Vaccine_Targets_WorkflowTarget_GI00The GI Number for the target strain. The example below is Bacillus anthracis Ames.2011-04-01 11:26:57.365 BST1603670752011-03-30 20:24:58.462 BST491769662011-03-31 23:56:58.874 BSTroot_directory00The directory in which to save the workflow results (FASTA, Blast, and HTML document).2011-04-01 11:25:46.130 BSTD:\Workflows\Ours\Live_Demo\Vaccine\demo2011-04-01 02:56:16.240 BSTD:\Workflows\Ours\Live_Demo\2011-04-01 02:56:00.575 BSTD:\Workflows\Ours\target_proteins.txt2011-03-25 18:40:49.587 GMTD:\Workflows\Ours\target2011-03-31 16:41:05.518 BSTSource_GI002251846402011-03-31 23:56:32.721 BSTThe GI number for the source strain. The example below is for Bacillus subtilis 168.2011-04-01 11:26:33.570 BSTprotein_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.Parallelize1net.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.Retry1.0100050003net.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.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtruecontents_file0text/plain0url_string0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtruecontents_file0text/plain0url_string0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtruein10text/plain1out11net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtrueparsed_uniprot0text/plainjava.lang.Stringtrueidentifier_name0text/plain1out11net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityACnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtrueparsed_uniprot0text/plainjava.lang.Stringtrueidentifier_name0text/plain1out11net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityPubMednet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.WSDLActivityhttp://www.ebi.ac.uk/webservices/citexplore/v1.0/service?wsdlsearchCitationsnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesearchCitations_inputluceneQueryString0email0outputFormat0offSet0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="searchCitations" name="parameters" qname="{http://webservice.cdb.ebi.ac.uk/}searchCitations"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="luceneQueryString" qname="searchCitations>luceneQueryString" /><s:basetype optional="true" unbounded="false" typename="string" name="outputFormat" qname="searchCitations>outputFormat" /><s:basetype optional="false" unbounded="false" typename="int" name="offSet" qname="searchCitations>offSet" /><s:basetype optional="true" unbounded="false" typename="string" name="email" qname="searchCitations>email" /></s:elements></s:complextype></s:extensions>falseluceneQueryString0'text/plain'falseoutputFormat0'text/plain'falseoffSet0'text/plain'falseemail0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesearchCitations_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="searchCitationsResponse" name="parameters" qname="{http://webservice.cdb.ebi.ac.uk/}searchCitationsResponse"><s:elements><s:complextype optional="true" unbounded="false" typename="resultListBean" name="return" qname="searchCitationsResponse>return"><s:elements><s:basetype optional="false" unbounded="false" typename="int" name="hitCount" qname="resultListBean>hitCount" /><s:basetype optional="false" unbounded="false" typename="int" name="offSet" qname="resultListBean>offSet" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="resultBean" name="resultBeanCollection" qname="resultListBean>resultBeanCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="resultBean" name="" qname="{http://webservice.cdb.ebi.ac.uk/}resultBean"><s:elements><s:complextype optional="true" unbounded="false" typename="citation" name="citation" qname="resultBean>citation"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="abstractText" qname="citation>abstractText" /><s:basetype optional="true" unbounded="false" typename="string" name="affiliation" qname="citation>affiliation" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="author" name="authorCollection" qname="citation>authorCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="author" name="" qname="{http://webservice.cdb.ebi.ac.uk/}author"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="author>citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="collectiveName" qname="author>collectiveName" /><s:basetype optional="true" unbounded="false" typename="string" name="fullName" qname="author>fullName" /><s:basetype optional="true" unbounded="false" typename="string" name="initials" qname="author>initials" /><s:basetype optional="true" unbounded="false" typename="string" name="initialsNonAscii" qname="author>initialsNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="author>lastName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastNameNonAscii" qname="author>lastNameNonAscii" /><s:basetype optional="true" unbounded="false" typename="short" name="orderIn" qname="author>orderIn" /><s:basetype optional="true" unbounded="false" typename="string" name="suffix" qname="author>suffix" /><s:basetype optional="true" unbounded="false" typename="string" name="suffixNonAscii" qname="author>suffixNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="valid" qname="author>valid" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:complextype optional="true" unbounded="false" typename="bookOrReport" name="bookOrReportDetails" qname="citation>bookOrReportDetails"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="bookOrReport>citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="comprisingTitle" qname="bookOrReport>comprisingTitle" /><s:basetype optional="true" unbounded="false" typename="string" name="comprisingTitleNonAscii" qname="bookOrReport>comprisingTitleNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="edition" qname="bookOrReport>edition" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="editor" name="editorCollection" qname="bookOrReport>editorCollection"><s:elementtype><s:complextype optional="false" unbounded="false" typename="editor" name="" qname="{http://webservice.cdb.ebi.ac.uk/}editor"><s:elements><s:basetype optional="true" unbounded="false" typename="int" name="citationId" qname="editor>citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="collectiveName" qname="editor>collectiveName" /><s:basetype optional="true" unbounded="false" typename="string" name="initials" qname="editor>initials" /><s:basetype optional="true" unbounded="false" typename="string" name="initialsNonAscii" qname="editor>initialsNonAscii" /><s:basetype optional="true" unbounded="false" typename="string" name="lastName" qname="editor>lastName" /><s:basetype optional="true" unbounded="false" typename="string" name="lastNameNonAscii" qname="editor>lastNameNonAscii" /><s:basetype optional="false" unbounded="false" typename="short" name="orderIn" qname="editor>orderIn" /><s:basetype