Tutorial_1_WorkflowUniProt_Accession2GeneID00proteinsgenescomparisonLine_Breakvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \r\n|\n net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 l('text/plain') 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeXPath_Servicexml_text0nodelist11net.sf.taverna.t2.activitiesxpath-activity1.4net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="UTF-8"?> <!-- BSI implementation of pepXML output for PEAKS Studio --><msms_pipeline_analysis xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML pepXML_v18_peaks_denovo.xsd" date="15-Jul-13 20:54" summary_xml="peptide.xml"> <msms_run_summary base_name="filename" raw_data_type="" raw_data=""> <spectrum_query spectrum="GSC-Block6-Mascot.mgf" start_scan="9552" end_scan="9552" precursor_neutral_mass="841.5027" assumed_charge="2" index="1"> <search_result> <search_hit hit_rank="1" peptide="VATVSLPR" protein="AP054|TRYP_PIG" num_tot_proteins="1" calc_neutral_pep_mass="841.5021" massdiff="0.7" protein_mw="24409.48"> <search_score name="Score (%)" value="99.94"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="GSC-Block6-Mascot.mgf" start_scan="9511" end_scan="9511" precursor_neutral_mass="841.5027" assumed_charge="2" index="2"> <search_result> <search_hit hit_rank="1" peptide="VATVSLPR" protein="AP054|TRYP_PIG" num_tot_proteins="1" calc_neutral_pep_mass="841.5021" massdiff="0.7" protein_mw="24409.48"> <search_score name="Score (%)" value="99.94"/> </search_hit> </search_result> </spectrum_query> <spectrum_query spectrum="GSC-Block6-Mascot.mgf" start_scan="9427" end_scan="9427" precursor_neutral_mass="841.5027" assumed_charge="2" index="3"> <search_result> <search_hit hit_rank="1" peptide="VATVSLPR" protein="AP054|TRYP_PIG" num_tot_proteins="1" calc_neutral_pep_mass="841.5021" massdiff="0.7" protein_mw="24409.48"> <search_score name="Score (%)" value="99.94"/> </search_hit> </search_result> </spectrum_query> </msms_run_summary> </msms_pipeline_analysis> /default:msms_pipeline_analysis/default:msms_run_summary/default:spectrum_query/default:search_result/default:search_hit/@protein default http://regis-web.systemsbiology.net/pepXML xsi http://www.w3.org/2001/XMLSchema-instance net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSpectral_Countingin11out111net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 1 text/plain java.lang.String true out1 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_Gene_Expression_and_Spectral_Countsin11in21out111net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 1 text/plain java.lang.String true in2 1 text/plain java.lang.String true out1 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGene_Expression_with_UniProt_Accessionsin11in21out111net.sf.taverna.t2.activitiesbeanshell-activity1.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity in1 1 text/plain java.lang.String true in2 1 text/plain java.lang.String true out1 1 1 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeTranscriptomics_Datavalue00 An NSC11 dataset in GEO 2014-04-16 15:06:22.667 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GSM1098404&id=13672&db=GeoDb_blob95 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeProteomics_Datavalue00 An NSC11 PRIDE dataset in pepXML 2014-04-16 15:05:21.109 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity