Get_differentially_eexprs_file00 Location of the gene expression data 2013-02-10 13:37:25.683 UTC phenotypeData00 Location of the phenotype data 2013-02-10 13:37:05.497 UTC cf00 This input port takes an integer 1 or 2 or 3, which represents the first, second or third coefficient that we want to export from top table (limma), when we test for differential expression. We tested for DE between HD and normal tissue in each brain region. Therefore cf = 1 -> caudate nucleus cf = 2 -> frontal lobe cf = 3 -> cerebellum 2013-02-10 13:36:30.70 UTC working_dir00 the desired working directory. This workflow saves the results in .txt files and therefore its useful for the user to provide a directory to save the results in. 2013-08-27 14:12:05.873 UTC \tmp\ 2013-08-27 14:12:11.648 UTC filename_gene_idsfile_DE_genesget_necessary_filesphenotype_file0expression_file0datadirectory0 Loads the files we defined at the input ports. Gene expression and phenotypic data 2013-02-10 14:05:23.668 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity expression_file 0 false phenotype_file 0 false datadirectory 0 false false localhost 6311 true false expression_file TEXT_FILE phenotype_file TEXT_FILE datadirectory STRING 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.Invokecreate_expression_setprobe_ids11 create expression set object to be used by limma to test for DE 2013-02-10 14:05:38.36 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity out1 0 0 probe_ids 1 1 false localhost 6311 true false out1 STRING probe_ids STRING_LIST 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.Invokelibraries Load necessary libraries. If not existing libraries need to be installed beforehand. these are : library(ArrayExpress) library(hgu133b.db) library(limma) 2013-02-10 14:07:31.61 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity false localhost 6311 true false 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.Invokecompute_DE_limmanet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.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.Invokeprobenames_to_entrez_genes_ids_Array_Bprobe_ids_new1 translates probe names to entrez gene ids. For array B. 2013-02-10 14:05:56.986 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity probe_ids_new 1 false false localhost 6311 true false probe_ids_new STRING_LIST 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_DE_genescf0cut_off0filename00file_DE00net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.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.Invokecut_offvalue00 cut_off value for exporting DE genes. Here it is defined as 0.05. for other p value cut offs this constant needs to be changed 2013-02-10 14:19:52.532 UTC net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 0.05 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_necessary_filesphenotype_filephenotypeDataget_necessary_filesexpression_fileexprs_fileget_necessary_filesdatadirectoryworking_dirprobenames_to_entrez_genes_ids_Array_Bprobe_ids_newcreate_expression_setprobe_idsget_DE_genescfcfget_DE_genescut_offcut_offvaluefilename_gene_idsget_DE_genesfilenamefile_DE_genesget_DE_genesfile_DE 