optional="true" unbounded="false" typename="string" name="suffix" qname="editor>suffix" /><s:basetype optional="true" unbounded="false" typename="string" name="suffixNonAscii" qname="editor>suffixNonAscii" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="extraInformation" qname="bookOrReport>extraInformation" /><s:basetype optional="true" unbounded="false" typename="string" name="isbn10" qname="bookOrReport>isbn10" /><s:basetype optional="true" unbounded="false" typename="string" name="isbn13" qname="bookOrReport>isbn13" /><s:basetype optional="true" unbounded="false" typename="string" name="numberOfPages" qname="bookOrReport>numberOfPages" /><s:basetype optional="true" unbounded="false" typename="byte" name="publicationDay" qname="bookOrReport>publicationDay" /><s:basetype optional="true" unbounded="false" typename="byte" name="publicationMonth" qname="bookOrReport>publicationMonth" /><s:basetype optional="true" unbounded="false" typename="short" name="publicationYear" qname="bookOrReport>publicationYear" /><s:basetype optional="true" unbounded="false" typename="string" name="publisher" qname="bookOrReport>publisher" /><s:basetype optional="true" unbounded="false" typename="string" name="seriesIssn" qname="bookOrReport>seriesIssn" /><s:basetype optional="true" unbounded="false" typename="string" name="seriesName" qname="bookOrReport>seriesName" /></s:elements></s:complextype><s:basetype optional="true" unbounded="false" typename="dateTime" name="cachedAt" qname="citation>cachedAt" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="chemical" name="chemicalCollection" qname="citation>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>id" /><s:basetype optional="true" unbounded="false" typename="string" name="name" qname="chemical>name" /><s:basetype optional="true" unbounded="false" typename="string" name="registryNumber" qname="chemical>registryNumber" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="comment" name="commentsAndCorrectionsCollection" qname="citation>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>citationId" /><s:basetype optional="true" unbounded="false" typename="string" name="externalId" qname="comment>externalId" /><s:basetype optional="true" unbounded="false" typename="string" name="note" qname="comment>note" /><s:basetype optional="false" unbounded="false" typename="byte" name="orderIn" qname="comment>orderIn" /><s:basetype optional="true" unbounded="false" typename="string" name="reference" qname="comment>reference" /><s:basetype optional="true" unbounded="false" typename="string" name="source" qname="comment>source" /><s:basetype optional="true" unbounded="false" typename="string" name="type" qname="comment>type" 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optional="true" unbounded="false" typename="string" name="validAuthorsConcatenation" qname="authorsConcatenation>validAuthorsConcatenation" /><s:basetype optional="true" unbounded="false" typename="string" name="validAuthorsConcatenation_clob" qname="authorsConcatenation>validAuthorsConcatenation_clob" /></s:elements></s:complextype></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="crossReference" name="crossReferenceAltSpliceFunCollection" qname="citation>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>dataSource" /><s:basetype optional="true" unbounded="false" typename="string" name="externalId" qname="crossReference>externalId" /><s:basetype optional="true" unbounded="false" 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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.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtruethreshold0text/plain0out10net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityA-Team: Vaccine Targets Analysisnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.StringtrueTid0text/plainjava.lang.StringtrueTSpecies0text/plainjava.lang.StringtrueSid0text/plainjava.lang.StringtrueSSpecies0text/plainjava.lang.StringtrueKPI0text/plainjava.lang.Stringtrueinput0text/plainjava.lang.StringtrueKDiagram0text/plainjava.lang.StringtrueGO0text/plainjava.lang.StringtrueInterPro0text/plainjava.lang.StringtruePubMed0text/plainjava.lang.StringtrueOC_R0text/plainjava.lang.StringtrueTitle0text/plainjava.lang.StringtrueOS0text/plain0output10net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringListMergeworkflowjava.lang.Stringtruestringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'0concatenated0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtruefilename0text/plainjava.lang.Stringtrueuniprot1text/plain1filenames11uniprot_ids1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050003net.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.BeanshellActivityworkflowjava.lang.Stringtrueroot0text/plainjava.lang.Stringtruegi_num0text/plain0path0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.TextFileWriterworkflowjava.lang.StringtrueoutputFile0'text/plain'java.lang.Stringtruefilecontents0'text/plain'0outputFile0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtrueroot0text/plainjava.lang.Stringtruesource_gi_num0text/plainjava.lang.Stringtruetarget_gi_num0text/plain0path0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringListMergeworkflowjava.lang.Stringtruestringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'0concatenated0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtract_proteins_using_a_giidExtract_proteins_using_a_gifasta_file_pathMicrobase_BlastPsubjectURLMicrobase_BlastPqueryURLGet_Source_Fasta_Urlcontents_fileGet_Target_Fasta_Urlcontents_fileString_to_listin1Find_Unique_ProteinsblastFileFind_Unique_ProteinstfastaKEGG_ResultsUniprot_idsGet_Uniprot_DataSearchTermget_identifiers_from_uniprotparsed_uniprotget_identifiers_from_uniprotidentifier_nameGene_Ontology_Resultsparsed_uniprotInterPro_Resultsparsed_uniprotget_identifiers_from_uniprot_2_2identifier_nameget_identifiers_from_uniprot_2_2parsed_uniprotsearchCitationsparameterssearchCitations_inputluceneQueryStringsearchCitations_inputemailsearchCitations_inputoutputFormatsearchCitations_inputoffSetsearchCitations_outputinputdeXMLerin1Merge_String_List_to_a_StringdataFlatten_ListinputlistMerge_String_List_to_a_String_2stringlistGet_Target_Filenamegi_numGet_Target_FilenamerootHeader_OutputIntroHeader_OutputSim_MHeader_OutputoutPutFileHeader_OutputTitleHeader_OutputSidHeader_OutputTidHeader_OutputTotalID_dGet_HTML_FilenamerootSim_Measure_StatementthresholdWrite_Protein_HTMLGOWrite_Protein_HTMLInterProWrite_Protein_HTMLPubMedWrite_Protein_HTMLKPIWrite_Protein_HTMLKDiagramWrite_Protein_HTMLTitleWrite_Protein_HTMLinputWrite_Protein_HTMLTidMerge_String_List_to_a_String_5stringlistFilename_SHIMfilenameFilename_SHIMuniprotExtract_proteins_using_a_gi_2idExtract_proteins_using_a_gi_2fasta_file_pathGet_Source_Filenamegi_numGet_Source_FilenamerootWrite_Text_FilefilecontentsWrite_Text_FileoutputFileGet_Blast_FilenamerootGet_Blast_Filenamesource_gi_numGet_Blast_Filenametarget_gi_numGet_EMBL_IDsthresholded_blastWorkflow27blast_fileMerge_String_List_to_a_String_3stringlistprotein_idsNCBIGitoKeggPathways_pathway_descriptionsGO_output_2NCBIGitoKeggPathways_URLInterProPubMed_Results_2outout_2531a8205-e72e-4a14-b99e-d72154909b922011-03-31 