Kegg_pathway_diagrams_with_enzymes_coloured_on_path_diagramSpecies00 The three letter species code 2010-03-13 08:05:45.460 GMT sac 2010-03-19 15:36:27.447 GMT KEGG 2010-03-13 08:05:23.807 GMT eco 2010-03-14 13:52:54.438 GMT hsa 2010-03-14 01:18:26.660 GMT eco 2010-03-13 08:06:06.679 GMT The three letter species code used by KEGG 2010-03-13 08:05:59.216 GMT bg_color11 The background colour for the boxes containing enzymes. 2010-03-14 01:11:59.113 GMT red #ff0000 2010-03-14 01:12:42.141 GMT red 2010-03-19 12:26:05.816 GMT The 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 GMT fg_color11 The 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 GMT green #00ff00 2010-03-14 01:13:09.889 GMT #00ff00 2010-03-19 12:26:12.816 GMT path_proteins11 D:\Drutex\path_proteins.txt 2010-03-19 12:55:59.921 GMT drugs_file11 D:\blastdb\drugs.fasta 2010-03-19 12:55:41.391 GMT DBSavePath00 D:\Drutex\ 2010-03-19 12:55:23.579 GMT Sequence100 Full 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 GMT D:\CSC8308\newman.fna 2010-03-19 15:37:42.730 GMT Sequence200 D:\CSC8308\newman.fna 2010-03-19 15:39:19.310 GMT Full 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 GMT source_file_path00 EMBL 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 GMT col_chrom.emb 2010-03-19 15:37:17.227 GMT target_file_path00 EMBL 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 GMT newman_chrom.emb 2010-03-19 15:34:22.161 GMT blast_bin_dir00 D:\mgcat_v15b\ 2010-03-19 15:33:51.436 GMT File path to folder which contains FormatDB.exe 2010-03-19 15:34:03.890 GMT KeggPathwayIDs A list of the pathways found. 2010-03-13 08:15:37.559 GMT path:hsa00010 2010-03-13 08:15:43.143 GMT keggimageurl The URLs of the images produced for the KeggImage output 2010-03-13 08:14:19.106 GMT http://soap.genome.jp/tmp/mark_pathway_www_api.126846700018802/hsa00010.png 2010-03-13 08:14:44.67 GMT The URLs of the images produced for the KeggImage output. 2010-03-13 08:14:48.935 GMT keggGeneNames hsa:5236 2010-03-13 08:17:09.171 GMT A list of the gene ids, that was given as input with the species code concatenated. 2010-03-13 08:17:01.144 GMT coloured_images List of pathway diagram with enzyme boxes coloured in specified colours 2010-03-14 01:10:28.178 GMT enzyme_list ec:1.1.1.27 2010-03-14 01:11:23.41 GMT List of enzyme id retrieve from Kegg using get_enzymes_by_gene 2010-03-14 01:11:07.986 GMT genes_list List of ids that are enzymes 2010-03-14 01:09:09.981 GMT hsa:160287 2010-03-14 01:09:28.521 GMT OutputtestWorkflow89part10part20string00net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.WebImageFetcher workflow java.lang.String true url 0 'text/x-taverna-web-url' java.lang.String true base 0 'text/x-taverna-web-url' 0 image 0 'image/*' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.WSDLActivity http://soap.genome.jp/KEGG.wsdl color_pathway_by_objects net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.WSDLActivity http://soap.genome.jp/KEGG.wsdl get_enzymes_by_gene net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.WSDLActivity http://soap.genome.jp/KEGG.wsdl get_genes_by_enzyme net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.WSDLActivity http://soap.genome.jp/KEGG.wsdl get_pathways_by_genes net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates workflow java.lang.String true stringlist 1 l('text/plain') 1 strippedlist 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.BeanshellActivity workflow java.lang.String true bg_color 0 text/plain java.lang.String true fg_color 0 text/plain java.lang.String true genes_list 1 text/plain 1 bg_colors 1 1 fg_colors 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Loop net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 1 l(l('')) 1 outputlist 1 UserNameHere 2010-03-16 12:45:55.247 GMT UserNameHere 2010-03-16 12:46:27.439 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 1 l(l('')) 1 outputlist 1 UserNameHere 2010-03-16 12:46:45.95 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true regex 0 'text/plain' java.lang.String true group 0 'text/plain' 1 filteredlist 1 UserNameHere 2010-03-18 20:59:54.509 GMT UserNameHere 2010-03-18 21:00:48.431 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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 .