Kegg_pathway_diagrams_with_enzymes_coloured_on_path_diagramSpecies00The three letter species code2010-03-13 08:05:45.460 GMTsac2010-03-19 15:36:27.447 GMTKEGG 2010-03-13 08:05:23.807 GMTeco2010-03-14 13:52:54.438 GMThsa2010-03-14 01:18:26.660 GMTeco2010-03-13 08:06:06.679 GMTThe three letter species code used by KEGG2010-03-13 08:05:59.216 GMTbg_color11The background colour for the boxes containing enzymes.2010-03-14 01:11:59.113 GMTred
#ff00002010-03-14 01:12:42.141 GMTred2010-03-19 12:26:05.816 GMTThe background colour for the boxes containing enzymes. Values can be given as strings or hexadecimal RGB colour codes.2010-03-14 01:12:30.165 GMTfg_color11The text colour for the boxes containing enzymes. Values can be given as strings or hexadecimal RGB colour codes.2010-03-14 01:12:54.809 GMTgreen
#00ff002010-03-14 01:13:09.889 GMT#00ff002010-03-19 12:26:12.816 GMTpath_proteins11D:\Drutex\path_proteins.txt2010-03-19 12:55:59.921 GMTdrugs_file11D:\blastdb\drugs.fasta2010-03-19 12:55:41.391 GMTDBSavePath00D:\Drutex\2010-03-19 12:55:23.579 GMTSequence100Full path to FastA file containg nucleotide genome sequence (NB this would be supplied by part 1 however due to an oversight only the genome sequence from one EMBL file is generated)2010-03-19 15:39:02.223 GMTD:\CSC8308\newman.fna2010-03-19 15:37:42.730 GMTSequence200D:\CSC8308\newman.fna2010-03-19 15:39:19.310 GMTFull path to FastA file containg nucleotide genome sequence (NB this would be supplied by part 1 however due to an oversight only the genome sequence from one EMBL file is generated)2010-03-19 15:39:08.616 GMTsource_file_path00EMBL file name for source (file must be in EMBL folder within path specificed in DBSavePath e.g. D:\Drutex\EMBL\)2010-03-19 15:36:49.446 GMTcol_chrom.emb2010-03-19 15:37:17.227 GMTtarget_file_path00EMBL file name for target (file must be in EMBL folder within path specificed in DBSavePath e.g. D:\Drutex\EMBL\)2010-03-19 15:36:04.705 GMTnewman_chrom.emb2010-03-19 15:34:22.161 GMTblast_bin_dir00D:\mgcat_v15b\2010-03-19 15:33:51.436 GMTFile path to folder which contains FormatDB.exe2010-03-19 15:34:03.890 GMTKeggPathwayIDsA list of the pathways found.2010-03-13 08:15:37.559 GMTpath:hsa000102010-03-13 08:15:43.143 GMTkeggimageurlThe URLs of the images produced for the KeggImage output2010-03-13 08:14:19.106 GMThttp://soap.genome.jp/tmp/mark_pathway_www_api.126846700018802/hsa00010.png2010-03-13 08:14:44.67 GMTThe URLs of the images produced for the KeggImage output.2010-03-13 08:14:48.935 GMTkeggGeneNameshsa:52362010-03-13 08:17:09.171 GMTA list of the gene ids, that was given as input with the species code concatenated.2010-03-13 08:17:01.144 GMTcoloured_imagesList of pathway diagram with enzyme boxes coloured in specified colours2010-03-14 01:10:28.178 GMTenzyme_listec:1.1.1.272010-03-14 01:11:23.41 GMTList of enzyme id retrieve from Kegg using get_enzymes_by_gene2010-03-14 01:11:07.986 GMTgenes_listList of ids that are enzymes2010-03-14 01:09:09.981 GMThsa:1602872010-03-14 01:09:28.521 GMTOutputtestWorkflow89part10part20string00net.sf.taverna.t2.activitiesdataflow-activity1.0net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Image_From_URL_2url0image00net.sf.taverna.t2.activitieslocalworker-activity1.0net.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-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecolor_pathway_by_objectsbg_color_list1fg_color_list1object_id_list1pathway_id0return00net.sf.taverna.t2.activitieswsdl-activity1.0net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://soap.genome.jp/KEGG.wsdlcolor_pathway_by_objectsnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_enzymes_by_genegenes_id0return11net.sf.taverna.t2.activitieswsdl-activity1.0net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://soap.genome.jp/KEGG.wsdlget_enzymes_by_genenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_genes_by_enzymeorg0enzyme_id0return11net.sf.taverna.t2.activitieswsdl-activity1.0net