20:50:26.494 BST4a513a74-4ff9-43e4-b869-e48ac1ac8ac52011-04-01 11:57:24.815 BST627bcf2b-9512-4e79-9f6b-470f3910b7652011-03-31 22:53:29.457 BSTb485a670-0c3e-4b3b-b0e8-9c969011217f2011-03-30 20:05:24.997 BSTb7314f4a-d93a-4582-b782-a1aef5b386f22011-03-25 15:22:44.991 GMT5c7ab668-f89d-4da0-a35a-8f08cf5348a62011-03-30 20:28:06.400 BSTb44d1586-4b9f-46e8-84e1-8bc9f901faa32011-03-31 23:45:25.780 BST2c17cf54-dbb3-42e5-8e1e-ee7d0360b7682011-03-31 17:38:23.5 BSTfaee7798-f653-4d07-b6bb-1c4e71e4222e2011-04-01 11:27:03.849 BST781051a8-81d5-4b14-9e4c-09c95ad8c9f82011-04-01 00:21:45.475 BSTc8ffe6bc-0577-4a7a-8f5a-5a29d311f8092011-03-30 20:25:19.255 BSTfc0f8722-ba6e-43bb-b1dd-0c2444028c302011-04-01 10:36:43.985 BST6353f76e-d241-4b18-910a-d4d19ec2ed712011-03-31 21:25:39.593 BST806afaae-4232-4141-97af-5dbd5a437fa32011-04-01 02:57:41.919 BST882b7448-8cd8-4abc-9474-168d797ade7e2011-04-01 01:54:29.114 BSTd009369e-c283-403f-9b0e-f0554631e1da2011-03-31 23:47:20.574 BST50b9c052-1ee1-423b-bc8c-05eeb82d39f22011-03-30 10:42:56.949 BSTa149bb84-02f1-4295-a75b-ed7282796efd2011-03-31 17:32:24.433 BST40ee0320-dc68-48e4-9ff8-2a8be39a33082011-03-31 21:48:34.121 BSTefe69d39-5ebc-4cd6-9102-ef61d7a3913e2011-03-30 10:47:51.219 BST08be2a06-ae0a-47c6-a0ec-306b17161c362011-03-31 15:42:08.915 BSTf93a61d2-330c-4418-a4bf-31434b3298b32011-03-31 23:55:41.429 BST8f8386df-6385-453c-9550-9c24583c92492011-03-28 13:56:08.131 BSTf6558964-cc08-45b1-8ead-2700014d51df2011-03-25 19:11:46.295 GMT595cc410-b061-4ba6-967d-9fe5861325612011-03-31 23:51:38.227 BST299440f3-f6cb-4917-90a8-f9e27b4f97922011-03-30 20:34:33.670 BSTdaf61cd4-8796-4f36-bc20-e765960d9f4b2011-03-31 19:23:55.564 BSTc50df741-8cbb-402a-a3aa-ce106a8a622b2011-04-01 01:54:00.923 BST71f23402-77b6-4c3e-bbea-d07686d36de92011-03-31 20:25:08.531 BST7cd5bdbd-66f3-4c98-9367-7126756d2f542011-04-01 00:51:28.171 BSTdc46f972-c7a8-409d-993a-7c3edb1e504c2011-04-01 11:54:48.474 BSTff808d5b-0681-427f-b2a3-90f89b5b91282011-03-31 22:49:45.469 BST5c4c34f7-7cea-4ace-9973-4051ecb08c852011-03-31 23:18:50.41 BST63826d21-9052-48ee-9725-0f828b9c68752011-03-31 23:57:29.611 BST1d3a29d6-0fa8-43ab-b83a-fcad500c3a342011-03-31 20:40:24.959 BSTb45c784f-e7d7-41e2-a19f-84365ccc64e52011-04-01 00:56:47.15 BST40329737-b8f1-41ed-839c-27d919202a352011-03-31 20:05:43.488 BSTComparison 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 BSTThe 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 BST2b36819c-4f4a-45f2-996c-e02cda8100182011-03-31 16:41:25.315 BSTVaccine Targets Workflow2011-03-31 23:46:11.901 BSTDrug Re-Purposing Workflow2011-03-31 22:53:13.693 BSTUniProt_ID_to_Kegg_PathwaysUniprot_ids00imports gi numbers to be used by the workflow to create the pathways
Tried this one and it worked2011-03-25 18:07:56.507 GMT215422388
2011-03-25 18:07:46.275 GMTtext/plain2010-03-15 17:26:56.908 GMTA8YYV32011-04-01 11:48:34.917 BSTThe UniProt identifier of the gene of interest.2011-04-01 11:46:15.448 BST2010-03-15 17:26:56.908 GMTimports gi numbers to be used by the workflow to create the pathways2010-03-19 03:48:31.724 GMTKEGGIDtext/plain2010-03-15 17:26:56.908 GMTkegg ids2010-03-19 03:50:43.170 GMTpathway_by_genespathway ids2010-03-19 03:51:34.611 GMTtext/plain2010-03-15 17:26:56.908 GMTpathway_descriptionspathway ids and corresponding pathways descriptions2010-03-19 03:51:25.813 GMTtext/plain2010-03-15 17:26:56.908 GMTkegg_descriptionsKegg Ids and corresponding Kegg descriptions2010-03-19 03:50:34.309 GMTURLcorresponding url to the pathway id2010-03-19 03:52:02.52 GMTimagecorresponding image to the pathway id2010-03-19 03:52:25.108 GMTmerge_pathwaysstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringListMergeworkflowjava.lang.Stringtruestringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'0concatenated0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringListMergeworkflowjava.lang.Stringtruestringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'0concatenated0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringListMergeworkflowjava.lang.Stringtruestringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'0concatenated0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringStripDuplicatesworkflowjava.lang.Stringtruestringlist1l('text/plain')1strippedlist1l('text/plain')net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.WSDLActivityhttp://soap.genome.jp/KEGG.wsdlbtitnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.WSDLActivityhttp://soap.genome.jp/KEGG.wsdlbtitnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.WSDLActivityhttp://soap.genome.jp/KEGG.wsdlbconvnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.BeanshellActivityworkflowjava.lang.Stringtrueinput0'text/plain'0output0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.BeanshellActivityworkflowjava.lang.Stringtrueinput0'text/plain'0output0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.BeanshellActivityworkflowjava.lang.Stringtrueinput0'text/plain'0output0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.BeanshellActivityworkflowjava.lang.Stringtrueinput0'text/plain'0output0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.WebImageFetcherworkflowjava.lang.Stringtrueurl0'text/x-taverna-web-url'java.lang.Stringtruebase0'text/x-taverna-web-url'0image0'image/*'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.WSDLActivityhttp://soap.genome.jp/KEGG.wsdlcolor_pathway_by_objectsnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.SplitByRegexworkflowjava.lang.Stringtruestring0'text/plain'java.lang.Stringtrueregex0'text/plain'1split1l('text/plain')net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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\nnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.SplitByRegexworkflowjava.lang.Stringtruestring0'text/plain'java.lang.Stringtrueregex0'text/plain'1split1l('text/plain')net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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\nnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.WSDLActivityhttp://soap.genome.jp/KEGG.wsdlget_pathways_by_genesnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.StringConstantActivitypinknet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivitypurplenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemerge_pathwaysstringlistmerge_pathways_2stringlistmerge_descriptionsstringlistRemove_duplicate_pathwaysstringlistbtitstringbtit1stringbconvstringremove_Nullsinputextract_gene_idsinputremove_nulls_2inputadd_uniprot_to_stringinputGet_image_from_URLurlcolor_pathway_by_objects_2pathway_idcolor_pathway_by_objects_2bg_color_listcolor_pathway_by_objects_2fg_color_listcolor_pathway_by_objects_2object_id_listsplit_by_regex_2regexsplit_by_regex_2stringsplit_by_regexregexsplit_by_regexstringget_pathways_by_genesgenes_id_listFlatten_ListinputlistFlatten_List_3inputlistKEGGIDpathway_by_genespathway_descriptionskegg_descriptionsURLimage446598ae-de47-4e9a-af0a-e192c2cb3b262011-04-01 