*gi\|(\w*)\| net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshell_2in01n22net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true in0 1 text/plain 2 n 2 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFlatten_List_10inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokerunMGCATcommand0workingdir0args0net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.LocalCommand workflow java.lang.String true command 0 'text/plain' java.lang.String true args 0 l('text/plain') java.lang.String true workingdir 0 text/plain 0 result 0 UserNameHere 2010-03-16 20:49:11.432 GMT UserNameHere 2010-03-16 20:40:07.800 GMT UserNameHere 2010-03-16 20:29:02.574 GMT UserNameHere 2010-03-16 20:38:23.832 GMT UserNameHere 2010-03-16 20:44:41.769 GMT UserNameHere 2010-03-16 16:23:31.917 GMT UserNameHere 2010-03-16 16:20:34.383 GMT UserNameHere 2010-03-16 20:41:02.274 GMT UserNameHere 2010-03-16 16:24:57.923 GMT UserNameHere 2010-03-16 21:02:05.625 GMT UserNameHere 2010-03-16 20:27:21.661 GMT UserNameHere 2010-03-16 20:45:44.987 GMT UserNameHere 2010-03-16 16:19:21.614 GMT UserNameHere 2010-03-16 20:46:31.676 GMT UserNameHere 2010-03-16 20:42:41.149 GMT UserNameHere 2010-03-16 20:47:19.965 GMT UserNameHere 2010-03-16 16:21:13.44 GMT UserNameHere 2010-03-16 20:33:31.554 GMT UserNameHere 2010-03-16 16:21:54.265 GMT UserNameHere 2010-03-16 20:34:16.471 GMT UserNameHere 2010-03-16 20:42:11.268 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMGCAT_Pathvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity D:\mgcat_v15b\mgcat.exe net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWorking_Dirvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity D:\blastdb\ net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.TextFileReader workflow java.lang.String true fileurl 0 'text/plain' 0 filecontents 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.SplitByRegex workflow java.lang.String true string 0 'text/plain' java.lang.String true regex 0 'text/plain' 1 split 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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 \n net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilter_List_of_Strings_by_regexstringlist1regex10regex20file20group0file0filteredlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FilterStringList workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true regex1 0 'text/plain' java.lang.String true file 0 text/plain java.lang.String true regex2 0 text/plain java.lang.String true file2 0 text/plain java.lang.String true group 0 text/plain 1 filteredlist 1 UserNameHere 2010-03-16 21:27:44.184 GMT UserNameHere 2010-03-16 20:01:11.947 GMT UserNameHere 2010-03-16 20:00:15.477 GMT UserNameHere 2010-03-16 20:06:18.820 GMT UserNameHere 2010-03-16 21:28:23.481 GMT UserNameHere 2010-03-16 17:07:30.131 GMT UserNameHere 2010-03-16 21:06:42.478 GMT UserNameHere 2010-03-16 20:20:57.123 GMT UserNameHere 2010-03-16 17:19:56.20 GMT UserNameHere 2010-03-16 21:29:56.300 GMT UserNameHere 2010-03-16 21:10:59.598 GMT UserNameHere 2010-03-16 21:26:18.741 GMT UserNameHere 2010-03-16 19:56:51.562 GMT UserNameHere 2010-03-16 21:18:09.286 GMT UserNameHere 2010-03-16 21:20:26.475 GMT UserNameHere 2010-03-16 19:57:29.691 GMT UserNameHere 2010-03-16 21:35:15.777 GMT UserNameHere 2010-03-16 19:59:13.375 GMT UserNameHere 2010-03-16 19:58:36.225 GMT UserNameHere 2010-03-16 17:31:11.731 GMT UserNameHere 2010-03-16 21:38:29.187 GMT UserNameHere 2010-03-16 20:06:50.350 GMT UserNameHere 2010-03-16 17:08:09.856 GMT UserNameHere 2010-03-16 19:53:25.572 GMT UserNameHere 2010-03-16 21:37:27.450 GMT UserNameHere 2010-03-16 21:29:13.59 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity ^file=.* net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRegex3value00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity ^file1=.