5548d9c9-bd5f-4fc6-837b-4fe9935ec707 2013-02-06 11:34:02.629 UTC 7a09762a-2c68-43d3-87a2-70c5e8f73c66 2013-02-09 19:57:32.282 UTC 22e9b9eb-b92e-460f-9622-7f1aff96981e 2013-02-05 15:44:58.356 UTC 2a7471db-928a-49f6-a66a-a5b685b3780e 2013-02-10 12:17:08.782 UTC 4cf63f2d-4be2-4307-b350-4069a2982687 2013-02-10 13:23:28.974 UTC 0563dc4b-563c-472f-81e3-c08ffcdee698 2013-02-09 18:45:41.407 UTC 68cdc139-59b3-4b2f-8c8b-2ca5a6a6ed4f 2013-02-10 14:15:48.191 UTC 8b237bf5-d9e7-48c2-97e5-6c1557b7776f 2011-10-24 07:40:00.69 UTC ba813f0b-1c79-47da-b1d6-4fe64ca37f6f 2013-02-09 20:09:43.841 UTC 74c24a75-440e-447c-b74b-8e47eaace057 2013-02-10 14:17:09.844 UTC 53aa8f13-6638-421e-81a1-903a7d6d4a46 2013-02-10 13:28:05.729 UTC d77fadfc-f7c4-44ee-9f8a-3184c080c1bc 2011-07-27 12:37:40.664 UTC 9f7c4c7b-2760-48ee-96d9-778fdeae25be 2013-02-09 17:11:00.288 UTC ccab3dc0-0ae0-46ed-984b-46cbf0bb2ac5 2013-08-27 15:00:07.27 UTC 38b14968-3465-48ea-938a-bdf33e7ae4f0 2013-02-09 17:06:41.237 UTC 28859247-6fe1-4abb-b57d-aa44019db2dc 2013-02-09 20:18:59.440 UTC d1f41a7e-b2b3-4114-ad64-17b200b78c87 2013-02-07 18:09:09.926 UTC 8b5c0f8d-4e68-46e9-b021-662a87ef3d58 2013-02-07 15:05:00.772 UTC c82cf035-b66f-436a-a223-38176e2c13d0 2013-02-09 17:08:26.193 UTC 46c42f3a-3fdd-4c05-845b-5d4326d07d75 2011-07-27 13:13:06.705 UTC e88bd9ca-0442-41a1-82c6-6fc78c16ff78 2011-07-27 11:22:13.130 UTC 06effb2a-395d-4df7-9773-2b7e81cf7ccb 2013-02-10 13:47:13.2 UTC 50f7c15b-5709-4662-b0f5-d6408b2ece96 2013-02-09 20:24:33.757 UTC a5ed14bd-8d64-4bbf-8a5c-c4ac54df6ce7 2011-07-27 12:20:53.487 UTC 71415f02-1d87-47fe-b9fa-19a3666f8fc0 2011-10-25 10:50:23.719 UTC c7c541c0-952d-41a9-a08c-95175b633427 2013-02-10 13:02:37.12 UTC e19b4e37-533b-4391-8e0d-ea3216fc0aa2 2013-02-09 18:17:43.403 UTC eb73f4cf-5ff9-4b25-a85d-a26278d80bd7 2011-07-27 15:44:18.798 UTC 4438a443-d190-41df-ae99-770948df13b0 2011-10-13 09:01:53.267 UTC dd6e9a9b-ead8-4b69-a479-89fc4539b052 2011-10-13 08:46:42.298 UTC 84c02ba8-1d13-48bf-82ea-af31d9273312 2013-02-10 14:05:24.723 UTC 2cd24e2b-ff49-4276-a08e-b43ab53ee48e 2013-02-09 16:09:24.811 UTC 0737eae5-079c-401f-a237-21c4ff566816 2011-07-27 12:24:40.450 UTC ca06ba1e-535e-4450-803d-916c5bb855bd 2013-02-09 18:32:54.190 UTC 857d309a-99cc-43ee-87af-acc30b26823f 2013-02-09 18:25:15.499 UTC ****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133b.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for DE. In this example we test for DE between HD and controls for each brain region. To test for DE between other variables, this information can be changed at the workflow "compute_DE_limma" 2013-08-28 15:16:25.568 UTC e71c3dcc-7b96-4e6d-8635-daa729b8b0d2 2013-02-09 20:21:45.273 UTC a75976a6-aa09-45d6-8555-031f877bf727 2013-08-27 15:20:59.239 UTC f589947d-9831-43da-8785-28583092db20 2013-02-09 16:19:15.570 UTC e5d7cefe-1bb7-43f5-b1a8-e33560e58955 2011-07-27 12:29:25.597 UTC 7c7e892f-8972-4ba2-990f-db556a0e085d 2013-02-10 13:49:12.460 UTC e69ac0bb-a3f9-4649-95d7-57c5cc9ff6b2 2013-02-10 13:37:06.780 UTC 7ec37103-e2ee-4a91-b8d2-3f73dd7c93eb 2011-10-19 18:26:57.228 UTC b2509878-da0e-4a0e-b492-998db9c5c0fb 2013-02-10 11:01:06.530 UTC 5f9292b9-fffb-44ef-9697-004505a8fd45 2011-07-27 