11:48:37.376 BSTa110afdb-d845-4164-8b6a-49f76cfb514d2011-03-31 11:19:46.601 BST1495f977-2aeb-4ca7-a79d-e9aa9472af272011-03-25 18:08:37.965 GMTf38c6560-baaa-400e-be8a-b02171e13db02011-03-31 15:02:01.586 BST31e58e2c-47a8-4ed4-a7ab-c6b8d1d671492011-03-31 14:42:16.155 BST89621269-d95c-45f4-b969-0bce9cccd1252011-03-31 11:19:29.823 BST358042ee-ccdc-43f4-8301-5e7448bfbd532011-03-25 11:49:22.194 GMT17596066-d978-42f2-a5a1-3082300be8ea2011-03-31 11:14:43.208 BSTc2ab2676-5a31-4889-9913-0601a8f0e2382011-03-31 13:58:25.963 BSTRetrieves 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 BST94c3b907-cb48-438b-bb8e-c64463e1303c2011-04-01 11:46:39.891 BST3542735a-febb-4b90-af1d-7571fa36d73e2011-03-28 12:03:17.584 BSTPaul Fisher2010-03-15 17:26:56.962 GMTNCBI Gi to Kegg Pathways2010-03-15 17:26:56.962 GMT2011-04-01 11:44:03.421 BSTb9b894bb-350e-47f2-81ba-e076e9f506082011-03-31 13:57:42.749 BSTThis 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 GMTd5d0df3b-2ac7-4a8d-85ce-223e0ff171322011-03-25 17:57:31.266 GMTUniProt ID to Kegg Pathways2011-04-01 11:43:57.585 BSTd456be95-e8be-419b-a86e-fa54751ae1b02011-03-31 14:50:44.6 BSTRetrieves 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 BSTaeba0128-e6e4-4246-8da0-b816c51b62cc2011-03-31 11:57:51.849 BSTnclteamc
and
Paul Fisher2010-03-19 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 GMTExtract_EMBL_Ids_from_BLASTthresholded_blast00Tab-delimited BLAST results.2011-04-01 11:38:49.491 BSTFile : C:\myblast.blast2011-04-01 11:39:11.736 BSTTab-delimited BLAST results. Add as file location.2011-04-01 11:38:57.38 BSTembl_idsextract_embl_from_blastunique_identifiers0out100net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtrueunique_identifiers0text/plain0out10net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_embl_from_blastunique_identifiersembl_idsdf44d724-29e3-4388-9ad7-c91b3c1554482011-03-28 14:23:43.718 BST9da54ff9-666e-4b37-9b51-4253ce2aa4e32011-03-28 14:15:58.425 BSTd59fa6cd-cf4d-4c4e-969b-2aaa6e715cb02011-03-28 14:17:58.13 BST7ecb3fae-7fa0-4a8e-9be2-0249d0d93c852011-03-28 14:06:16.349 BSTExtract EMBL Ids from BLAST2011-04-01 11:35:52.859 BSTReturns the EMBL ids from a tab-delimited FASTA file (retrieved from the GenBank file).2011-04-01 11:36:42.612 BST2ee1bf16-50b0-43d9-a017-33d197bdced92011-03-28 16:48:23.946 BST8d2027c6-c223-4e1c-a388-a9a76d1fe9a12011-03-28 16:47:49.242 BST685f9123-2cda-440d-bddc-56c89ff31a2a2011-03-28 14:19:20.984 BST61754d49-84e4-465f-bb1b-14932249c1692011-03-28 16:43:03.711 BSTfc421123-fbb0-4793-9d33-6144808b1a632011-03-28 16:46:55.748 BSTfed9062a-2a7d-4f65-bd56-6192178619f42011-03-28 14:21:28.705 BSTb0f93f0d-7821-4056-a53f-07961afb42642011-03-28 16:56:29.848 BSTc2d1d84b-5fe7-44f7-8623-be156fdb70222011-03-28 14:24:09.153 BSTbdc2723f-dc2c-48e1-ac6c-8cacd3da705d2011-03-28 14:17:17.190 BST97ca9486-2650-4c74-8fed-55434ecfcb5f2011-03-28 14:22:49.653 BSTc149a342-53fe-4a09-ad40-fbb63a4a525a2011-03-29 18:44:24.857 BST7fc42d35-5cce-471c-97da-98bbef355bc52011-03-28 14:11:24.932 BST947351f6-7bd1-4045-a085-20ac5321adb92011-03-28 16:45:50.692 BST98909241-55c4-432e-b98c-88852aad7c022011-03-31 23:18:42.548 BST17305750-742e-4a5e-8e90-5c24284450122011-03-28 16:57:30.14 BSTab1440e1-4318-4124-adc4-2288c3bc61012011-03-28 14:14:35.23 BST84eb7e30-96bb-4aaf-bf80-449579424f0b2011-03-28 14:13:10.264 BST3aab4589-ed9a-47f1-9bd1-286581af7f222011-03-28 14:12:25.862 BSTcf58c3d7-d887-4d76-ae34-88c1c8db722e2011-03-28 14:20:09.898 BSTa02d4f7b-c8cf-4d4b-928c-ba1a261b55d22011-03-28 16:44:55.235 BSTe07c0f89-8abe-4fba-9c4b-09969b7c5e8c2011-03-28 14:08:00.146 BSTc58ba6c6-bca5-4037-a14c-227dd20ef3352011-04-01 11:36:42.674 BST031fa9b7-183c-499a-b269-f3b8faf127522011-03-28 14:06:55.834 BST19c5e68c-d782-48bb-9e23-c1231a2d1b4e2011-04-01 11:39:11.814 BST1ae5ea65-68cb-47b1-9f19-dd02451f09812011-03-28 14:10:13.533 BSTExtract_unique_proteins_from_blast_resultsblastFile00The 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 GMTinputs the xml format of the blast results2010-03-19 03:21:20.950 GMTC:\Users\You2011-03-24 15:20:32.41 GMTThe 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 GMTC:\Users\You\Documents\my_blast_results.tab2011-03-24 15:21:18.503 GMTThe URL or file path location of the tab-delimited format of the Blast results.2011-03-24 15:20:06.729 GMTtfasta00Fasta file of the target proteins to extract the sequences. Add as file location.2011-03-24 15:21:53.195 GMTFasta file of the target proteins to extract the sequences. 2011-03-24 15:21:32.450 GMTFile : C:\Users\You\Documents\target_fasta.faa2011-03-24 15:22:34.14 GMTfasta file of the target proteins to extract the sequences2010-03-19 03:19:27.444 GMTFile 2011-03-24 15:21:59.270 GMTunique_identifiersUnique 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 GMTgi|321313668|ref|YP_004205955.1|
gi|321312432|ref|YP_004204719.1|
gi|321314996|ref|YP_004207283.1|2011-03-24 15:28:18.998 GMTblasted_identifiersIdentifiers 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 GMTgi|321313668|ref|YP_004205955.1|
gi|321312432|ref|YP_004204719.1|
gi|321314996|ref|YP_004207283.1|2011-03-24 15:27:27.684 GMTRead_Text_Filefileurl0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.2net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.TextFileReaderworkflowjava.lang.Stringtruefileurl0'text/plain'0filecontents0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtruexml_result0text/plain0gi_lines_val0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtruegi_val0text/plainjava.lang.Stringtruetfasta_in0text/plain0cfasta_out0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_Filefileurlextract_blast_idsxml_resultfind_unique_proteinsgi_valfind_unique_proteinstfasta_inunique_identifiersblasted_identifiers737d3624-b4d2-4a08-b274-cc14742bce4c2011-03-29 17:38:42.291 BSTfetchEnsemblSeqsAndBlast2010-03-15 11:30:59.109 GMTcc480ca8-ff58-4ff6-9949-17d47f4449ac2011-03-29 17:40:41.746 BSTnclteamc2010-03-19 03:15:57.858 GMT93e32a3d-4e18-465b-8d3f-d2705d281a242011-03-29 17:44:59.100 BSTBela Tiwari2010-03-15 11:30:59.109 GMTWorkflow outputs a list of proteins encoded by the target genomes that do not have sequences similarity to those encoded by the source genome2010-03-19 03:18:26.823 GMTc39cf70b-850d-4f5a-a83e-d6570a9c468c2011-03-28 11:10:21.821 