plotGenomicspecies00 hsap 2013-05-28 11:59:42.854 UTC NGD species short name. Choice of: hsap, mmus, rnor. 2013-05-29 10:44:13.190 UTC version00 71_1 2013-05-28 14:27:44.40 UTC NGD version, usually the Ensembl version followed by "_1". 2013-05-28 14:27:41.0 UTC gene00 Ensembl gene display_label, e.g. BDNF (Bdnf); or gene_stable_id, e.g. ENSG00000176697. 2013-05-28 12:06:24.745 UTC BDNF 2013-05-28 12:05:51.25 UTC library00 jaspar 2013-05-28 12:02:12.887 UTC A motif library to use. Choice of: jaspar, transfac, genomatix. (The last accessible only to local registered users.) 2013-05-29 10:46:51.71 UTC motif_name11 CREB1 2013-05-28 12:13:23.318 UTC A list of motifs to be plotted, from Jaspar or Transfac Professional motif libraries. Motifs can be entered either as a list of dataset types e.g. (for Jaspar): MA0018.1, PB0108.1, PB0010.1; or as a list of transcription factor names, e.g. (for Jaspar): CREB1, Atf1_2, Egr1_1. Click 'Add value' to use the example transcription factor name (CREB1). Use 'Add value' to add additional motifs. Delete all elements from the input list, or replace the example value with xsi:nil to to plot only the areas. 2013-10-07 14:24:57.152 UTC area_types11 xsi:nil 2013-05-29 10:45:18.415 UTC A list of NGD area type(s) to be plotted. Click "Add value" and use the default null value (xsi:nil) to plot all the area types. Delete the default null value (xsi:nil), and then click 'Add value' to enter particular area types, e.g.: CREB, cisRED Search Region. Enter one type per list element. 2013-10-07 14:19:32.421 UTC separate_motifs00 False 2013-05-28 12:07:25.986 UTC When this flag is set to 'True' , different motifs assigned to the same tf_name (e.g. the motifs MA0018.1 and MA0018.2 for the tf_name CREB1) are ploted in separate lines. 2013-05-29 10:44:46.414 UTC user00 public 2013-05-28 14:15:23.864 UTC Authenticating user. 2013-05-29 10:44:26.318 UTC passwd00 Authenticating user password. None (encoded as xsi:nil) for the user 'public'. 2013-05-29 10:43:32.205 UTC xsi:nil 2013-05-28 14:28:48.73 UTC file_namefile_dataPlotGenomicResponseinput0PlotGenomicResult00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false PlotGenomicResult 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="PlotGenomicResponse" name="PlotGenomicResponse" qname="{ngp}PlotGenomicResponse"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="ArrayFilesArray" name="PlotGenomicResult" qname="{ngp}PlotGenomicResponse&gt;PlotGenomicResult"><s:elementtype><s:complextype optional="false" unbounded="false" typename="ArrayFiles" name="" qname="{ngp}ArrayFiles"><s:elements><s:basetype optional="true" unbounded="false" typename="base64Binary" name="file_data" qname="{ngp}ArrayFiles&gt;file_data" /><s:basetype optional="true" unbounded="false" typename="string" name="file_name" qname="{ngp}ArrayFiles&gt;file_name" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> 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.InvokePlotGenomicResponse_PlotGenomicResultinput0PlotGenomicResult11net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false PlotGenomicResult 1 l('text/xml') 1 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:arraytype optional="true" unbounded="false" wrapped="true" typename="ArrayFilesArray" name="PlotGenomicResult" qname="{ngp}PlotGenomicResponse&gt;PlotGenomicResult"><s:elementtype><s:complextype optional="false" unbounded="false" typename="ArrayFiles" name="" qname="{ngp}ArrayFiles"><s:elements><s:basetype optional="true" unbounded="false" typename="base64Binary" name="file_data" qname="{ngp}ArrayFiles&gt;file_data" /><s:basetype optional="true" unbounded="false" typename="string" name="file_name" qname="{ngp}ArrayFiles&gt;file_name" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:extensions> 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.InvokePlotGenomicResult_PlotGenomicResultinput0file_data00file_name00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false