6da1587e3d 2011-03-28 16:34:34.815 BST 6845039f-9b62-49dc-ac9d-8ba4deeafde0 2011-04-01 11:53:15.561 BST 2011-04-01 11:51:09.357 BST d7ce24f5-f65b-4b2b-8500-6d35cf027d1c 2011-03-28 19:02:12.80 BST 1752f7dd-badb-4e4a-a2f1-d50327f80d60 2011-03-30 16:46:50.149 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 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&gt;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&gt;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&gt;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&gt;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&gt;subjectFileId" /><s:basetype optional="true" unbounded="false" typename="string" name="queryFileId" qname="submitBlastPJob&gt;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&gt;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&gt;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&gt;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.InvokeaquireSubjectFileparametersSubjectUrlInputoutputSubjectUrlInputurlsubjectURLsubjectFileIDinputaquireSubjectFileparametersaquireQueryFileparametersQueryUrlInputoutputQueryUrlInputurlqueryURLqueryFileIDinputaquireQueryFileparameterssubmitBlastPJobparameterssubmitBlastPJob_inputoutputsubmitBlastPJob_inputsubjectFileIdsubjectFileIDreturnsubmitBlastPJob_inputqueryFileIdqueryFileIDreturnJobIDinputsubmitBlastPJobparametersAwaitJobCompletionJobIDJobIDreturngetBlastReportparametersgetBlastReport_inputoutputgetBlastReport_inputjobIdJobIDreturngetBlastReport_outputinputgetBlastReportparametersJobIDOutputJobIDreturnBlastReportgetBlastReport_outputreturnFinalStatusAwaitJobCompletionStatus 5ce9aec8-494f-45dd-a978-3d7156430652 2011-03-16 14:42:27.305 GMT cd88505f-a3f1-4bde-af4a-aa287edf5642 2011-03-16 17:04:35.157 GMT 573e2324-2806-494a-8127-37eda623cd97 2011-03-18 11:45:08.987 GMT ec74ad83-bc35-4801-9f1a-5895a07707a4 2011-03-16 17:11:23.916 GMT 63f00396-c32e-4320-a732-6c682f2464fb 2011-03-16 19:07:15.429 GMT 78ba349d-a426-46bb-b842-57cad76582ef 2011-03-18 12:22:51.796 GMT 4d26090f-0bef-4024-ba16-8a69f3690998 2011-03-16 22:52:59.767 GMT 14b5dde3-dfd6-4c04-b254-78c13051998a 2011-03-16 19:38:23.32 GMT 00226a02-118c-419e-96df-2dd8869cbfa0 2011-03-16 16:51:12.261 GMT a2f6d3f7-262b-47b5-9fd1-e191935a19a9 2011-03-16 17:07:31.320 GMT e0a458bb-2f5c-43e7-b582-745c970a1966 2011-03-16 17:41:03.200 GMT f5981737-10a0-4fc4-9672-3130a03656ab 2011-03-16 17:40:41.255 GMT 3b70d4ae-354f-477e-a277-41712da51770 2011-03-16 17:31:43.390 GMT 660f7075-7cd0-4c7c-8240-5ef305e3d081 2011-03-16 17:39:20.697 GMT e9287f94-ee6e-483b-8c8b-5284afc5213e 2011-03-16 15:34:27.528 GMT 71ce1c05-e453-4cab-b2e1-ee49bb4534dc 2011-03-16 14:28:03.443 GMT 66e94c9e-a25e-4df1-bcf9-988548430342 2011-03-16 14:29:06.933 GMT 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 16:25:55.280 BST UserNameHere 2011-03-30 16:29:15.546 BST UserNameHere 2011-03-30 16:27:49.467 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_uniprotparsed_uniprotget_identifiers_from_uniprot_2_2identifier_nameGOvalueEBI_OLS_TermInfoOntology_Idget_identifiers_from_uniprot_2_2out1GO_deXMLerin1EBI_OLS_TermInfoOntology_termMerge_String_List_to_a_Stringgo_defsGO_deXMLerout1Merge_String_List_to_a_Stringgo_idsget_identifiers_from_uniprot_2_2out1GO_ResultsMerge_String_List_to_a_Stringconcatenated 2011-03-30 16:14:48.557 BST c88315af-4ce4-43fb-b48d-45cc0e9424b2 2011-03-28 18:57:59.270 BST Used parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from Gene Ontology and outputs it in text format. 