BST8dd7abc2-2a03-403f-b241-90fe56b28a302011-04-01 11:33:12.635 BST9adf3d21-e3ce-44cb-b1d1-f58b89a7045d2011-03-29 18:02:43.52 BST782c8659-5afb-4518-a8c3-0376a08848162011-03-24 13:52:32.878 GMT7045bed3-10bd-4d68-9c66-0135b0ed2dde2011-03-24 15:28:27.232 GMT63e1f905-8094-472f-9564-694024af6d412011-03-29 17:51:04.462 BSTThis 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 GMTaf914252-ebc4-432f-992e-e2b0d39017f92011-03-29 17:39:30.204 BST60c8aba2-6a4b-4c8c-b66a-bbbf02104f942011-03-29 17:56:11.11 BST4626edc0-7e50-4e5d-8b94-7a2dfcd251752011-03-29 17:43:35.769 BST133c1ed5-3710-4e6a-956e-265beacfa6c42011-03-28 11:06:19.156 BST498004e2-20fa-4e68-beb8-c37363ed1d7c2011-03-29 19:06:48.198 BSTThe 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 GMTThe 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 BSTA-Team2011-04-01 11:32:13.835 BST1b646021-1281-4a60-87d2-30ff347c440e2011-03-29 17:32:31.887 BSTb2579890-b32e-4be4-975b-28659feea68f2011-03-24 13:12:29.54 GMT4de394ba-bb1d-40bb-9091-6814ed44a0222011-03-29 18:03:07.210 BSTExtract unique proteins from blast results2010-03-19 03:16:29.89 GMTc1f4908c-1669-4b80-bba1-13a2024ef9f42011-03-25 19:44:27.821 GMT150d4e84-1ab0-445e-a68f-59c9520fcb132011-03-29 18:00:45.354 BSTa3deee76-a760-4d32-a267-c6b198eafc6f2011-03-29 17:31:59.467 BST8192e733-05b6-4855-9246-997adf9d9da82011-03-25 20:01:56.11 GMT0bf98650-2884-406a-98a0-557f9de13e1c2011-03-29 17:35:46.991 BST4d837fd7-5124-4e7c-964b-17de794236cc2011-03-24 15:25:33.719 GMT2010-03-19 03:14:00.733 GMT6d6d19ae-76d8-4e21-a247-3a200324d0be2011-03-29 18:05:10.408 BST3bf00d4e-1435-4e32-b252-cd4db7d34aa42011-03-29 17:30:29.191 BST407de167-b803-49a3-8d88-330ea6dad2cd2011-03-29 17:53:15.739 BST07a797c2-caa6-48b9-bbde-148dfc94b6bd2011-03-29 17:51:41.951 BSTb066272d-8732-4505-a7b1-aa424a011c422011-03-29 17:37:52.118 BSTEBI_OLS_TermInfoOntology_Id00Ontology term identifier to retrive information about. For example: GO:0008150.2011-03-30 10:54:12.634 BSTtext/plain2011-03-30 10:54:12.634 BSTOntology_termtext/xml2011-03-30 10:54:12.634 BSTtext/plain2011-03-30 10:54:12.634 BSTgetTermMetadataparameters0attachmentList11parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/ontology-lookup/OntologyQuery.wsdlgetTermMetadatanet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeInput_parameterstermId0ontologyName0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getTermMetadata" name="parameters" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}getTermMetadata"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="termId" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}>getTermMetadata>termId" /><s:basetype optional="false" unbounded="false" typename="string" name="ontologyName" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}>getTermMetadata>ontologyName" /></s:elements></s:complextype></s:extensions>java.lang.StringtruetermId0'text/plain'java.lang.StringtrueontologyName0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeUnwrap_resultinput0getTermMetadataReturn00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getTermMetadataResponse" name="parameters" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}getTermMetadataResponse"><s:elements><s:arraytype optional="false" unbounded="false" wrapped="false" typename="Map" name="getTermMetadataReturn" qname="{http://www.ebi.ac.uk/ontology-lookup/OntologyQuery}>getTermMetadataResponse>getTermMetadataReturn"><s:elementtype><s:complextype optional="false" unbounded="false" typename="mapItem" name="" qname="{http://xml.apache.org/xml-soap}mapItem"><s:elements><s:basetype optional="false" unbounded="false" typename="anyType" name="key" qname="{http://xml.apache.org/xml-soap}mapItem>key" /><s:basetype optional="false" unbounded="false" typename="anyType" name="value" qname="{http://xml.apache.org/xml-soap}mapItem>value" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>java.lang.Stringtrueinput0'text/xml'0getTermMetadataReturn0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.StringConstantActivityGOnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetTermMetadataparametersInput_parameterstermIdInput_parametersontologyNameUnwrap_resultinputOntology_term4eaf1d8b-b3dc-478f-8337-bc4213714abb2011-03-30 10:54:12.741 BST672f9ccb-befa-40ea-ad98-ed1905681a362011-03-30 10:59:32.867 BST95e54190-f04b-4903-b7b1-11f40bb672de2011-03-30 11:01:12.1 BST5991ef38-c361-422d-82ab-5c100a76112c2011-03-30 10:55:35.943 BSTEBI_OLS_TermInfo2011-03-30 10:54:12.659 BSTGet 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 BSTHamish McWilliam2011-03-30 10:54:12.659 BSTWorkflow40Entry_Id00Domain00getEntry_output_entryValuesgetEntryparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/ebisearch/service.ebi?wsdlgetEntrynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetEntry_inputentry0fields1domain0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getEntry" name="parameters" qname="{http://www.ebi.ac.uk/EBISearchService}getEntry"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="domain" qname="{http://www.ebi.ac.uk/EBISearchService}>getEntry>domain" /><s:basetype optional="false" unbounded="false" typename="string" name="entry" qname="{http://www.ebi.ac.uk/EBISearchService}>getEntry>entry" /><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="fields" qname="{http://www.ebi.ac.uk/EBISearchService}>getEntry>fields"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>falsedomain0'text/plain'falseentry0'text/plain'falsefields1l('text/plain')0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetEntry_outputinput0entryValues11net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getEntryResponse" name="parameters" qname="{http://www.ebi.ac.uk/EBISearchService}getEntryResponse"><s:elements><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="entryValues" qname="{http://www.ebi.ac.uk/EBISearchService}>getEntryResponse>entryValues"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'1entryValues1l('text/plain')net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.WSDLActivityhttp://www.ebi.ac.uk/ebisearch/service.ebi?wsdllistFieldsnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokelistFields_inputdomain0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="listFields" name="parameters" qname="{http://www.ebi.ac.uk/EBISearchService}listFields"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="domain" qname="{http://www.ebi.ac.uk/EBISearchService}>listFields>domain" /></s:elements></s:complextype></s:extensions>falsedomain0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokelistFields_outputinput0arrayOfFieldNames11net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="listFieldsResponse" name="parameters" qname="{http://www.ebi.ac.uk/EBISearchService}listFieldsResponse"><s:elements><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="arrayOfFieldNames" qname="{http://www.ebi.ac.uk/EBISearchService}>listFieldsResponse>arrayOfFieldNames"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'1arrayOfFieldNames1l('text/plain')net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringConcatworkflowjava.lang.Stringtruestring10'text/plain'java.lang.Stringtruestring20'text/plain'0output0UserNameHere2011-03-30 