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://soap.genome.jp/KEGG.wsdlget_genes_by_enzymenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_pathways_by_genesgenes_id_list1return11net.sf.taverna.t2.activitieswsdl-activity1.0net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://soap.genome.jp/KEGG.wsdlget_pathways_by_genesnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_Listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_2inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRemove_String_Duplicatesstringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringStripDuplicatesworkflowjava.lang.Stringtruestringlist1l('text/plain')1strippedlist1l('text/plain')net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshellgenes_list1bg_color0fg_color0bg_colors11fg_colors11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtruebg_color0text/plainjava.lang.Stringtruefg_color0text/plainjava.lang.Stringtruegenes_list1text/plain1bg_colors11fg_colors1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loopnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_3inputlist1outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist1l(l(''))1outputlist1UserNameHere2010-03-16 12:45:55.247 GMTUserNameHere2010-03-16 12:46:27.439 GMTnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_4inputlist1outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist1l(l(''))1outputlist1UserNameHere2010-03-16 12:46:45.95 GMTnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_5inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_6inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_7inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_8inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeNested_workflowdrugs_file1path_proteins0DBSavePath0output22net.sf.taverna.t2.activitiesdataflow-activity1.0net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_9inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_2_2inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_3_2inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.FlattenListworkflow[Btrueinputlist2l(l(''))1outputlist1l('')net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_list_of_strings_extracting_match_to_a_regexstringlist1group0regex0filteredlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.RegularExpressionStringListworkflowjava.lang.Stringtruestringlist1l('text/plain')java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruegroup0'text/plain'1filteredlist1UserNameHere2010-03-18 20:59:54.509 GMTUserNameHere2010-03-18 21:00:48.431 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20:49:11.432 GMTUserNameHere2010-03-16 20:40:07.800 GMTUserNameHere2010-03-16 20:29:02.574 GMTUserNameHere2010-03-16 20:38:23.832 GMTUserNameHere2010-03-16 20:44:41.769 GMTUserNameHere2010-03-16 16:23:31.917 GMTUserNameHere2010-03-16 16:20:34.383 GMTUserNameHere2010-03-16 20:41:02.274 GMTUserNameHere2010-03-16 16:24:57.923 GMTUserNameHere2010-03-16 21:02:05.625 GMTUserNameHere2010-03-16 20:27:21.661 GMTUserNameHere2010-03-16 20:45:44.987 GMTUserNameHere2010-03-16 16:19:21.614 GMTUserNameHere2010-03-16 20:46:31.676 GMTUserNameHere2010-03-16 20:42:41.149 GMTUserNameHere2010-03-16 20:47:19.965 GMTUserNameHere2010-03-16 16:21:13.44 GMTUserNameHere2010-03-16 20:33:31.554 GMTUserNameHere2010-03-16 16:21:54.265 GMTUserNameHere2010-03-16 20:34:16.471 GMTUserNameHere2010-03-16 20:42:11.268 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21:27:44.184 GMTUserNameHere2010-03-16 20:01:11.947 GMTUserNameHere2010-03-16 20:00:15.477 GMTUserNameHere2010-03-16 20:06:18.820 GMTUserNameHere2010-03-16 21:28:23.481 GMTUserNameHere2010-03-16 17:07:30.131 GMTUserNameHere2010-03-16 21:06:42.478 GMTUserNameHere2010-03-16 20:20:57.123 GMTUserNameHere2010-03-16 17:19:56.20 GMTUserNameHere2010-03-16 21:29:56.300 GMTUserNameHere2010-03-16 21:10:59.598 GMTUserNameHere2010-03-16 21:26:18.741 GMTUserNameHere2010-03-16 19:56:51.562 GMTUserNameHere2010-03-16 