Protein_3D_VisualizationhasJmol3DStructureVisualizationUniProt_Record_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.1net.sf.taverna.t2.activities.stringconstant.StringConstantActivity P68871net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokefetch_jmol_filejmol_file_location0jmol_file00net.sf.taverna.t2.activitiesdataflow-activity1.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokelimitlimit0input2output11net.sf.taverna.t2.activitiesbeanshell-activity1.1net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true limit 0 text/plain java.lang.String true input 2 text/plain 1 output 1 net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokelimit_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.1net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 5net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeUniProt-to-PDBUniProt_Record1has3DStructure (PDB_Record)22net.sf.taverna.t2.activitiessadi-activity0.2.0net.sf.taverna.t2.activities.sadi.SADIActivity http://biordf.net/sparql http://sadiframework.org/registry/ http://sadiframework.org/examples/uniprot2pdb UniProt_Record AnnotatedUniProtRecord has3DStructure (PDB_Record) net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokerenderProteinStructurePDB_Record1hasJmol3DStructureVisualization (Thing)22net.sf.taverna.t2.activitiessadi-activity0.2.0net.sf.taverna.t2.activities.sadi.SADIActivity http://biordf.net/sparql http://sadiframework.org/registry/ http://sadiframework.org/services/renderProteinStructure PDB_Record renderProteinStructure_Output hasJmol3DStructureVisualization (Thing) net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokefetch_jmol_filejmol_file_locationlimitoutputlimitlimitlimit_valuevaluelimitinputrenderProteinStructurehasJmol3DStructureVisualization (Thing)UniProt-to-PDBUniProt_RecordUniProt_Record_valuevaluerenderProteinStructurePDB_RecordUniProt-to-PDBhas3DStructure (PDB_Record)hasJmol3DStructureVisualizationfetch_jmol_filejmol_file Uniprot Protein Visualization 2010-05-01 12:18:46.96 PDT Jmol 3D visualization of a protein structure. 2010-05-01 12:21:28.862 PDT Protein 3D Visualization 2010-05-01 12:22:01.230 PDT David Withers 2010-05-01 12:17:12.903 PDT Fetch_Jmol_filejmol_file_location00jmol_filesplitURLregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.1net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.SplitByRegex workflow java.lang.String true string 0 'text/plain' java.lang.String true regex 0 'text/plain' 1 split 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.1net.sf.taverna.t2.activities.stringconstant.StringConstantActivity =net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeselectLastUrlin1out00net.sf.taverna.t2.activitiesbeanshell-activity1.1net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true in 1 text/plain 0 out 0 net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Web_Page_from_URLurl0contents00net.sf.taverna.t2.activitieslocalworker-activity1.1net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.WebPageFetcher workflow java.lang.String true url 0 'text/x-taverna-web-url' java.lang.String true base 0 'text/x-taverna-web-url' 0 contents 0 'text/plain,text/html' net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0net.sf.taverna.t2.coreworkflowmodel-impl1.1net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesplitURLregexregex_valuevaluesplitURLstringjmol_file_locationselectLastUrlinsplitURLsplitGet_Web_Page_from_URLurlselectLastUrloutjmol_fileGet_Web_Page_from_URLcontents SADI jmol example 2010-01-07 10:32:08.517 PST Fetch Jmol file 2010-05-01 12:23:32.363 PDT SADI Jmol example 2010-01-07 10:32:47.70 PST An example workflow showing use of the SADI activity 2010-01-07 10:33:38.407 PST Fetches a jmol file from a url 2010-05-01 12:24:03.300 PDT David Withers 2010-01-07 10:31:42.495 PST