2011-04-01 11:55:40.31 BST 0523fd65-210c-421c-a12d-86216a61de19 2011-03-30 16:14:43.704 BST 9fedbdd2-dde5-4b08-ab50-80991ea7c41c 2011-03-28 18:55:56.909 BST 9e103ba0-8dce-4f23-a7f4-165bd80a8f93 2011-03-30 10:56:21.121 BST 21781546-1ad8-4dea-81d0-6780a7ec9e66 2011-03-30 16:35:51.793 BST 2011-04-01 11:54:34.135 BST GO Data from GO ID 2011-03-30 16:15:03.966 BST 5f08104a-de65-423f-b532-dc7eb89c28ce 2011-03-28 16:39:56.913 BST a7da9321-f578-410e-93b3-2115c326a8d4 2011-03-30 16:15:18.613 BST 7ae7f0a1-1f28-48e1-8c41-7c6da1587e3d 2011-03-28 16:34:34.815 BST fda20a14-917b-454a-a88e-4d4cf58e24c6 2011-03-28 18:34:50.789 BST acd0a40b-a688-473f-8618-1bdbd2046096 2011-03-28 16:33:17.871 BST d7ce24f5-f65b-4b2b-8500-6d35cf027d1c 2011-03-28 19:02:12.80 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 2011-03-28 16:28:59.317 BST 2011-03-30 16:15:18.518 BST 473b328e-5f9a-4db9-b31a-c868afc8da4c 2011-03-30 10:55:52.642 BST a129e83f-4d68-4d84-bb21-b7b2c29cdab9 2011-03-30 12:01:49.842 BST ef9de97c-ca76-479e-b933-d396f043e138 2011-03-28 16:39:02.585 BST 416a5592-70f9-4c5f-af15-397bd21af3cb 2011-03-28 19:15:54.482 BST 19dbb793-e604-4c3c-82a6-e2fe1be4d084 2011-03-29 11:06:03.489 BST fb843096-2675-4579-9a51-05f43e15ba79 2011-03-28 17:54:29.330 BST Untitled workflow #14 2011-03-28 16:28:59.317 BST 2011-04-01 11:54:33.870 BST 3117ba0d-f09f-4956-ad74-7761dbf998d9 2011-03-28 19:18:13.311 BST 2011-03-28 16:28:59.317 BST bf867204-2ced-4bc2-9c7a-20da8438de9a 2011-04-01 11:55:51.865 BST f5c68892-7c8c-4bba-96cf-6e4094272de2 2011-03-28 18:51:46.105 BST 11d4d655-87f9-4a31-88f1-eef56a3a03ee 2011-03-28 16:58:53.309 BST 73ae7c45-6300-40e1-86c2-5da602996ff8 2011-03-30 10:59:35.473 BST 33afbd5c-d9a6-4e58-a255-ac744742875a 2011-03-28 18:38:03.893 BST 7f7920cf-259e-4947-8a28-bbd0bf0d5de4 2011-03-28 18:59:44.143 BST b4078147-9bbb-45c3-a045-dc6090bf95bb 2011-03-30 11:01:16.668 BST 6ad18fe7-29cc-4cd2-ad50-6b2b62c7be8c 2011-03-30 16:23:46.939 BST e276142b-824b-4fca-94b4-5a7402085b73 2011-03-30 10:59:54.93 BST Determine_Average_Identity_of_BLAST_resultsblast_file00 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.txt 2011-03-28 11:41:26.692 BST File : D:\Workflows\Ours\blast_results 2011-03-28 11:41:21.424 BST overallSimilarityaverage_identityblast_file0out100net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true blast_file 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.Invokeaverage_identityblast_fileblast_fileoverallSimilarityaverage_identityout1 bd3db62e-7772-4c70-b67b-4a264023adbf 2011-03-28 11:44:34.517 BST Determine Average Identity of BLAST results 2011-04-01 11:34:13.83 BST db16decf-8a95-4f1e-b627-e2dd988bbe04 2011-03-28 12:16:57.540 BST c7c15b62-55f3-4568-8f02-e1b8fb351949 2011-03-28 12:17:39.213 BST 90be7e33-afc5-4ecb-82bf-712e2a39bc8d 2011-03-28 11:45:51.374 BST 94985fbf-dde2-47ce-9e29-a7b1b373d6c2 2011-03-28 12:20:14.167 BST 9114a2d0-9f1a-4e01-abe2-1a99fc294929 2011-04-01 11:35:18.232 BST Using a tab-delimited BLAST result, averages the maximum identity for each source protein. Used as a method to compare species or strain similarity. 2011-04-01 11:35:07.169 BST 59b138d5-5cb4-4a34-a8cb-f4dfd035ef8b 2011-03-28 11:42:41.787 BST 29dd4ffc-1662-49c8-85d9-afb9581a70da 2011-03-28 12:04:20.997 BST 6d9879d5-59c9-49d9-8edf-5e5764681977 2011-03-29 18:57:56.789 BST Get_identifiers_from_UniProtSearchTerm00 Search term for UniProt. 2011-04-01 11:40:37.777 BST MecA 2011-04-01 11:40:48.902 BST 2011-03-28 17:43:19.351 BST parsed_datafieldNamevalue00net.