11:23:54.423 UTC 02ef7030-4e2c-4167-8f92-53637a130a97 2013-02-09 18:43:35.627 UTC d1634299-0fd9-4913-9805-7c77be8ca49b 2013-02-10 14:22:26.288 UTC 265af27e-8eb2-48d5-a9d2-8805f5dd662a 2013-02-09 19:31:00.912 UTC 1b0bf25c-eef8-4fc9-b08a-b97f5fbd7fce 2013-02-05 18:24:48.878 UTC 03179cd5-0e09-4a1a-b2d8-1f5eea946cf7 2011-10-24 07:36:54.639 UTC 84ec68c4-533c-4da0-a492-f87defa9921a 2013-02-10 13:45:22.103 UTC 34a0e230-efaa-4910-945f-8608f6b541b3 2011-07-27 14:27:59.846 UTC 91fde642-56c7-43d5-bcb2-4aa3740c67db 2013-02-09 18:30:43.241 UTC ab1188e6-8089-473d-8efb-70a18ac5afcc 2011-10-19 18:20:25.832 UTC 31d1f631-6ee6-49a1-bd23-14fa32a5719a 2011-07-27 12:28:32.538 UTC 15c9ef40-2422-44a3-9ad6-b5731924f758 2013-02-10 10:56:51.918 UTC 34a6cff3-2033-4599-884f-7743c535443d 2013-02-09 19:38:35.772 UTC Get differentially expressed genes for Array B (one brain region) 2013-02-10 13:46:15.401 UTC 3a1d446b-2bcb-4024-a595-f79c1fd6725d 2013-02-09 18:27:03.230 UTC da2c79da-4bb8-4f24-a842-d2f2e15ab584 2013-02-10 14:08:31.174 UTC 5077cacd-aed1-4380-8b39-d5bc1c5fe841 2013-02-07 15:08:02.268 UTC f66526ee-833d-4a51-a130-fd972dcb4164 2011-07-27 10:59:42.981 UTC 06eb476e-fe84-4d91-911f-2cfa00143622 2013-08-27 14:12:10.555 UTC 07de2939-df2e-48a1-b0de-5dc0c1e0d7f5 2011-07-27 13:04:24.867 UTC f3994354-ff08-4a1e-a7fb-84be9ab6805c 2013-02-10 14:19:52.614 UTC 6c6b960b-fbec-44e8-917d-0526eceb5a33 2011-10-19 18:30:39.94 UTC 1424161d-f78d-4e50-8a47-65eb55eab79b 2013-02-10 13:36:35.217 UTC c6c630d9-4b95-4497-8851-7e5b1104a934 2013-02-09 18:22:29.750 UTC f78a1474-4ea5-4e92-ad39-d84b07d24f10 2011-07-27 13:32:09.513 UTC 78de8bc6-d7c4-4454-90e1-a2149c323eb1 2013-02-10 10:51:53.745 UTC a444b8fd-f6cb-4f00-8606-6db1f00df700 2011-07-27 14:31:53.366 UTC 934dcf9d-3054-4aba-8dda-a141aa7804e9 2013-02-10 14:05:38.736 UTC Eleni Mina 2013-02-10 13:42:59.422 UTC ec0798f7-25e5-4cc4-9ea7-18349d8ca585 2013-02-09 18:53:51.128 UTC 537888c0-27e6-4229-aecd-c63d75bf58fa 2013-02-07 14:59:08.799 UTC a74868f8-37e9-4800-ba3a-715137c259c9 2013-02-10 11:06:17.702 UTC e9806396-10ad-46b6-b2f2-49a6f2cf0bec 2011-07-27 12:59:24.833 UTC 936ab012-1643-4a2e-b301-ac175629e184 2011-07-27 13:24:52.237 UTC 75e8eb60-e9ae-46d8-9e55-623f22f2b148 2013-02-10 13:37:26.846 UTC 88de8d8f-fdc9-45a2-a70f-28212f6b874e 2013-02-10 10:47:14.945 UTC 381cb695-82bb-461f-b7d8-696f6695125a 2013-02-06 15:28:21.750 UTC 8cdd65c7-4b3c-44cc-b287-3e231824f8a4 2011-10-24 07:37:59.172 UTC dcaeec7a-2088-4a1d-a87c-ec1580518aef 2013-02-09 18:49:36.978 UTC 06281a52-a6e7-4acd-aae1-44e304189445 2013-02-10 14:05:58.60 UTC c16667f8-75a7-4315-aaea-1beb9e66ead3 2011-10-19 18:28:46.180 UTC ce69f001-c3fc-4846-9da3-d12b9cc26608 2013-02-09 16:36:49.473 UTC b9094592-489f-4b11-9037-7d8ec4d39231 2013-02-07 15:11:34.554 UTC 42f29aed-be98-442e-8041-2eee91912c14 2013-02-10 11:01:15.969 UTC ab8213df-5d5d-48ca-b319-9328bde073c9 2013-08-27 14:32:33.119 UTC 367b97d8-c7d3-41fc-b645-7d7a2b57bdec 2013-02-07 15:05:38.182 UTC 54c4445c-d7ac-422a-8f8a-0c3f98ebeb65 2013-02-09 19:53:25.912 UTC 4c3bbd52-245f-4143-bbbb-112e83817d7d 2013-08-27 14:53:00.303 UTC 29e20d00-da2e-42a0-a63c-7bfa83b6aac1 2013-02-10 12:28:28.204 UTC 5c20b887-e2a2-43f4-9e19-a7fc0334cb52 