21:18:09.286 GMTUserNameHere2010-03-16 21:20:26.475 GMTUserNameHere2010-03-16 19:57:29.691 GMTUserNameHere2010-03-16 21:35:15.777 GMTUserNameHere2010-03-16 19:59:13.375 GMTUserNameHere2010-03-16 19:58:36.225 GMTUserNameHere2010-03-16 17:31:11.731 GMTUserNameHere2010-03-16 21:38:29.187 GMTUserNameHere2010-03-16 20:06:50.350 GMTUserNameHere2010-03-16 17:08:09.856 GMTUserNameHere2010-03-16 19:53:25.572 GMTUserNameHere2010-03-16 21:37:27.450 GMTUserNameHere2010-03-16 21:29:13.59 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20:16:21.695 GMTUserNameHere2010-03-16 20:13:24.460 GMTUserNameHere2010-03-16 20:12:12.586 GMTUserNameHere2010-03-16 20:14:42.471 GMTnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGroup_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeINI_Filevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivityD:\mgcat_v15b\mgcat.ininet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_File_2fileurl0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.TextFileReaderworkflowjava.lang.Stringtruefileurl0'text/plain'0filecontents0UserNameHere2010-03-16 22:27:39.980 GMTUserNameHere2010-03-16 22:29:02.510 GMTUserNameHere2010-03-16 22:26:37.122 GMTUserNameHere2010-03-16 22:25:43.329 GMTUserNameHere2010-03-16 22:18:02.467 GMTnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expression_2string0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.0net.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-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRegex1_2value00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity\nnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_list_of_strings_extracting_match_to_a_regex_2stringlist1group0regex0filteredlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.RegularExpressionStringListworkflowjava.lang.Stringtruestringlist1l('text/plain')java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruegroup0'text/plain'1filteredlist1UserNameHere2010-03-16 22:45:05.540 GMTUserNameHere2010-03-16 22:45:51.185 GMTUserNameHere2010-03-16 22:45:13.563 GMTnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGroup1value00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex2value00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivityTotal.coverage.among.all.sequences.(.*)\%net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeThresholderseqSim0reqSim0net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.StringtrueseqSim0text/plainjava.lang.StringtruereqSim0text/plain0cont0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeAskmessage0title0answer00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.ui.AskWorkerworkflowjava.lang.Stringtruetitle0'text/plain'java.lang.Stringtruemessage0'text/plain'0answer0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMessagevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivityPlease enter the minimum required strain similaritynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTitlevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivityGenome similaritynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeINI_Pathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivityD:\mgcat_v15b\mgcat.ininet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_3target_file_path0source_file_path0progpath0base_dir0database_dir00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.Stringtruebase_dir0text/plainjava.lang.Stringtruetarget_file_path0text/plainjava.lang.Stringtruesource_file_path0text/plainjava.lang.Stringtrueprogpath0text/plain0database_dir0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWorkflow89part1Workflow89part2Get_Image_From_URL_2urlcolor_pathway_by_objectsbg_color_listcolor_pathway_by_objectsfg_color_listcolor_pathway_by_objectsobject_id_listcolor_pathway_by_objectspathway_idget_enzymes_by_genegenes_idget_genes_by_enzymeorgget_genes_by_enzymeenzyme_idget_pathways_by_genesgenes_id_listFlatten_ListinputlistFlatten_List_2inputlistRemove