http://www.ebi.ac.uk/pride/archive/files/21260108 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Web_Page_from_URLurl0contents00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity url 0 'text/x-taverna-web-url' java.lang.String true base 0 'text/x-taverna-web-url' java.lang.String true contents 0 'text/plain,text/html' 0 workflow org.embl.ebi.escience.scuflworkers.java.WebPageFetcher net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeImport_into_R_and_Plotin11genes11proteins11comparison00net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity in1 1 false genes 1 1 proteins 1 1 comparison 0 0 false localhost 6311 false false in1 STRING_LIST genes DOUBLE_LIST proteins DOUBLE_LIST comparison PNG_FILE net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSpreadsheetImportfileurl0A11net.sf.taverna.t2.activitiesspreadsheet-import-activity1.4net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportActivity 0 0 22 17748 NaN false false true USER_DEFINED PORT_PER_COLUMN , net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSplit_string_into_string_list_by_regular_expressionregexLine_BreakvalueSplit_string_into_string_list_by_regular_expressionstringUniProt_Accession2GeneIDXPath_Servicexml_textGet_Web_Page_from_URLcontentsSpectral_Countingin1XPath_ServicenodelistMerge_Gene_Expression_and_Spectral_Countsin1Gene_Expression_with_UniProt_Accessionsout1Merge_Gene_Expression_and_Spectral_Countsin2Spectral_Countingout1Gene_Expression_with_UniProt_Accessionsin1Split_string_into_string_list_by_regular_expressionsplitGene_Expression_with_UniProt_Accessionsin2SpreadsheetImportAGet_Web_Page_from_URLurlProteomics_DatavalueImport_into_R_and_Plotin1Merge_Gene_Expression_and_Spectral_Countsout1SpreadsheetImportfileurlTranscriptomics_DatavalueproteinsImport_into_R_and_PlotproteinsgenesImport_into_R_and_PlotgenescomparisonImport_into_R_and_Plotcomparison f7a1fc68-9925-43ce-b2d1-a0dbbbc5e066 2014-04-10 09:09:31.535 UTC 377082d0-1474-4fe0-9cfc-8fcf9449c94b 2014-04-02 14:22:29.207 UTC 87c345fc-044d-4656-8deb-a16fd04d8b9e 2014-04-10 11:15:19.532 UTC 735f6139-20f2-468b-a6ca-14dfee9b9418 2014-04-11 16:54:46.876 UTC d5fbe6ed-62a0-4f47-acf0-13fa9321213f 2014-04-10 12:52:43.959 UTC 87307f57-e714-4e1c-ac90-f79838cc6905 2014-04-10 15:01:49.82 UTC 51f76764-7d7e-465d-bc6c-398f5a6b58cc 2014-04-11 15:57:35.685 UTC d06bc0b7-a90e-4bac-8d0a-d9ff81309cdc 2014-04-10 09:16:16.42 UTC ddfa4cc8-a398-4160-9e3a-a9f3568a4fb9 2014-04-16 12:03:22.782 UTC 88fe3117-7d15-49a8-99c1-585ee7158795 2014-04-10 15:59:49.288 UTC e14a86c4-93c8-4f73-9e5b-a1d6e619aa4a 2014-04-11 15:17:57.932 UTC 7082c3ae-cfa5-4d23-ac55-4952a7043337 2014-04-10 12:23:22.739 UTC cf054a74-765d-4faa-a5ed-b0d9e4ede462 2014-04-10 08:40:34.585 UTC e5eaf78a-aed7-4554-af5e-cbf9c354513c 2014-04-11 15:43:53.151 UTC 40a3a5ed-896e-4125-bc88-602823b43d31 2014-04-10 12:40:06.982 UTC e74bea4e-444b-4aaf-9622-56d78619f374 2014-04-10 12:40:16.974 UTC 84909816-b0c4-4c89-8afa-8aba6fcc96ed 2014-04-16 14:57:14.725 UTC 6705059c-4373-4885-921a-7c7565187731 2014-04-16 13:49:36.233 UTC a40ec4c2-9337-4c42-a7a0-33523637085c 2014-04-10 09:00:27.760 UTC be5930c5-5cbf-4063-83ab-76fb4c05c5d6 2014-04-03 10:21:21.355 UTC Tutorial 1 Workflow 2014-04-16 13:49:05.105 UTC b3ab0050-3755-4dd1-bc1a-eb712a5569d8 2014-04-11 10:50:32.36 UTC 624b2bb9-20bd-4031-b5cd-5209a7e8eefc 2014-04-10 08:41:13.446 UTC eda0ccc4-391a-4fc1-98fb-6e42065d4c82 