file_data 0 'application/octet-stream' 0 file_name 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="ArrayFiles" name="" qname="{ngp}ArrayFiles"><s:elements><s:basetype optional="true" unbounded="false" typename="base64Binary" name="file_data" qname="{ngp}ArrayFiles&gt;file_data" /><s:basetype optional="true" unbounded="false" typename="string" name="file_name" qname="{ngp}ArrayFiles&gt;file_name" /></s:elements></s:complextype></s:extensions> 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.InvokePlotGenomicPlotGenomic0PlotGenomicResponse00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://webservices.nencki-genomics.org/genomic?wsdl PlotGenomic 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.InvokePlotGenomic_2authenticate0parameters0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity authenticate 0 'text/xml' false parameters 0 'text/xml' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="PlotGenomic" name="PlotGenomic" qname="{ngp}PlotGenomic"><s:elements><s:complextype optional="true" unbounded="false" typename="Authenticate" name="authenticate" qname="{ngp}PlotGenomic&gt;authenticate"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="username" qname="{ngp}Authenticate&gt;username" /><s:basetype optional="true" unbounded="false" typename="string" name="version" qname="{ngp}Authenticate&gt;version" /><s:basetype optional="true" unbounded="false" typename="string" name="password" qname="{ngp}Authenticate&gt;password" /><s:basetype optional="true" unbounded="false" typename="string" name="species" qname="{ngp}Authenticate&gt;species" /></s:elements></s:complextype><s:complextype optional="true" unbounded="false" typename="Parameters" name="parameters" qname="{ngp}PlotGenomic&gt;parameters"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="stringArray" name="area_types" qname="{ngp}Parameters&gt;area_types"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="library" qname="{ngp}Parameters&gt;library" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="stringArray" name="motif_name" qname="{ngp}Parameters&gt;motif_name"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="boolean" name="seperate_motifs" qname="{ngp}Parameters&gt;seperate_motifs" /><s:basetype optional="false" unbounded="false" typename="string" name="gene" qname="{ngp}Parameters&gt;gene" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions> 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.Invokeauthenticatepassword0username0species0version0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity username 0 'text/plain' false version 0 'text/plain' false password 0 'text/plain' false species 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="Authenticate" name="authenticate" qname="{ngp}PlotGenomic&gt;authenticate"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="username" qname="{ngp}Authenticate&gt;username" /><s:basetype optional="true" unbounded="false" typename="string" name="version" qname="{ngp}Authenticate&gt;version" /><s:basetype optional="true" unbounded="false" typename="string" name="password" qname="{ngp}Authenticate&gt;password" /><s:basetype optional="true" unbounded="false" typename="string" name="species" qname="{ngp}Authenticate&gt;species" /></s:elements></s:complextype></s:extensions> 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.Invokeinputarea_types1gene0library0motif_name1seperate_motifs0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity area_types 1 l('text/plain') false library 0 'text/plain' false motif_name 1 l('text/plain') false seperate_motifs 0 'text/plain' false gene 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="true" unbounded="false" typename="Parameters" name="parameters" qname="{ngp}PlotGenomic&gt;parameters"><s:elements><s:arraytype