2013-02-10 13:03:01.901 UTC 33f60dbe-c6ac-4854-b14c-c2c12dc31592 2013-02-09 19:41:52.995 UTC 77b30169-7a25-4934-8833-07158935ec63 2011-10-13 08:33:44.864 UTC 1b5c0647-8a05-4428-be04-d8be0f8ed981 2013-02-10 11:53:34.887 UTC 3241ac1a-5d92-429a-a965-e5454e6dc586 2013-10-31 16:13:36.273 UTC c58c01e5-e73f-45ad-82b7-2c50871b6f4d 2013-02-10 14:16:35.343 UTC ee48d96b-067d-4ccc-9df7-1268bf77cda3 2013-02-09 17:13:43.494 UTC d3a61584-5a2e-4224-8804-dfbb2beb5cf6 2013-02-10 12:48:02.221 UTC b845c4a9-b441-412b-be2e-a8bdbf193ffb 2013-02-10 11:53:24.772 UTC 051d461f-9481-4d40-accf-225de1875bcc 2013-02-09 17:05:59.992 UTC 4d9f7945-2fd6-401b-9558-a4199c53c3bb 2013-02-09 18:51:04.914 UTC 24cc847e-60c0-4beb-bd86-3b5d579defcb 2011-10-19 18:45:10.347 UTC 4dd45b55-4f2f-444c-80f0-3d36aa8297ec 2011-07-27 14:21:17.785 UTC c5c2ba52-8878-42b8-ad0f-6b7cba7e8015 2013-02-09 19:48:00.942 UTC b7961d31-adac-451b-882a-09fd23f4d2c3 2013-02-05 16:37:21.891 UTC eb6e04bb-d77d-4677-b595-235188f3633b 2013-02-05 16:38:35.132 UTC 29ba22f5-da16-4e29-8e4a-f5469bf06ff9 2013-02-07 15:02:29.141 UTC b24bb765-fc5c-4d72-85f4-7a1622240b97 2013-02-09 20:30:07.737 UTC aed06c63-d43b-4336-a606-4a9c5434e790 2011-07-27 12:19:31.387 UTC 1648c9ad-d65b-4622-be19-407de14426b3 2013-08-28 15:16:28.860 UTC Workflow22fit_modelCreate_design_matrixnet.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity false localhost 6311 true false 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.Invokecreate_contrast_matrixnet.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity false localhost 6311 true false 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.Invokefit_modeltmp_out00net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity tmp_out 0 0 false localhost 6311 true false tmp_out STRING 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.Invokeload_librariesnet.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity false localhost 6311 true false 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.Invokefit_modelfit_modeltmp_out b7a51fd2-15cb-4a20-bd72-9e9563615485 2011-10-25 11:13:32.411 UTC 2832eef5-5e59-41ee-b2c5-1d83288948c6 2013-02-05 18:34:56.416 UTC 55bdd327-dc3f-4c88-8620-a8dba010ed07 2011-10-25 10:55:38.659 UTC 044e93f4-4062-4177-9fbd-1527f10666d4 2011-10-25 10:46:33.495 UTC 1eec2f04-3d77-4f0a-83f9-2c1110f48f02 2011-07-27 12:55:52.286 UTC 6d230f26-b0af-47ba-a292-9c19b1f7663e 2011-10-25 12:12:06.83 UTC 5a3343b7-50c1-4c8b-b11f-4cc50920f7d6 2011-10-13 09:23:49.1 UTC f8fa71bd-a121-4c0a-be6b-760dde6bcb36 2011-10-25 11:01:08.763 UTC 177aa755-7ff4-46cb-88f7-739d31b71307 2011-10-25 11:08:43.523 UTC 5ee2dfad-45d8-4866-bb76-54567d9f51cf 2011-07-27 12:56:47.272 UTC de9fc05c-5f2a-42b4-9ea6-a29958eb1bea 2011-10-25 10:45:54.313 UTC 7197d16c-f159-4a95-be26-9a0498f52cd5 2011-10-25 10:51:35.427 UTC 23fbeacd-ebab-4c29-81ff-e63eb86da0ce 2011-10-25 11:08:23.971 UTC e4ce6d39-964c-4c5a-ae3c-83543ab0ebbb 2011-07-27 14:30:33.262 UTC a6cd7517-7956-4317-a57b-741e661134fb 2013-02-10 10:12:41.442 UTC e1671ff6-9e20-472c-be65-142c5fa2d39f 2011-10-25 10:48:55.621 UTC 17356852-e4da-484a-b5ec-db5cb06740a8 2011-10-25 10:45:29.447 UTC af61248d-9f53-43a4-bfa4-b3f5b398fe9a 2011-10-25 11:03:52.195 UTC a5b4e04f-206d-49fe-9af5-7a5947d7b199 2011-07-27 13:24:02.872 UTC da056906-21e4-424f-83d7-e5fc3ce54e40 2011-10-25 10:51:09.547 UTC abff9c0b-9054-444a-a15d-82355f2cfaef 2011-07-29 14:30:03.715 UTC 28684882-8f95-44f9-a973-d0bd99c7cac9 2011-07-27 14:29:52.678 UTC gets as input an expression set object. 