* net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWrite_Text_Filefilecontents0outputFile0net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.TextFileWriter workflow java.lang.String true outputFile 0 'text/plain' java.lang.String true filecontents 0 'text/plain' 0 outputFile 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConcatenate_stringsstringlist1output00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringConcat workflow java.lang.String true stringlist 1 'text/plain' 0 output 0 UserNameHere 2010-03-16 20:16:21.695 GMT UserNameHere 2010-03-16 20:13:24.460 GMT UserNameHere 2010-03-16 20:12:12.586 GMT UserNameHere 2010-03-16 20:14:42.471 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity D:\mgcat_v15b\mgcat.ini net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.TextFileReader workflow java.lang.String true fileurl 0 'text/plain' 0 filecontents 0 UserNameHere 2010-03-16 22:27:39.980 GMT UserNameHere 2010-03-16 22:29:02.510 GMT UserNameHere 2010-03-16 22:26:37.122 GMT UserNameHere 2010-03-16 22:25:43.329 GMT UserNameHere 2010-03-16 22:18:02.467 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.SplitByRegex workflow java.lang.String true string 0 'text/plain' java.lang.String true regex 0 'text/plain' 1 split 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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 \n net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList workflow java.lang.String true stringlist 1 l('text/plain') java.lang.String true regex 0 'text/plain' java.lang.String true group 0 'text/plain' 1 filteredlist 1 UserNameHere 2010-03-16 22:45:05.540 GMT UserNameHere 2010-03-16 22:45:51.185 GMT UserNameHere 2010-03-16 22:45:13.563 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity Total.coverage.among.all.sequences.(.*)\% net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.BeanshellActivity workflow java.lang.String true seqSim 0 text/plain java.lang.String true reqSim 0 text/plain 0 cont 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity net.sourceforge.taverna.scuflworkers.ui.AskWorker workflow java.lang.String true title 0 'text/plain' java.lang.String true message 0 'text/plain' 0 answer 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity Please enter the minimum required strain similarity net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity Genome similarity net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity D:\mgcat_v15b\mgcat.ini net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.BeanshellActivity workflow java.lang.String true base_dir 0 text/plain java.lang.String true target_file_path 0 text/plain java.lang.String true source_file_path 0 text/plain java.lang.String true progpath 0 text/plain 0 database_dir 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWorkflow89part1SpeciesWorkflow89part2Filter_list_of_strings_extracting_match_to_a_regexfilteredlistGet_Image_From_URL_2urlcolor_pathway_by_objectsreturncolor_pathway_by_objectsbg_color_listFlatten_List_6outputlistcolor_pathway_by_objectsfg_color_listFlatten_List_8outputlistcolor_pathway_by_objectsobject_id_listRemove_String_Duplicatesstrippedlistcolor_pathway_by_objectspathway_idFlatten_List_10outputlistget_enzymes_by_genegenes_idWorkflow89stringget_genes_by_enzymeorgSpeciesget_genes_by_enzymeenzyme_idFlatten_Listoutputlistget_pathways_by_genesgenes_id_listBeanshell_2nFlatten_Listinputlistget_enzymes_by_genereturnFlatten_List_2inputlistget_genes_by_enzymereturnRemove_String_DuplicatesstringlistFlatten_List_2outputlistBeanshellgenes_listRemove_String_DuplicatesstrippedlistBeanshellbg_colorbg_colorBeanshellfg_colorfg_colorFlatten_List_3inputlistBeanshellbg_colorsFlatten_List_4inputlistBeanshellfg_colorsFlatten_List_5inputlistFlatten_List_3outputlistFlatten_List_6inputlistFlatten_List_5outputlistFlatten_List_7inputlistFlatten_List_4outputlistFlatten_List_8inputlistFlatten_List_7outputlistNested_workflowdrugs_filedrugs_fileNested_workflowpath_proteinspath_proteinsNested_workflowDBSavePathDBSavePathFlatten_List_9inputlistNested_workflowoutputFlatten_List_2_2inputlistFlatten_List_9outputlistFlatten_List_3_2inputlistFlatten_List_2_2outputlistFilter_list_of_strings_extracting_match_to_a_regexstringlistFlatten_List_3_2outputlistFilter_list_of_strings_extracting_match_to_a_regexgroupGroupvalueFilter_list_of_strings_extracting_match_to_a_regexregexRegexvalueBeanshell_2in0Workflow89stringFlatten_List_10inputlistget_pathways_by_genesreturnrunMGCATcommandMGCAT_PathvaluerunMGCATworkingdirWorking_DirvaluerunMGCATargsINI_FilevalueRead_Text_FilefileurlINI_PathvalueSplit_