16:39:34.159 BSTnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetEntryparametersgetEntry_inputentrygetEntry_inputfieldsgetEntry_inputdomaingetEntry_outputinputlistFieldsparameterslistFields_inputdomainlistFields_outputinputConcatenate_two_stringsstring1Concatenate_two_stringsstring2getEntry_output_entryValuesfac4bed3-abac-4864-8df7-8c97c5d9faba2011-03-28 18:22:17.369 BST28d4438b-5326-4ec1-9c46-1ee3b08cb23b2011-03-28 19:08:29.809 BST4cc17549-3f52-4a93-adb4-52746c2e31a32011-03-28 19:12:01.629 BST4db4c4e5-4f28-448c-8ab8-ab579454d6ee2011-03-28 18:27:54.841 BST5d320077-d00d-48c4-ad88-009a51fd10a12011-03-28 18:25:30.628 BST6dc968df-61ce-43fe-b497-5701fa930ff42011-03-30 16:39:39.780 BST3cc20f68-58e9-4f62-ac8b-4f78e38149062011-03-28 18:55:42.38 BST6d71ee52-0f98-499a-b48d-ea6586d334b92011-03-28 19:11:45.502 BST0ff56878-b4d2-4b72-b768-ecfa144973932011-03-28 18:57:50.617 BSTa8e6c66a-2319-47dd-9b2b-cf4642a180be2011-03-28 19:07:07.123 BSTUse_UniProt_to_retrieve_InterPro_dataparsed_uniprot00The file location of the parsed Uniprot file (see http://www.myexperiment.org/workflows/26.html).2011-04-01 11:53:45.625 BSTEB_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.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtrueparsed_uniprot0text/plainjava.lang.Stringtrueidentifier_name0text/plain1out11net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtruein10text/plain0out10net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringListMergeworkflowjava.lang.Stringtruego_defs1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtruego_ids1text/plain0concatenated0UserNameHere2011-03-30 16:27:49.467 BSTUserNameHere2011-03-30 16:29:15.546 BSTUserNameHere2011-03-30 16:25:55.280 BSTnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringListMergeworkflowjava.lang.Stringtruestringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'0concatenated0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityInterPronet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeInterPro_ResultsEntry_IdInterPro_ResultsDomainget_identifiers_from_uniprot_2_2parsed_uniprotget_identifiers_from_uniprot_2_2identifier_nameto_Lower_Case_2in1Merge_String_List_to_a_Stringgo_idsMerge_String_List_to_a_Stringgo_defsMerge_String_List_to_a_String_2stringlistEB_Eye_Resultsef9de97c-ca76-479e-b933-d396f043e1382011-03-28 16:39:02.585 BST4ed40fd8-b13c-4aa2-8977-3299887636742011-03-28 17:56:58.784 BSTf5c68892-7c8c-4bba-96cf-6e4094272de22011-03-28 18:51:46.105 BST427f85e8-da08-4e29-800f-8479992b79e52011-03-30 16:48:37.456 BSTfda20a14-917b-454a-a88e-4d4cf58e24c62011-03-28 18:34:50.789 BST2c33a9b5-8e1e-449a-9bf3-07b1ad48beab2011-03-30 16:41:33.953 BST2a76c6a1-b3d1-4ca2-9459-ddf3945932502011-04-01 11:53:46.891 BST2011-04-01 11:51:41.635 BSTUntitled workflow #142011-03-28 16:28:59.317 BSTeccaf02b-b85b-4894-9974-c4c49a1686732011-03-30 16:40:30.44 BST3117ba0d-f09f-4956-ad74-7761dbf998d92011-03-28 19:18:13.311 BSTUse UniProt to retrieve InterPro data2011-04-01 11:51:41.323 BST9fedbdd2-dde5-4b08-ab50-80991ea7c41c2011-03-28 18:55:56.909 BSTUsed 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 BSTf5b50570-afa2-4768-a298-a7bd35e90e112011-03-28 19:28:47.180 BST5bc429c4-927b-4d7e-b4c8-9f8cd17838b72011-03-30 17:22:18.272 BST416a5592-70f9-4c5f-af15-397bd21af3cb2011-03-28 19:15:54.482 BSTUsed parsed Uniprot results (see workflow2011-04-01 11:52:07.242 BST33afbd5c-d9a6-4e58-a255-ac744742875a2011-03-28 18:38:03.893 BST5f08104a-de65-423f-b532-dc7eb89c28ce2011-03-28 16:39:56.913 BST2011-03-28 16:28:59.317 BST7b3873e1-cd30-4e5c-ab3a-4e0178648eb62011-03-30 16:43:19.253 BST2011-03-28 16:28:59.317 BSTff900e9f-7b8d-43fc-be47-cc638b4266d42011-03-28 19:00:51.178 BST7f7920cf-259e-4947-8a28-bbd0bf0d5de42011-03-28 18:59:44.143 BST11d4d655-87f9-4a31-88f1-eef56a3a03ee2011-03-28 16:58:53.309 BSTacd0a40b-a688-473f-8618-1bdbd20460962011-03-28 16:33:17.871 BST7ae7f0a1-1f28-48e1-8c41-7c6da1587e3d2011-03-28 16:34:34.815 BST6845039f-9b62-49dc-ac9d-8ba4deeafde02011-04-01 11:53:15.561 BST2011-04-01 11:51:09.357 BSTd7ce24f5-f65b-4b2b-8500-6d35cf027d1c2011-03-28 19:02:12.80 BST1752f7dd-badb-4e4a-a2f1-d50327f80d602011-03-30 16:46:50.149 BSTc88315af-4ce4-43fb-b48d-45cc0e9424b22011-03-28 18:57:59.270 BSTfb843096-2675-4579-9a51-05f43e15ba792011-03-28 17:54:29.330 BSTWorkflow8subjectURL00queryURL00JobIDOutputBlastReportFinalStatusaquireSubjectFileparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdlaquireInputFilenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSubjectUrlInputurl0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFile" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="url" qname="aquireInputFile>url" /></s:elements></s:complextype></s:extensions>falseurl0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubjectFileIDinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFileResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFileResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="aquireInputFileResponse>return" /></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'0return0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.WSDLActivityhttp://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdlaquireInputFilenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeQueryUrlInputurl0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFile" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFile"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="url" qname="aquireInputFile>url" /></s:elements></s:complextype></s:extensions>falseurl0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokequeryFileIDinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="aquireInputFileResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}aquireInputFileResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="aquireInputFileResponse>return" /></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'0return0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.WSDLActivityhttp://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdlsubmitBlastPJobnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesubmitBlastPJob_inputsubjectFileId0queryFileId0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="submitBlastPJob" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}submitBlastPJob"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="subjectFileId" qname="submitBlastPJob>subjectFileId" /><s:basetype optional="true" unbounded="false" typename="string" name="queryFileId" qname="submitBlastPJob>queryFileId" /></s:elements></s:complextype></s:extensions>falsesubjectFileId0'text/plain'falsequeryFileId0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJobIDinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="submitBlastPJobResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}submitBlastPJobResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="submitBlastPJobResponse>return" /></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'0return0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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>truenet.