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 0 0 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 0 0 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 1000 5000 3 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeparse_uniprotfile_direct_dataUniprot_searchresultUniprot_searchfieldnamefieldNamevalueUniprot_searchsearchtermSearchTermparsed_dataparse_uniprotoutput 2011-04-01 11:41:03.139 BST dc311c4e-25e3-4e86-96f4-b8889e83f3e8 2011-04-01 01:54:27.607 BST b5a6390c-d9bd-4baa-a233-b4e8b03d6a43 2011-04-01 11:42:19.583 BST Get identifiers from UniProt 2011-04-01 11:41:30.876 BST 733461a4-348d-4198-b6ba-899bbf28ba64 2011-03-28 17:43:19.611 BST 2011-03-28 17:43:19.515 BST 2011-03-28 17:43:19.515 BST 2011-04-01 11:41:31.126 BST Untitled workflow #4 2011-03-28 17:43:19.515 BST From a search term, retrieves the complete list of identifiers from UniProt, including GO ids, InterPro ids, PubMed ids, and many more. 2011-04-01 11:42:12.22 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 5000 0 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 0 'text/plain' 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 3 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtraction_of_infoxml_resultGet_Nucleotide_GBSeq_XMLoutputTextWrite_Text_FileoutputFilefasta_file_pathWrite_Text_FilefilecontentsExtraction_of_infofastas_outGet_Nucleotide_GBSeq_XMLididfile_outputWrite_Text_FileoutputFile 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 58b39f65-b805-41ee-b49f-e4803a284183 2011-04-01 00:55:35.727 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&gt;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.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&gt;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_inputoutputgetJobState_inputjobIdJobIDgetJobState_outputinputgetJobStateparametersStatusgetJobState_outputreturn 4e01e2d8-674e-4af5-8df0-317b9ecaa9f2 2011-03-16 19:37:52.588 GMT d5767d0c-5a85-4f35-a4fc-8ef5e5bbf60c 2011-03-18 12:22:47.500 GMT c73c43fa-0789-480d-99c8-8207a12fdbaf 2011-03-16 17:37:44.858 GMT Genome_GI_to_Protein_FASTAfasta_file_path00 This is where the workflow will save the fasta file 2010-03-18 23:57:05.740 GMT Where the workflow will save the FASTA file 2011-04-01 11:30:13.915 BST C:\Users\You\Desktop\myfasta.faa 2011-04-01 11:30:31.513 BST id11 225184640 2011-04-01 11:30:02.741 BST The workflow uses the gi no to retrieve the xml genbank entry 2010-03-18 23:58:02.898 GMT The GI number for the species used to retrieve the FASTA protein sequences. The example is Bacillus anthracis 168. 2011-04-01 11:29:38.51 BST 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 5000 0 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 0 'text/plain' 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 3 net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtraction_of_infoxml_resultGet_Nucleotide_GBSeq_XMLoutputTextWrite_Text_FileoutputFilefasta_file_pathWrite_Text_FilefilecontentsExtraction_of_infofastas_outGet_Nucleotide_GBSeq_XMLididfile_outputWrite_Text_FileoutputFile bda21c6c-8327-48ca-8339-37ac15c63cf3 2011-04-01 11:30:31.607 BST 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 Uses the GI id to retrieve the GenBank entry. Using a beanscript, the workflow then parses the required data for the creation of the protein FASTA file. 2011-04-01 11:31:30.797 BST 81f6a23a-091d-478f-b425-a30931c05b65 2011-04-01 11:31:34.672 BST nclteamc 2010-03-18 23:54:52.375 GMT A-Team 2011-04-01 11:30:41.482 BST 6beeaaf5-900a-438a-8791-76184cbcb463 2011-03-24 19:03:54.809 GMT d224eb34-ce3a-4a01-af3c-f5ea28079a4f 2011-04-01 00:55:02.915 BST Extract proteins using a gi - output as fasta file 2010-03-18 23:55:22.983 GMT 1d96c07a-cea5-43e0-b42a-09a4a98457ba 2011-04-01 11:29:39.458 BST Genome GI to Protein FASTA 2011-04-01 11:30:55.750 BST