DAS_sequence_retrieval_and_parsing_with_JDASIDs00 O35502,P99999 2011-05-30 04:01:34.907 CEST You can input more than one ID using comma-separated values. You can use different types of IDs depending on the DAS coordinate system (http://www.dasregistry.org/help_coordsys.jsp) you decided to use. If you selected a DAS source of type "Protein Sequence" and authority "UniProt" you could use UniProt (TrEMBL and SwissProt) accessions. For instance "P37173". If you selected a DAS source of type "Chromosome", authority "GRCh_37" and organism "Homo sapiens" you could use a chromosome ID. For instance "1". 2011-05-30 04:01:22.608 CEST DasSource00 Input a DAS reference source following this format "http://www.server.com/das/source/". Find a public list of available DAS reference sources providing sequence information in the DAS registry … http://www.dasregistry.org/listSources.jsp … or create your own DAS source with easyDAS … http://www.ebi.ac.uk/panda-srv/easydas/ 2011-05-30 04:01:54.364 CEST http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/ 2011-05-30 02:29:17.129 CEST start00 The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence. 2011-05-30 04:02:13.175 CEST 11 2011-05-30 04:02:18.694 CEST stop00 32 2011-05-30 04:02:39.38 CEST The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence. 2011-05-30 04:02:22.298 CEST Sequence_Custom_Format This output was achieved using the JDAS library … http://code.google.com/p/jdas/ To be able to use this workflow with JDAS copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs. 2011-05-30 04:07:04.130 CEST Sequence_DAS_format Have a look to the specification to know more about the DAS format ... http://www.biodas.org/documents/spec-1.6.html#sequence 2011-05-30 04:04:25.201 CEST Service_status 200 2011-05-30 04:03:56.367 CEST HTTP response status codes ... http://en.wikipedia.org/wiki/List_of_HTTP_status_codes 2011-05-30 04:03:51.296 CEST DAS_sequence_retrievalDasSource0start0stop0ID0Sequence_DAS_format00Service_status00net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJDASsequenceXML0sequenceText00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity sequenceXML 0 text/plain java.lang.String true sequenceText 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_by_regexstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivity string 0 'text/plain' java.lang.String true regex 0 'text/plain' java.lang.String true split 1 1 workflow org.embl.ebi.escience.scuflworkers.java.SplitByRegex UserNameHere 2011-05-30 03:58:05.622 CEST net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity , net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeDAS_sequence_retrievalDasSourceDasSourceDAS_sequence_retrievalstartstartDAS_sequence_retrievalstopstopDAS_sequence_retrievalIDsplit_by_regexsplitJDASsequenceXMLDAS_sequence_retrievalSequence_DAS_formatsplit_by_regexstringIDssplit_by_regexregexregex_valuevalueSequence_Custom_FormatJDASsequenceTextSequence_DAS_formatDAS_sequence_retrievalSequence_DAS_formatService_statusDAS_sequence_retrievalService_status Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS copy this file … http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar … to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs. 2011-05-30 04:10:18.475 CEST c8c59c76-0444-4a87-965c-100b1233efea 2011-05-30 03:39:25.578 CEST a1708814-616b-42b3-9486-98014544eb48 2011-05-30 03:34:49.44 CEST 87adc1b2-2043-4a77-9d88-fe4b2aed17e7 2011-05-30 03:20:22.554 CEST 076007bb-74d1-4ba5-b581-64618dd0c897 2011-05-30 03:25:43.94 CEST ba998355-bec5-4575-a66f-676391e68f33 2011-05-30 03:44:57.378 CEST f15449de-8120-43a2-97fa-9c2d90eb9474 2011-05-30 02:51:35.544 CEST af896ceb-6fa5-45a0-806f-db8a2430bf72 2011-05-30 03:36:12.651 CEST 8bf845ff-13c9-408c-a47a-f18f1df2e0a8 2011-05-30 03:58:59.698 CEST 4dcda7cd-4679-4df6-b557-350488e980f6 2011-05-30 02:53:31.861 CEST DAS sequence retrieval and parsing with JDAS 2011-05-30 04:10:24.871 CEST 816d6ae4-580f-406e-a837-7d16c1a3717d 2011-05-30 03:55:19.696 