Extract_proteins_from_xml_blast_resultsblastFile00 filepath of blast results in order to import them in 2010-03-19 03:42:16.938 GMT tfasta00 imported fasta of target proteins 2010-03-19 03:43:58.712 GMT list_of_proteins00 filepath used to save the list of proteins of interest 2010-03-19 03:41:38.406 GMT end_file_path00 filepath used to save a fasta format of the proteins of interest 2010-03-19 03:44:31.67 GMT Read_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 1net.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 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeExtract_unique_proteinsxml_result0gi_lines_val00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true xml_result 0 text/plain 0 gi_lines_val 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.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 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTfasta_parsergi_val0tfasta_in0cfasta_out00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true gi_val 0 text/plain java.lang.String true tfasta_in 0 text/plain 0 cfasta_out 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.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 0net.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 1net.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 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_gisgi_lines_in0gis00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true gi_lines_in 0 text/plain 0 gis 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.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 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeWrite_Text_File_2filecontents0outputFile0net.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 1net.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 0net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeRead_Text_FilefileurlblastFileExtract_unique_proteinsxml_resultRead_Text_FilefilecontentsTfasta_parsergi_valExtract_unique_proteinsgi_lines_valTfasta_parsertfasta_intfastaWrite_Text_FilefilecontentsTfasta_parsercfasta_outWrite_Text_FileoutputFileend_file_pathextract_gisgi_lines_inExtract_unique_proteinsgi_lines_valWrite_Text_File_2filecontentsextract_gisgisWrite_Text_File_2outputFilelist_of_proteins 2010-03-19 03:31:14.148 GMT The workflow extracts a list of proteins from the target genome that may be known drugs using the blast similarity results. 2010-03-19 03:39:32.810 GMT Bela Tiwari 2010-03-15 11:30:59.109 GMT fetchEnsemblSeqsAndBlast 2010-03-15 11:30:59.109 GMT This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you.Shortcomings:The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created.All files created in the working directory are not yet coded to be deleted via the workflow. Ideally there would be an option that a user could choose that would set the files to be kept or deleted after use. 2010-03-15 11:30:59.109 GMT Extract proteins from xml blast results 2010-03-19 03:35:24.348 GMT 2010-03-19 03:31:29.374 GMT nclteamc 2010-03-19 03:31:22.978 GMT