DAS_features_retrieval_and_parsing_with_JDASIDs00 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". 2011-06-01 18:02:00.987 BST O35502,P99999 2011-06-01 17:52:23.956 BST 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/ 2011-06-01 18:02:13.393 BST http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/ 2011-06-01 17:52:09.237 BST 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. 2011-06-01 18:02:23.330 BST 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. 2011-06-01 18:02:48.751 BST Features_DAS_format Have a look to the specification to know more about the DAS format ... http://www.biodas.org/documents/spec-1.6.html#features 2011-06-01 18:03:25.265 BST Service_status HTTP response status codes ... http://en.wikipedia.org/wiki/List_of_HTTP_status_codes 2011-06-01 18:03:36.624 BST 200 2011-06-01 18:03:43.327 BST Features_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. 2011-06-01 18:03:04.407 BST DAS_features_retrievalID0DasSource0start0stop0Features_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.Invokesplit_by_regexregex0string0split11net.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 02:58:05.622 BST 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.InvokeJDASfeaturesXML0featuresText00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivity featuresXML 0 text/plain java.lang.String true featuresText 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.InvokeDAS_features_retrievalIDsplit_by_regexsplitDAS_features_retrievalDasSourceDasSourceDAS_features_retrievalstartstartDAS_features_retrievalstopstopsplit_by_regexregexregex_valuevaluesplit_by_regexstringIDsJDASfeaturesXMLDAS_features_retrievalFeatures_DAS_formatFeatures_DAS_formatDAS_features_retrievalFeatures_DAS_formatService_statusDAS_features_retrievalService_statusFeatures_custom_formatJDASfeaturesText b976dd39-e516-4822-8659-da1deb0fb8aa 2011-06-01 18:00:01.554 BST b681062d-ff02-4b1b-b4fa-2f66180715dc 2011-06-01 18:03:44.296 BST 8068892f-36ca-4115-a21c-fed00b6fa9d2 2011-06-01 18:05:41.245 BST 064f4ec4-f0ad-4c1b-a8ce-9a87015f96e6 2011-06-01 17:59:13.259 BST Retrieve Protein or Genome features 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. 2011-06-01 18:05:40.41 BST 480db7ab-dd76-41f5-807e-b29e2e1be8c0 2011-06-01 17:53:06.471 BST DAS features retrieval and parsing with JDAS 2011-06-01 18:05:07.730 BST a024e92e-5283-4f74-86ba-005cbef495f6 2011-06-01 17:21:28.994 BST DAS_features_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 00:52:17.550 BST P37173 2011-05-30 00:52:18.805 BST DasSource00 Input a DAS annotation source following this format "http://www.server.com/das/source/". Find a public list of available DAS annotation 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/ 2011-06-01 17:06:39.442 BST http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/ 2011-05-30 00:28:16.88 BST 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 01:17:50.251 BST 11 2011-05-30 00:55:19.329 BST 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 01:18:12.559 BST 34 2011-05-30 00:55:40.282 BST Features_DAS_format Have a look to the specification to know more about the DAS format ... http://www.biodas.org/documents/spec-1.6.html#features 2011-06-01 17:08:05.240 BST Service_status HTTP response status codes ... http://en.wikipedia.org/wiki/List_of_HTTP_status_codes 2011-05-30 01:22:21.891 BST 200 2011-05-30 01:22:25.299 BST Get_FeaturesID0range0DasSource0responseBody00status00net.sf.taverna.t2.activitiesrest-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.rest.RESTActivity GET {DasSource}features?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_FeaturesIDIDGet_Featuresrangecreate_rangerangeGet_FeaturesDasSourceDasSourcecreate_rangestartstartcreate_rangestopstopFeatures_DAS_formatGet_FeaturesresponseBodyService_statusGet_Featuresstatus 1666f142-70c6-49a3-b19b-c833bc6a22a8 2011-05-30 01:01:31.744 BST 92ff601d-9ad6-4731-b9a7-6e3d292b2be7 2011-05-30 00:57:19.424 BST 730c1649-36b7-4a8f-9243-1bc86b91803a 2011-05-30 01:06:27.364 BST a8bada53-c671-4e50-ade0-8e34c32901e6 2011-05-30 01:18:01.306 BST 2b8cbaeb-375e-40c9-ad77-7e4ab49c057f 2011-05-30 01:03:47.677 BST edf775f1-683a-4fbe-a7c2-dfa731ca84b5 2011-05-30 00:34:56.825 BST 93e3904a-0744-418f-a528-a56516e0c746 2011-05-30 00:59:54.881 BST Retrieve Protein or Genome features (annotations) using the Distributed Annotation System (DAS). 2011-06-01 17:05:03.417 BST Rafael C. Jimenez 2011-05-30 00:51:35.732 BST 0211c48c-94f4-460c-a68a-999184c28c0b 2011-06-01 17:08:23.88 BST 79201635-7ebc-4498-aa96-286c5e6279b4 2011-05-30 01:16:24.682 BST fc528ec7-bb47-49dc-81ee-c39d697fff3d 2011-05-30 01:11:31.834 BST 5ac5004d-9ed3-4196-9388-c6a66dfe1ad6 2011-05-30 01:09:39.158 BST 733432d7-c241-4e41-a456-7a66a34d8d9b 2011-05-30 00:58:53.465 BST 9644404d-5f8d-492a-b3d8-c745997f3aa0 2011-05-30 01:13:55.383 BST DAS features retrieval 2011-06-01 17:05:16.463 BST b1b262e0-bddb-47d9-80f8-507b98956113 2011-05-30 01:08:08.718 BST 5ca5196d-90d7-458c-8c9a-f5baee1bc0d9 2011-06-01 17:03:02.20 BST 2602b9f0-2792-4dff-9128-09ced4486819 2011-06-01 17:59:03.41 BST 73bbadd7-3fb6-4f7c-abe3-3da636e96b34 2011-05-30 01:23:53.286 BST