CEST 9b8849d8-a1d3-4a7d-8106-2e37c0d5d2c9 2011-05-30 03:33:28.950 CEST 87c07b0a-bc75-49d6-b490-0c1b896f54cb 2011-05-30 03:37:59.703 CEST e7a97f0d-7f82-451d-bde5-ef8f5f5f17ec 2011-05-30 04:11:00.444 CEST 564e88c0-046e-4781-90ea-3ec4d6984241 2011-05-30 02:56:05.576 CEST c5ec8b42-23e2-40cb-b7ee-83aa3cc460f6 2011-05-30 02:47:40.436 CEST 0a47eda6-25d1-4832-99e9-54ffcb3f5372 2011-05-30 02:57:50.895 CEST 77093bcd-f2fa-400d-918c-26fbe2c6cff6 2011-05-30 03:51:39.304 CEST DAS_sequence_retrievalID00 You can use different types of IDs depending on the DAS coordinate system (http://www.dasregistry.org/help_coordsys.jsp) you decided to use. If you selected a DAS source of type "Protein Sequence" and authority "UniProt" you could use UniProt (TrEMBL and SwissProt) accessions. For instance "P37173". If you selected a DAS source of type "Chromosome", authority "GRCh_37" and organism "Homo sapiens" you could use a chromosome ID. For instance "1". 2011-05-30 01:52:17.550 CEST P37173 2011-05-30 01:52:18.805 CEST DasSource00 http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/ 2011-05-30 01:28:16.88 CEST Input a DAS reference source following this format "http://www.server.com/das/source/". Find a public list of available DAS reference sources providing sequence information in the DAS registry … http://www.dasregistry.org/listSources.jsp … or create your own DAS source with easyDAS … http://www.ebi.ac.uk/panda-srv/easydas/ 2011-05-30 02:15:09.967 CEST start00 11 2011-05-30 01:55:19.329 CEST The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence. 2011-05-30 02:17:50.251 CEST stop00 The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence. 2011-05-30 02:18:12.559 CEST 34 2011-05-30 01:55:40.282 CEST Sequence_DAS_format Have a look to the specification to know more about the DAS format ... http://www.biodas.org/documents/spec-1.6.html#sequence 2011-05-30 02:23:33.888 CEST Service_status HTTP response status codes ... http://en.wikipedia.org/wiki/List_of_HTTP_status_codes 2011-05-30 02:22:21.891 CEST 200 2011-05-30 02:22:25.299 CEST Get_SequenceID0range0DasSource0responseBody00status00net.sf.taverna.t2.activitiesrest-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.rest.RESTActivity GET {DasSource}sequence?segment={ID}{range} text/plain application/xml String false false false range java.lang.String ID java.lang.String DasSource java.lang.String net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_rangestart0stop0range00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity start 0 text/plain java.lang.String true stop 0 text/plain java.lang.String true range 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_SequenceIDIDGet_Sequencerangecreate_rangerangeGet_SequenceDasSourceDasSourcecreate_rangestartstartcreate_rangestopstopSequence_DAS_formatGet_SequenceresponseBodyService_statusGet_Sequencestatus 9644404d-5f8d-492a-b3d8-c745997f3aa0 2011-05-30 02:13:55.383 CEST a8bada53-c671-4e50-ade0-8e34c32901e6 2011-05-30 02:18:01.306 CEST 733432d7-c241-4e41-a456-7a66a34d8d9b 2011-05-30 01:58:53.465 CEST 93e3904a-0744-418f-a528-a56516e0c746 2011-05-30 01:59:54.881 CEST fc528ec7-bb47-49dc-81ee-c39d697fff3d 2011-05-30 02:11:31.834 CEST 1666f142-70c6-49a3-b19b-c833bc6a22a8 2011-05-30 02:01:31.744 CEST 5ac5004d-9ed3-4196-9388-c6a66dfe1ad6 2011-05-30 02:09:39.158 CEST 730c1649-36b7-4a8f-9243-1bc86b91803a 2011-05-30 02:06:27.364 CEST edf775f1-683a-4fbe-a7c2-dfa731ca84b5 2011-05-30 01:34:56.825 CEST 79201635-7ebc-4498-aa96-286c5e6279b4 2011-05-30 02:16:24.682 CEST Retrieve Protein or Genome sequences using the Distributed Annotation System (DAS). 2011-05-30 02:16:33.776 CEST 73bbadd7-3fb6-4f7c-abe3-3da636e96b34 2011-05-30 02:23:53.286 CEST 92ff601d-9ad6-4731-b9a7-6e3d292b2be7 2011-05-30 01:57:19.424 CEST Rafael C. Jimenez 2011-05-30 01:51:35.732 CEST DAS sequence retrieval 2011-05-30 01:52:03.426 CEST 2b8cbaeb-375e-40c9-ad77-7e4ab49c057f 2011-05-30 02:03:47.677 CEST b1b262e0-bddb-47d9-80f8-507b98956113 2011-05-30 02:08:08.718 CEST