string_into_string_list_by_regular_expressionstringRead_Text_FilefilecontentsSplit_string_into_string_list_by_regular_expressionregexRegex1valueFilter_List_of_Strings_by_regexstringlistSplit_string_into_string_list_by_regular_expressionsplitFilter_List_of_Strings_by_regexregex1Regex2valueFilter_List_of_Strings_by_regexregex2Regex3valueFilter_List_of_Strings_by_regexfile2Sequence2Filter_List_of_Strings_by_regexgroupGroup_2valueFilter_List_of_Strings_by_regexfileSequence1Write_Text_FilefilecontentsConcatenate_stringsoutputWrite_Text_FileoutputFileINI_PathvalueConcatenate_stringsstringlistFilter_List_of_Strings_by_regexfilteredlistRead_Text_File_2fileurlWorking_DirvalueSplit_string_into_string_list_by_regular_expression_2stringRead_Text_File_2filecontentsSplit_string_into_string_list_by_regular_expression_2regexRegex1_2valueFilter_list_of_strings_extracting_match_to_a_regex_2stringlistSplit_string_into_string_list_by_regular_expression_2splitFilter_list_of_strings_extracting_match_to_a_regex_2groupGroup1valueFilter_list_of_strings_extracting_match_to_a_regex_2regexregex2valueThresholderseqSimFilter_list_of_strings_extracting_match_to_a_regex_2filteredlistThresholderreqSimAskanswerAskmessageMessagevalueAsktitleTitlevalueBeanshell_3target_file_pathtarget_file_pathBeanshell_3source_file_pathsource_file_pathBeanshell_3progpathblast_bin_dirBeanshell_3base_dirDBSavePathKeggPathwayIDsFlatten_List_10outputlistkeggimageurlcolor_pathway_by_objectsreturnkeggGeneNamesWorkflow89stringcoloured_imagesGet_Image_From_URL_2imageenzyme_listFlatten_Listoutputlistgenes_listRemove_String_DuplicatesstrippedlistOutputFilter_list_of_strings_extracting_match_to_a_regexfilteredlisttestBeanshell_3database_dir Kegg pathway diagrams 2010-03-12 18:40:11.636 GMT Kegg pathway diagrams with enzymes coloured on path diagram 2010-03-14 13:49:59.744 GMT Find 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 GMT Jannetta Steyn 2010-03-12 18:39:29.404 GMT Find 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 GMT for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures 2010-03-12 18:39:23.38 GMT WorkflowforProteinSequenceAnalysisdrugs_file11 Enter a list of protein IDs. e.g: Q96TS5 Q12575 AAA33739 Q96TS6 AAA33741 2010-03-14 16:35:01.56 GMT D:\blastdb\drugs.fasta 2010-03-18 18:51:50.306 GMT text/plain 2010-03-14 16:35:01.56 GMT Path to known drug targets file - amino acid sequences in FastA format. 2010-03-18 18:48:35.820 GMT D:\Drutex\ 2010-03-18 18:48:41.242 GMT Path 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 GMT Path 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 GMT path_proteins00 D:\Drutex\path_proteins.txt 2010-03-18 18:51:39.73 GMT Path 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 GMT DBSavePath00 DBSavePath - 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 GMT D:\Drutex\ 2010-03-18 18:52:55.724 GMT DBSavePath - 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 GMT DBSavePath - 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 2010-03-18 18:52:49.958 GMT outputlocal_create_blastdbcommand0args1net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.LocalCommand workflow java.lang.String true command 0 'text/plain' java.lang.String true args 1 l('text/plain') 0 result 0 UserNameHere 2010-03-16 13:55:15.191 GMT UserNameHere 2010-03-16 13:56:35.777 GMT UserNameHere 2010-03-16 10:59:51.399 GMT UserNameHere 2010-03-15 15:15:42.513 GMT UserNameHere 2010-03-16 11:00:03.8 GMT UserNameHere 2010-03-16 13:57:09.852 GMT UserNameHere 2010-03-16 13:55:43.225 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.StringConstantActivity D:\bin\formatdb.exe net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.BeanshellActivity workflow java.lang.String true fastAFileName 0 text/plain java.lang.String true DBSavePath 0 text/plain 1 cmdArgsList 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.TextFileReader workflow java.lang.String true fileurl 0 'text/plain' 0 filecontents 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.SplitByRegex workflow java.lang.String true string 0 'text/plain' java.lang.String true regex 0 'text/plain' 1 split 1 UserNameHere 2010-03-17 16:07:24.464 GMT UserNameHere 2010-03-17 16:05:25.448 