_String_DuplicatesstringlistBeanshellgenes_listBeanshellbg_colorBeanshellfg_colorFlatten_List_3inputlistFlatten_List_4inputlistFlatten_List_5inputlistFlatten_List_6inputlistFlatten_List_7inputlistFlatten_List_8inputlistNested_workflowdrugs_fileNested_workflowpath_proteinsNested_workflowDBSavePathFlatten_List_9inputlistFlatten_List_2_2inputlistFlatten_List_3_2inputlistFilter_list_of_strings_extracting_match_to_a_regexstringlistFilter_list_of_strings_extracting_match_to_a_regexgroupFilter_list_of_strings_extracting_match_to_a_regexregexBeanshell_2in0Flatten_List_10inputlistrunMGCATcommandrunMGCATworkingdirrunMGCATargsRead_Text_FilefileurlSplit_string_into_string_list_by_regular_expressionstringSplit_string_into_string_list_by_regular_expressionregexFilter_List_of_Strings_by_regexstringlistFilter_List_of_Strings_by_regexregex1Filter_List_of_Strings_by_regexregex2Filter_List_of_Strings_by_regexfile2Filter_List_of_Strings_by_regexgroupFilter_List_of_Strings_by_regexfileWrite_Text_FilefilecontentsWrite_Text_FileoutputFileConcatenate_stringsstringlistRead_Text_File_2fileurlSplit_string_into_string_list_by_regular_expression_2stringSplit_string_into_string_list_by_regular_expression_2regexFilter_list_of_strings_extracting_match_to_a_regex_2stringlistFilter_list_of_strings_extracting_match_to_a_regex_2groupFilter_list_of_strings_extracting_match_to_a_regex_2regexThresholderseqSimThresholderreqSimAskmessageAsktitleBeanshell_3target_file_pathBeanshell_3source_file_pathBeanshell_3progpathBeanshell_3base_dirKeggPathwayIDskeggimageurlkeggGeneNamescoloured_imagesenzyme_listgenes_listOutputtestKegg pathway diagrams2010-03-12 18:40:11.636 GMTKegg pathway diagrams with enzymes coloured on path diagram2010-03-14 13:49:59.744 GMTFind pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - just duplicating the specified colours. However with almost no Taverna documentation to speak of, none of my efforts wanted to work so far.2010-03-14 13:52:16.638 GMTJannetta Steyn2010-03-12 18:39:29.404 GMTFind pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.2010-03-13 07:59:28.240 GMTfor each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures2010-03-12 18:39:23.38 GMTWorkflowforProteinSequenceAnalysisdrugs_file11Enter a list of protein IDs. e.g:
Q96TS5
Q12575
AAA33739
Q96TS6
AAA337412010-03-14 16:35:01.56 GMTD:\blastdb\drugs.fasta2010-03-18 18:51:50.306 GMTtext/plain2010-03-14 16:35:01.56 GMTPath to known drug targets file - amino acid sequences in FastA format.2010-03-18 18:48:35.820 GMTD:\Drutex\2010-03-18 18:48:41.242 GMTPath to known drug targets file - amino acid sequences in FastA format.
NB MUST be the path as a value, NOT as a file location.2010-03-18 18:53:13.516 GMTPath to known drug targets file - amino acid sequences in FastA format.
NB MUST be the path as a value, NOT as a file location. Also don't forget the final slash as in example.2010-03-18 18:49:10.739 GMTpath_proteins00D:\Drutex\path_proteins.txt2010-03-18 18:51:39.73 GMTPath to list of unique proteins found in pathogen but not in non-pathogen (i.e. from section 2). File must be a text file with a list of FULL paths to protein files. Protein files must contain a single amino acid sequence in FastA format.
NB MUST be the path as a value, NOT as a file location. Also don't forget the final slash as in example.2010-03-18 18:51:19.637 GMTDBSavePath00DBSavePath - Workflow wide path, effectively the current working directory. This where the blast database and blast output files will be saved.2010-03-18 18:52:38.756 GMTD:\Drutex\2010-03-18 18:52:55.724 GMTDBSavePath - Workflow wide path, effectively the current working directory. This where the blast database and blast output files will be saved.
MUST be path as a value NOT file location. MUST contain final slash as in example.2010-03-18 18:53:04.626 GMTDBSavePath - Workflow wide path, effectively the current working directory. This where the blast database and blast output files will be saved.