2014-04-10 13:08:51.483 UTC 7354473c-a3c2-4752-b285-b267c41e9087 2014-04-10 08:15:54.465 UTC 6c4ba1c2-3708-4a96-ab21-cbdd82b5b8e8 2014-04-10 15:54:40.567 UTC b7346f77-1103-4430-9997-cb117b25edf6 2014-04-11 16:54:52.226 UTC c01cdbda-d2cd-4c6f-9bb8-c0bc4d495091 2014-04-16 13:50:50.429 UTC c2b94f14-12b5-429c-96ae-dd5e0e5eaf79 2014-04-16 13:15:06.252 UTC 98b40c74-c10c-4b14-bd4c-29c4d8ffbc43 2014-04-10 16:17:20.46 UTC 8c49db86-eb5a-448b-817c-dae6ca926896 2014-04-16 15:06:32.393 UTC Fetch and combine transcriptomics and proteomics data from NSC11 cells in GEO and PRIDE respectively. Apply spectral counting on the proteomics data. The workflow demonstrates how to combine data from different domains (here microarray- based transcriptomics and mass spectrometry-based proteomics) and do something useful with the data. The workflow also demonstrates spreadsheet import and XPath parsing of XML data. This workflow is for tutorial/educational use only. The cells were not grown under the same conditions, nor should raw spectral counts be used for protein quantitation. 2014-04-16 15:02:12.143 UTC e11e5eb7-82d9-42d4-aee3-f3462932fb7c 2014-04-11 16:36:57.105 UTC 581e568c-49d2-4a54-ab34-978faaaec19b 2014-04-02 14:37:18.987 UTC cb6e07cf-8588-4297-9ee1-5505982d973a 2014-04-10 15:17:51.740 UTC c57e9e39-1db0-48f5-b883-a723ec6060f8 2014-04-16 13:47:59.649 UTC 963eeaf2-59e5-408b-bc02-2f6ae11ba787 2014-04-11 16:09:13.74 UTC 89b73b19-d3ae-466f-8019-aac6b57b9e0d 2014-04-16 14:12:58.88 UTC 978fed05-38dd-4826-bc6a-b93eaf39bff6 2014-04-11 16:58:50.676 UTC 0b54c7ac-972f-4ca0-8494-e535850716c6 2014-04-02 14:25:58.123 UTC a26c08b7-7e05-4f47-9da8-0039d5170a37 2014-04-10 15:39:04.889 UTC f30f6906-0636-476d-b588-853fe07f2f3f 2014-04-10 12:08:43.147 UTC 738b4a62-4f61-4cdf-8608-661e5363e889 2014-04-10 09:13:26.849 UTC 5360f122-eed4-4112-9a21-249f4b4efb8a 2014-04-10 12:14:18.163 UTC b61f4e66-e576-4759-bddb-4f9ef449a19e 2014-04-11 11:36:41.551 UTC 8de03077-c99d-4660-b500-ec441dd985e9 2014-04-10 14:25:57.19 UTC de7e6bf1-ddcb-42f3-8280-2cc043a34694 2014-04-10 12:29:19.963 UTC d7c1af36-1cdc-40fa-a768-e9df1962ea89 2014-04-10 08:14:50.661 UTC 97e44e28-288e-486d-92eb-1c6f66baa512 2014-04-10 15:06:51.756 UTC acf37402-dd22-465a-9190-9131b4c834f8 2014-04-11 15:08:13.152 UTC a8ba2d22-55de-4daa-aa18-a2a4c2152cfe 2014-04-16 13:17:08.935 UTC d3280eac-3e7b-48a0-822b-c29064b6fe1e 2014-04-11 15:57:07.989 UTC a804cb58-a544-40fa-8d14-31c5b207423f 2014-04-10 08:30:58.865 UTC 5b91fabf-15e4-4ff7-b062-fe0fdf5fa642 2014-04-10 14:44:02.496 UTC 4618e389-988f-480c-9d3a-4a55d0780eb8 2014-04-10 14:54:22.930 UTC f7731663-8a5f-42e0-9b73-f54949c478e9 2014-04-10 08:54:07.797 UTC f77a6da1-880e-41c6-983e-109ba286f2cc 2014-04-16 14:11:20.887 UTC e11a1854-fbcf-484d-bc14-2baea456dbc8 2014-04-16 13:58:34.35 UTC f675de97-39db-4e5c-a96c-3ec0e52d0d5f 2014-04-11 16:58:43.78 UTC 6442390d-c8e6-4834-a784-125715892471 2014-04-10 11:52:45.785 UTC Magnus Palmblad 2014-04-16 13:48:33.815 UTC 2d69ebe6-33c5-4eba-bac8-b4528a7cbcbb 2014-04-10 13:01:00.792 UTC 52813653-20da-473e-94c8-5b0e7eb13d2b 2014-04-10 15:24:46.552 UTC e42d0d79-0dc1-4bf0-9c56-e36365a175e5 2014-04-10 15:57:52.632 UTC 9f5bb45d-d6cc-4435-96e6-a589df51186d 2014-04-10 12:19:50.337 UTC fa212469-d680-4249-9b3b-ec982ba66db6 2014-04-10 14:45:36.694 UTC a77778ec-35f7-438d-9d63-361dad292bfb 2014-04-16 12:08:16.371 UTC