2011-07-27 14:30:32.454 UTC 78f8a50c-d40a-48a7-9c33-dbcc26c6655d 2011-10-25 12:37:42.804 UTC 8f862e3c-0897-488e-803c-5956f51aeed4 2011-07-27 13:30:01.349 UTC 5bee9f25-38c3-4eed-a3b9-2c39b93dc967 2011-10-26 07:47:03.665 UTC 47f38461-58bb-4dc1-8ea5-af65db4cbe52 2013-02-06 11:31:26.930 UTC Workflow5cf00cut_off00filenamefile_DEget_top_ranked_probesets_for_coef_1cf0net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity cf 0 false probe_limma_file 0 0 false localhost 6311 true false cf INTEGER probe_limma_file STRING 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.Invokeannotate_top_ranked_with_gene_ids_coef_1net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity false localhost 6311 true false 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_unique_logs_p.values_at_gene_level_coef_1filename00net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity filename 0 0 false localhost 6311 true false filename STRING 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.Invokeexport_DE_tablecut_off0filename_diff00net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity cut_off 0 false filename_diff 0 0 false localhost 6311 false false cut_off DOUBLE filename_diff STRING 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_top_ranked_probesets_for_coef_1cfcfexport_DE_tablecut_offcut_offfilenameget_unique_logs_p.values_at_gene_level_coef_1filenamefile_DEexport_DE_tablefilename_diff 0d72e7f0-f832-4406-9ea4-32ee0de36216 2013-08-27 14:52:57.462 UTC 43bb79a1-518f-4ba4-8944-635543a34605 2013-02-09 18:26:49.707 UTC 207c8bc2-c1e3-4a2e-b239-a6246657d19d 2013-02-10 11:22:45.641 UTC b1ebb30d-82c5-46d5-8818-181100645b84 2013-02-10 12:15:54.602 UTC c63819c0-d6e0-4f55-8726-ac41a3bb40cd 2013-02-10 13:02:02.843 UTC 4fbe307f-f33e-4048-80dd-4810979fefa3 2013-02-05 18:36:04.986 UTC 9fbf4e03-73ec-412e-8557-8842ac936f9f 2013-02-07 14:58:23.281 UTC ec477cde-d584-476e-9b28-5712c5cea1fa 2013-02-09 18:22:21.1 UTC 22ae16a6-e816-466c-950e-871dcf094a99 2013-02-10 13:23:26.808 UTC 4f0df006-206f-47ec-bdba-e9caeaa390a0 2013-02-09 18:30:38.209 UTC ca274b95-e893-4608-9b4c-4783c0a40d2a 2013-02-07 15:07:57.738 UTC 84f996d5-f17c-4d92-9350-5c9ab4e10e79 2013-02-10 11:16:31.108 UTC 6a1ad012-e4b6-4f91-98ba-44f63136d4e4 2011-11-07 14:32:08.851 UTC 3656639f-18e3-445d-bf41-5ec5006186f4 2011-11-07 14:57:57.979 UTC a0434406-578d-4a54-9a71-d0e735f45d79 2013-02-09 18:17:31.40 UTC 833377ff-5f21-4b0a-a497-a724e35ae14d 2013-08-27 15:00:04.782 UTC cdfac4be-7ba6-4ebc-95f4-11a1a65093e6 2013-02-09 19:38:18.319 UTC cddeb86d-e60d-4698-a5b1-d680d02db7f9 2013-02-10 10:47:10.985 UTC 40d8f4bb-9dc4-4811-ada4-ee6f00d7b518 2011-11-07 14:33:28.625 UTC c738a14c-ed4d-49bf-8eaa-18dfc2beb0d0 2013-02-07 15:01:01.313 UTC 19adc730-6754-4091-b594-bff217cc29d2 2013-02-09 18:45:31.114 UTC 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