AworkflowversionoftheEMBOSStutorialoutputPlotprophetOutputtmapPlotsequenceidvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity swallid:ops2_* net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeprophecyNamevalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity Ops2 Sequences net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeprophecyTypevalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity G net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesendvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 1171 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesbeginvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 110 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvoketranseqSequenceIDvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity embl:xlrhodop net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemsfFormatvalue00net.sf.taverna.t2.activitiesstringconstant-activity0.8net.sf.taverna.t2.activities.stringconstant.StringConstantActivity msf net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketmapsequences_direct_data0outfile_url00outfile00report00Graphics_in_Postscript00Graphics_in_PNG11Graphics_in_Postscript_url00Graphics_in_PNG_url00net.sf.taverna.t2.activitiessoaplab-activity0.8net.sf.taverna.t2.activities.soaplab.SoaplabActivity http://www.ebi.ac.uk/soaplab/emboss4/services/protein_2d_structure.tmap 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeformatSequencessequence_direct_data0osformat0report00outseq_url00outseq00net.sf.taverna.t2.activitiessoaplab-activity0.8net.sf.taverna.t2.activities.soaplab.SoaplabActivity http://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeprophetsequence_direct_data0infile_direct_data0outfile00report00outfile_url00net.sf.taverna.t2.activitiessoaplab-activity0.8net.sf.taverna.t2.activities.soaplab.SoaplabActivity http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_profiles.prophet 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeseqret1sequence_usa0report00outseq_url00outseq00net.sf.taverna.t2.activitiessoaplab-activity0.8net.sf.taverna.t2.activities.soaplab.SoaplabActivity http://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeprophecytype0sequence_direct_data0name0outfile_url00report00outfile00net.sf.taverna.t2.activitiessoaplab-activity0.8net.sf.taverna.t2.activities.soaplab.SoaplabActivity http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_profiles.prophecy 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketranseqsend0sequence_usa0sbegin0outseq00outseq_url00report00net.sf.taverna.t2.activitiessoaplab-activity0.8net.sf.taverna.t2.activities.soaplab.SoaplabActivity http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_translation.transeq 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeplotsequences_direct_data0report00Graphics_in_PNG_url00Graphics_in_Postscript_url00Graphics_in_Postscript00Graphics_in_PNG11net.sf.taverna.t2.activitiessoaplab-activity0.8net.sf.taverna.t2.activities.soaplab.SoaplabActivity http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.prettyplot 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeemmasequence_direct_data0report00dendoutfile_url00dendoutfile00outseq_url00outseq00net.sf.taverna.t2.activitiessoaplab-activity0.8net.sf.taverna.t2.activities.soaplab.SoaplabActivity http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma 0 1.0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl0.8net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketmapsequences_direct_dataformatSequencesoutseqformatSequencessequence_direct_dataseqret1outseqformatSequencesosformatmsfFormatvalueprophetsequence_direct_datatranseqoutseqprophetinfile_direct_dataprophecyoutfileseqret1sequence_usasequenceidvalueprophecytypeprophecyTypevalueprophecysequence_direct_dataemmaoutseqprophecynameprophecyNamevaluetranseqsendsendvaluetranseqsequence_usatranseqSequenceIDvaluetranseqsbeginsbeginvalueplotsequences_direct_dataemmaoutseqemmasequence_direct_dataseqret1outseqoutputPlotplotGraphics_in_PNGprophetOutputprophetoutfiletmapPlottmapGraphics_in_PNG Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools. 2009-06-29 15:44:01.803 BST Tom Oinn 2009-06-29 15:44:01.803 BST A workflow version of the EMBOSS tutorial 2009-06-29 15:44:01.803 BST