optional="true" unbounded="false" wrapped="true" typename="stringArray" name="area_types" qname="{ngp}Parameters&gt;area_types"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="library" qname="{ngp}Parameters&gt;library" /><s:arraytype optional="true" unbounded="false" wrapped="true" typename="stringArray" name="motif_name" qname="{ngp}Parameters&gt;motif_name"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="boolean" name="seperate_motifs" qname="{ngp}Parameters&gt;seperate_motifs" /><s:basetype optional="false" unbounded="false" typename="string" name="gene" qname="{ngp}Parameters&gt;gene" /></s:elements></s:complextype></s:extensions> 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.InvokePlotGenomicResponseinputPlotGenomicPlotGenomicResponsePlotGenomicResponse_PlotGenomicResultinputPlotGenomicResponsePlotGenomicResultPlotGenomicResult_PlotGenomicResultinputPlotGenomicResponse_PlotGenomicResultPlotGenomicResultPlotGenomicPlotGenomicPlotGenomic_2outputPlotGenomic_2authenticateauthenticateoutputPlotGenomic_2parametersinputoutputauthenticatepasswordpasswdauthenticateusernameuserauthenticatespeciesspeciesauthenticateversionversioninputarea_typesarea_typesinputgenegeneinputlibrarylibraryinputmotif_namemotif_nameinputseperate_motifsseparate_motifsfile_namePlotGenomicResult_PlotGenomicResultfile_namefile_dataPlotGenomicResult_PlotGenomicResultfile_data 3f5a6655-7146-4ce5-a0f4-127e5b7f6492 2013-01-30 14:11:04.2 UTC 3b0ea844-8c28-4757-abff-406eaed6af3f 2013-05-28 12:14:02.307 UTC 1a070fe6-1cd1-483f-8000-4c31db083945 2013-05-29 10:06:29.701 UTC ad9440c5-8267-4673-9bf7-926ef0027ddb 2013-01-30 14:14:39.844 UTC ae23039b-d052-4288-9b7d-d9a397732aa8 2013-05-28 15:09:06.944 UTC b6fdb555-8f48-4c4a-b07a-f3566cd74374 2013-10-07 14:54:58.229 UTC plotGenomic 2013-05-29 10:30:00.510 UTC 3784e32f-7056-458d-aa2e-98f745ecd7d3 2013-05-07 15:12:02.516 UTC fab523a4-4930-447a-b840-73940bf84cf4 2013-02-12 14:20:40.269 UTC This workflow returns a graphical representation of selected Nencki Genomics Database (www.nencki-genomics.org) content in the ± 10 kb flank of the transcription start site of a chosen gene. More precisely, it returns instances of selected area types, and instances of selected motif types that intersect any of the returned area instances. The results are returned as three files: a pdf file with the plot, and two tab-separated files with the details of areas and motifs shown in the plot. Publication doi: 10.1093/database/bat069 2013-10-07 14:53:14.1 UTC Michal Dabrowski 2013-10-07 14:26:14.811 UTC 01f00ffe-79d5-4d9b-a1fa-4b38975d0516 2013-05-07 15:05:20.974 UTC 63d2f608-1c1b-4841-99af-3bcedcbccb31 2013-05-29 10:55:03.369 UTC b06417e2-41e3-43bb-bd83-5ce97369a002 2013-05-07 15:32:58.64 UTC c2079e9b-e861-46e0-a4de-b226caf1347b 2013-05-29 10:42:51.391 UTC 9eac03e7-eea4-4727-b753-a9785adf3e57 2013-05-28 14:08:23.126 UTC a0d6e59d-2bec-48c9-8d10-acf54bfdf45d 2013-01-30 14:12:54.237 UTC e0f607af-c8c7-4b89-a5ec-ca33847a7af9 2013-01-30 14:03:52.279 UTC 6d9a2fbc-44f5-4b05-a907-9cdb340336d0 2013-05-28 14:49:51.502 UTC 230d3047-b951-4d85-9217-3f77c9434c8d 2013-05-28 12:19:35.367 UTC fa13a19a-8181-4901-b3c6-5751fd61a118 2013-05-28 14:16:13.351 UTC b21f95e8-d5a2-452a-b7e8-9409a60dca79 2013-05-07 15:34:31.513 UTC fb7f1f5a-8a2f-4ecc-aa22-fd5ebc80b4c8 2013-10-07 14:26:15.44 UTC 5001a02e-8490-4985-8f4b-26fe16ac9aa0 2013-10-07 14:14:00.108 UTC d2e97b71-edce-4444-8d48-2254db832d33 2013-03-07 11:23:51.333 UTC 7d5479f5-e28f-4cdf-a2d4-4d344e12e927 2013-10-07 14:21:36.370 UTC 11bc9729-a9d3-4602-abf1-3304769888d4 2013-05-28 14:05:59.817 UTC 1c36b34c-2dc5-4526-bca8-be3a0b54773d 2013-05-28 15:07:42.500 UTC 766e1489-c7c1-4664-982e-ae652d4e81da 2013-05-28 14:06:49.904 UTC 0e32ef8c-50ac-40c1-9d8e-9a2fb7f1a901 2013-05-29 11:11:27.473 UTC 96a20c80-6058-4edd-ae77-088f04773fc5 2013-05-29 10:56:25.663 UTC 7a2a2c3f-2fa6-493b-9286-4bd01d93879c 2013-03-07 11:22:23.814 UTC 024d7030-b679-4458-8505-1b0528edef29 2013-01-30 14:06:45.400 UTC 4056daaa-4e55-4ae9-b2d0-db02f8bc1559 2013-02-12 16:05:33.770 UTC