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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 \n net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity net.sourceforge.taverna.scuflworkers.ui.AskWorker workflow java.lang.String true title 0 'text/plain' java.lang.String true message 0 'text/plain' 0 answer 0 UserNameHere 2010-03-18 14:38:38.654 GMT UserNameHere 2010-03-18 14:37:37.630 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity Please enter the maximum E value at which proteins will be considered significantly similar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity Protein similarity threshold net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokelocal_create_blastdbcommandFormatDB_Pathvaluelocal_create_blastdbargscreate_formatdb_cmdArgscmdArgsListcreate_formatdb_cmdArgsfastAFileNamedrugs_filecreate_formatdb_cmdArgsDBSavePathDBSavePathRead_Text_Filefileurlpath_proteinsSplit_string_into_string_list_by_regular_expressionstringRead_Text_FilefilecontentsSplit_string_into_string_list_by_regular_expressionregexregex1valueNested_workflowsequenceFileNameSplit_string_into_string_list_by_regular_expressionsplitNested_workflowDBSaveLocationDBSavePathNested_workflow_2blast_out_pathsNested_workflowblastoutNested_workflow_2DBSaveLocationDBSavePathNested_workflow_2reqEValAskanswerAskmessageMessagevalueAsktitleTitlevalueoutputNested_workflow_2complete Mariana de Oliveira Braga Teixeira Monteiro 2010-03-14 16:35:04.971 GMT This 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 GMT Workflow for Protein Sequence Analysis 2010-03-14 16:35:04.971 GMT Workflow37blast_out_paths00DBSaveLocation00reqEVal00completeBeanshellblastOutPath0DBSaveLocation0eValTol0complete11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true blastOutPath 0 text/plain java.lang.String true eValTol 0 text/plain java.lang.String true DBSaveLocation 0 text/plain 1 complete 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBeanshellblastOutPathblast_out_pathsBeanshellDBSaveLocationDBSaveLocationBeanshelleValTolreqEValcompleteBeanshellcompleteWorkflow25DBSaveLocation00sequenceFileName00blastoutcreate_blastall_cmdArgssequenceFileName0DBSaveLocation0group0regex0cmdArgsList11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true sequenceFileName 0 'text/plain' java.lang.String true DBSaveLocation 0 text/plain java.lang.String true regex 0 text/plain java.lang.String true group 0 text/plain 1 cmdArgsList 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.LocalworkerActivity net.sourceforge.taverna.scuflworkers.io.LocalCommand workflow java.lang.String true command 0 'text/plain' java.lang.String true args 1 l('text/plain') 0 blastOut 0 UserNameHere 2010-03-17 15:39:28.685 GMT UserNameHere 2010-03-18 09:16:48.220 GMT UserNameHere 2010-03-18 09:13:44.623 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 0 0 0 net.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.StringConstantActivity D:\bin\blastall.exe net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.StringConstantActivity 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_blastall_cmdArgssequenceFileNamesequenceFileNamecreate_blastall_cmdArgsDBSaveLocationDBSaveLocationcreate_blastall_cmdArgsgroupGroupvaluecreate_blastall_cmdArgsregexregexvaluerunBlastSearchargscreate_blastall_cmdArgscmdArgsListrunBlastSearchcommandBlastall_pathvalueblastoutrunBlastSearchblastOutWorkflow89part100part200stringConcatenate_two_stringsstring10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringConcat workflow java.lang.String true string1 0 'text/plain' java.lang.String true string2 0 'text/plain' 0 output 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringConcat workflow java.lang.String true string1 0 'text/plain' java.lang.String true string2 0 'text/plain' 0 output 0 'text/plain' net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.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.Parallelize 1 net.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.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeConcatenate_two_stringsstring1part1Concatenate_two_stringsstring2string2_valuevalueConcatenate_two_strings_2string1Concatenate_two_stringsoutputConcatenate_two_strings_2string2part2stringConcatenate_two_strings_2output