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.Retry1.0100050000net.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.WSDLActivityhttp://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdlgetBlastReportnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetBlastReport_inputjobId0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getBlastReport" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getBlastReport"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="jobId" qname="getBlastReport>jobId" /></s:elements></s:complextype></s:extensions>falsejobId0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetBlastReport_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getBlastReportResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getBlastReportResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="getBlastReportResponse>return" /></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'0return0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaquireSubjectFileparametersSubjectUrlInputurlsubjectFileIDinputaquireQueryFileparametersQueryUrlInputurlqueryFileIDinputsubmitBlastPJobparameterssubmitBlastPJob_inputsubjectFileIdsubmitBlastPJob_inputqueryFileIdJobIDinputAwaitJobCompletionJobIDgetBlastReportparametersgetBlastReport_inputjobIdgetBlastReport_outputinputJobIDOutputBlastReportFinalStatus5ce9aec8-494f-45dd-a978-3d71564306522011-03-16 14:42:27.305 GMTcd88505f-a3f1-4bde-af4a-aa287edf56422011-03-16 17:04:35.157 GMT573e2324-2806-494a-8127-37eda623cd972011-03-18 11:45:08.987 GMTec74ad83-bc35-4801-9f1a-5895a07707a42011-03-16 17:11:23.916 GMT63f00396-c32e-4320-a732-6c682f2464fb2011-03-16 19:07:15.429 GMT78ba349d-a426-46bb-b842-57cad76582ef2011-03-18 12:22:51.796 GMT4d26090f-0bef-4024-ba16-8a69f36909982011-03-16 22:52:59.767 GMT14b5dde3-dfd6-4c04-b254-78c13051998a2011-03-16 19:38:23.32 GMT00226a02-118c-419e-96df-2dd8869cbfa02011-03-16 16:51:12.261 GMTa2f6d3f7-262b-47b5-9fd1-e191935a19a92011-03-16 17:07:31.320 GMTe0a458bb-2f5c-43e7-b582-745c970a19662011-03-16 17:41:03.200 GMTf5981737-10a0-4fc4-9672-3130a03656ab2011-03-16 17:40:41.255 GMT3b70d4ae-354f-477e-a277-41712da517702011-03-16 17:31:43.390 GMT660f7075-7cd0-4c7c-8240-5ef305e3d0812011-03-16 17:39:20.697 GMTe9287f94-ee6e-483b-8c8b-5284afc5213e2011-03-16 15:34:27.528 GMT71ce1c05-e453-4cab-b2e1-ee49bb4534dc2011-03-16 14:28:03.443 GMT66e94c9e-a25e-4df1-bcf9-9885484303422011-03-16 14:29:06.933 GMTGO_Data_from_GO_IDparsed_uniprot00File location of the parsed Uniprot results2011-03-30 16:11:49.141 BSTFile location of the parsed Uniprot results. To generate this file, see http://www.myexperiment.org/workflows/26.html2011-03-30 16:14:06.340 BSTGO_Resultsget_identifiers_from_uniprot_2_2parsed_uniprot0identifier_name0out111net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtrueparsed_uniprot0text/plainjava.lang.Stringtrueidentifier_name0text/plain1out11net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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.Retry1.0100050000net.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.BeanshellActivityworkflowjava.lang.Stringtruein10text/plain0out10net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivityGOnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringListMergeworkflowjava.lang.Stringtruego_defs1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtruego_ids1text/plain0concatenated0UserNameHere2011-03-30 16:25:55.280 BSTUserNameHere2011-03-30 16:29:15.546 BSTUserNameHere2011-03-30 16:27:49.467 BSTnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_identifiers_from_uniprot_2_2parsed_uniprotget_identifiers_from_uniprot_2_2identifier_nameEBI_OLS_TermInfoOntology_IdGO_deXMLerin1Merge_String_List_to_a_Stringgo_defsMerge_String_List_to_a_Stringgo_idsGO_Results2011-03-30 16:14:48.557 BSTc88315af-4ce4-43fb-b48d-45cc0e9424b22011-03-28 18:57:59.270 BSTUsed 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 BST0523fd65-210c-421c-a12d-86216a61de192011-03-30 16:14:43.704 BST9fedbdd2-dde5-4b08-ab50-80991ea7c41c2011-03-28 18:55:56.909 BST9e103ba0-8dce-4f23-a7f4-165bd80a8f932011-03-30 10:56:21.121 BST21781546-1ad8-4dea-81d0-6780a7ec9e662011-03-30 16:35:51.793 BST2011-04-01 11:54:34.135 BSTGO Data from GO ID2011-03-30 16:15:03.966 BST5f08104a-de65-423f-b532-dc7eb89c28ce2011-03-28 16:39:56.913 BSTa7da9321-f578-410e-93b3-2115c326a8d42011-03-30 16:15:18.613 BST7ae7f0a1-1f28-48e1-8c41-7c6da1587e3d2011-03-28 16:34:34.815 BSTfda20a14-917b-454a-a88e-4d4cf58e24c62011-03-28 18:34:50.789 BSTacd0a40b-a688-473f-8618-1bdbd20460962011-03-28 16:33:17.871 BSTd7ce24f5-f65b-4b2b-8500-6d35cf027d1c2011-03-28 19:02:12.80 BSTff900e9f-7b8d-43fc-be47-cc638b4266d42011-03-28 19:00:51.178 BST4ed40fd8-b13c-4aa2-8977-3299887636742011-03-28 17:56:58.784 BST2011-03-28 16:28:59.317 BST2011-03-30 16:15:18.518 BST473b328e-5f9a-4db9-b31a-c868afc8da4c2011-03-30 10:55:52.642 BSTa129e83f-4d68-4d84-bb21-b7b2c29cdab92011-03-30 12:01:49.842 BSTef9de97c-ca76-479e-b933-d396f043e1382011-03-28 16:39:02.585 BST416a5592-70f9-4c5f-af15-397bd21af3cb2011-03-28 19:15:54.482 BST19dbb793-e604-4c3c-82a6-e2fe1be4d0842011-03-29 11:06:03.489 BSTfb843096-2675-4579-9a51-05f43e15ba792011-03-28 17:54:29.330 BSTUntitled workflow #142011-03-28 16:28:59.317 BST2011-04-01 11:54:33.870 BST3117ba0d-f09f-4956-ad74-7761dbf998d92011-03-28 19:18:13.311 BST2011-03-28 16:28:59.317 BSTbf867204-2ced-4bc2-9c7a-20da8438de9a2011-04-01 11:55:51.865 BSTf5c68892-7c8c-4bba-96cf-6e4094272de22011-03-28 18:51:46.105 BST11d4d655-87f9-4a31-88f1-eef56a3a03ee2011-03-28 16:58:53.309 BST73ae7c45-6300-40e1-86c2-5da602996ff82011-03-30 10:59:35.473 BST33afbd5c-d9a6-4e58-a255-ac744742875a2011-03-28 18:38:03.893 BST7f7920cf-259e-4947-8a28-bbd0bf0d5de42011-03-28 18:59:44.143 BSTb4078147-9bbb-45c3-a045-dc6090bf95bb2011-03-30 11:01:16.668 BST6ad18fe7-29cc-4cd2-ad50-6b2b62c7be8c2011-03-30 16:23:46.939 BSTe276142b-824b-4fca-94b4-5a7402085b732011-03-30 10:59:54.93 BSTDetermine_Average_Identity_of_BLAST_resultsblast_file00Add file location of tab-delimited BLAST results to be thresholded2011-03-28 11:41:06.278 BSTFile : D:\Workflows\Ours\blast_results.txt2011-03-28 