MUST be path as a value NOT file location2010-03-18 18:52:49.958 GMToutputlocal_create_blastdbcommand0args1net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.LocalCommandworkflowjava.lang.Stringtruecommand0'text/plain'java.lang.Stringtrueargs1l('text/plain')0result0UserNameHere2010-03-16 13:55:15.191 GMTUserNameHere2010-03-16 13:56:35.777 GMTUserNameHere2010-03-16 10:59:51.399 GMTUserNameHere2010-03-15 15:15:42.513 GMTUserNameHere2010-03-16 11:00:03.8 GMTUserNameHere2010-03-16 13:57:09.852 GMTUserNameHere2010-03-16 13:55:43.225 GMTnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFormatDB_Pathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivityD:\bin\formatdb.exenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_formatdb_cmdArgsfastAFileName0DBSavePath0cmdArgsList11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.StringtruefastAFileName0text/plainjava.lang.StringtrueDBSavePath0text/plain1cmdArgsList1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_Filefileurl0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.TextFileReaderworkflowjava.lang.Stringtruefileurl0'text/plain'0filecontents0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.SplitByRegexworkflowjava.lang.Stringtruestring0'text/plain'java.lang.Stringtrueregex0'text/plain'1split1UserNameHere2010-03-17 16:07:24.464 GMTUserNameHere2010-03-17 16:05:25.448 GMTnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex1value00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity\nnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeNested_workflowsequenceFileName0DBSaveLocation0blastout00net.sf.taverna.t2.activitiesdataflow-activity1.0net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeNested_workflow_2blast_out_paths0DBSaveLocation0reqEVal0complete11net.sf.taverna.t2.activitiesdataflow-activity1.0net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeAskmessage0title0answer00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.ui.AskWorkerworkflowjava.lang.Stringtruetitle0'text/plain'java.lang.Stringtruemessage0'text/plain'0answer0UserNameHere2010-03-18 14:38:38.654 GMTUserNameHere2010-03-18 14:37:37.630 GMTnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMessagevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivityPlease enter the maximum E value at which proteins will be considered significantly similarnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTitlevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivityProtein similarity thresholdnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokelocal_create_blastdbcommandlocal_create_blastdbargscreate_formatdb_cmdArgsfastAFileNamecreate_formatdb_cmdArgsDBSavePathRead_Text_FilefileurlSplit_string_into_string_list_by_regular_expressionstringSplit_string_into_string_list_by_regular_expressionregexNested_workflowsequenceFileNameNested_workflowDBSaveLocationNested_workflow_2blast_out_pathsNested_workflow_2DBSaveLocationNested_workflow_2reqEValAskmessageAsktitleoutputMariana de Oliveira Braga Teixeira Monteiro2010-03-14 16:35:04.971 GMTThis workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.2010-03-14 16:35:04.971 GMTWorkflow for Protein Sequence Analysis2010-03-14 16:35:04.971 GMTWorkflow37blast_out_paths00DBSaveLocation00reqEVal00completeBeanshellblastOutPath0DBSaveLocation0eValTol0complete11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.StringtrueblastOutPath0text/plainjava.lang.StringtrueeValTol0text/plainjava.lang.StringtrueDBSaveLocation0text/plain1complete1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshellblastOutPathBeanshellDBSaveLocationBeanshelleValTolcompleteWorkflow25DBSaveLocation00sequenceFileName00blastoutcreate_blastall_cmdArgssequenceFileName0DBSaveLocation0group0regex0cmdArgsList11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowjava.lang.StringtruesequenceFileName0'text/plain'java.lang.StringtrueDBSaveLocation0text/plainjava.lang.Stringtrueregex0text/plainjava.lang.Stringtruegroup0text/plain1cmdArgsList1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokerunBlastSearchargs1command0blastOut00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivitynet.sourceforge.taverna.scuflworkers.io.LocalCommandworkflowjava.lang.Stringtruecommand0'text/plain'java.lang.Stringtrueargs1l('text/plain')0blastOut0UserNameHere2010-03-17 15:39:28.685 GMTUserNameHere2010-03-18 09:16:48.220 GMTUserNameHere2010-03-18 09:13:44.623 GMTnet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBlastall_pathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivityD:\bin\blastall.exenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGroupvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregexvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity.*\\(.*\..*)net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_blastall_cmdArgssequenceFileNamecreate_blastall_cmdArgsDBSaveLocationcreate_blastall_cmdArgsgroupcreate_blastall_cmdArgsregexrunBlastSearchargsrunBlastSearchcommandblastoutWorkflow89part100part200stringConcatenate_two_stringsstring10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringConcatworkflowjava.lang.Stringtruestring10'text/plain'java.lang.Stringtruestring20'text/plain'0output0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConcatenate_two_strings_2string10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivityorg.embl.ebi.escience.scuflworkers.java.StringConcatworkflowjava.lang.Stringtruestring10'text/plain'java.lang.Stringtruestring20'text/plain'0output0'text/plain'net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokestring2_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity:net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce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