11:41:26.692 BSTFile : D:\Workflows\Ours\blast_results2011-03-28 11:41:21.424 BSToverallSimilarityaverage_identityblast_file0out100net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtrueblast_file0text/plain0out10net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeaverage_identityblast_fileoverallSimilaritybd3db62e-7772-4c70-b67b-4a264023adbf2011-03-28 11:44:34.517 BSTDetermine Average Identity of BLAST results2011-04-01 11:34:13.83 BSTdb16decf-8a95-4f1e-b627-e2dd988bbe042011-03-28 12:16:57.540 BSTc7c15b62-55f3-4568-8f02-e1b8fb3519492011-03-28 12:17:39.213 BST90be7e33-afc5-4ecb-82bf-712e2a39bc8d2011-03-28 11:45:51.374 BST94985fbf-dde2-47ce-9e29-a7b1b373d6c22011-03-28 12:20:14.167 BST9114a2d0-9f1a-4e01-abe2-1a99fc2949292011-04-01 11:35:18.232 BSTUsing 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 BST59b138d5-5cb4-4a34-a8cb-f4dfd035ef8b2011-03-28 11:42:41.787 BST29dd4ffc-1662-49c8-85d9-afb9581a70da2011-03-28 12:04:20.997 BST6d9879d5-59c9-49d9-8edf-5e57646819772011-03-29 18:57:56.789 BSTGet_identifiers_from_UniProtSearchTerm00Search term for UniProt. 2011-04-01 11:40:37.777 BSTMecA2011-04-01 11:40:48.902 BST2011-03-28 17:43:19.351 BSTparsed_datafieldNamevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.2net.sf.taverna.t2.activities.stringconstant.StringConstantActivityAlltextnet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.SoaplabActivityhttp://phoebus.cs.man.ac.uk:1977/axis/services/seq_analysis.parse_uniprot01.00net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0000net.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.SoaplabActivityhttp://phoebus.cs.man.ac.uk:1977/axis/services/uniprotsequence.uniprot01.00net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050003net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeparse_uniprotfile_direct_dataUniprot_searchfieldnameUniprot_searchsearchtermparsed_data2011-04-01 11:41:03.139 BSTdc311c4e-25e3-4e86-96f4-b8889e83f3e82011-04-01 01:54:27.607 BSTb5a6390c-d9bd-4baa-a233-b4e8b03d6a432011-04-01 11:42:19.583 BSTGet identifiers from UniProt2011-04-01 11:41:30.876 BST733461a4-348d-4198-b6ba-899bbf28ba642011-03-28 17:43:19.611 BST2011-03-28 17:43:19.515 BST2011-03-28 17:43:19.515 BST2011-04-01 11:41:31.126 BSTUntitled workflow #42011-03-28 17:43:19.515 BSTFrom 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 BSTExtract_proteins_using_a_gi___output_as_fasta_file_fasta_file_path00This is where the workflow will save the fasta file2010-03-18 23:57:05.740 GMTid11The workflow uses the gi no to retrieve the xml genbank entry2010-03-18 23:58:02.898 GMTfile_outputprotein output for specified gi in fasta format2010-03-18 23:58:47.780 GMTExtraction_of_infoxml_result0fastas_out00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtruexml_result0text/plain0fastas_out0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.TextFileWriterworkflowjava.lang.StringtrueoutputFile0'text/plain'java.lang.Stringtruefilecontents0'text/plain'0outputFile0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorkerworkflowjava.lang.Stringtrueid0'text/plain'0outputText0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050003net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtraction_of_infoxml_resultWrite_Text_FileoutputFileWrite_Text_FilefilecontentsGet_Nucleotide_GBSeq_XMLidfile_output6beeaaf5-900a-438a-8791-76184cbcb4632011-03-24 19:03:54.809 GMTThe 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 GMTExtract proteins using a gi - output as fasta file 2010-03-18 23:55:22.983 GMTnclteamc2010-03-18 23:54:52.375 GMT58b39f65-b805-41ee-b49f-e4803a2841832011-04-01 00:55:35.727 BSTWorkflow3JobID00StatusgetJobStateparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://blast.ncl.ac.uk:8080/TavernaBlastService/services/blast?wsdlgetJobStatenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobState_inputjobId0output00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getJobState" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getJobState"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="jobId" qname="getJobState>jobId" /></s:elements></s:complextype></s:extensions>falsejobId0'text/plain'0output0'text/xml'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobState_outputinput0return00net.sf.taverna.t2.activitieswsdl-activity1.2net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getJobStateResponse" name="parameters" qname="{http://cxf.blast.csc8308.ncl.ac.uk/}getJobStateResponse"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="return" qname="getJobStateResponse>return" /></s:elements></s:complextype></s:extensions>java.lang.Stringfalseinput0'text/xml'0return0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetJobStateparametersgetJobState_inputjobIdgetJobState_outputinputStatus4e01e2d8-674e-4af5-8df0-317b9ecaa9f22011-03-16 19:37:52.588 GMTd5767d0c-5a85-4f35-a4fc-8ef5e5bbf60c2011-03-18 12:22:47.500 GMTc73c43fa-0789-480d-99c8-8207a12fdbaf2011-03-16 17:37:44.858 GMTGenome_GI_to_Protein_FASTAfasta_file_path00This is where the workflow will save the fasta file2010-03-18 23:57:05.740 GMTWhere the workflow will save the FASTA file2011-04-01 11:30:13.915 BSTC:\Users\You\Desktop\myfasta.faa2011-04-01 11:30:31.513 BSTid112251846402011-04-01 11:30:02.741 BSTThe workflow uses the gi no to retrieve the xml genbank entry2010-03-18 23:58:02.898 GMTThe 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 BSTfile_outputprotein output for specified gi in fasta format2010-03-18 23:58:47.780 GMTExtraction_of_infoxml_result0fastas_out00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtruexml_result0text/plain0fastas_out0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.TextFileWriterworkflowjava.lang.StringtrueoutputFile0'text/plain'java.lang.Stringtruefilecontents0'text/plain'0outputFile0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorkerworkflowjava.lang.Stringtrueid0'text/plain'0outputText0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050003net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtraction_of_infoxml_resultWrite_Text_FileoutputFileWrite_Text_FilefilecontentsGet_Nucleotide_GBSeq_XMLidfile_outputbda21c6c-8327-48ca-8339-37ac15c63cf32011-04-01 11:30:31.607 BSTThe 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 GMTUses 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 BST81f6a23a-091d-478f-b425-a30931c05b652011-04-01 11:31:34.672 BSTnclteamc2010-03-18 23:54:52.375 GMTA-Team2011-04-01 11:30:41.482 BST6beeaaf5-900a-438a-8791-76184cbcb4632011-03-24 19:03:54.809 GMTd224eb34-ce3a-4a01-af3c-f5ea28079a4f2011-04-01 00:55:02.915 BSTExtract proteins using a gi - output as fasta file 2010-03-18 23:55:22.983 GMT1d96c07a-cea5-43e0-b42a-09a4a98457ba2011-04-01 11:29:39.458 BSTGenome GI to Protein FASTA2011-04-01 11:30:55.750 BST