Render_gene_via_BioGPSgene_id00 The gene id. The required format of the id depends upon the plugin chosen. 2012-02-10 20:03:39.370 GMT 1016 2012-02-10 20:03:44.742 GMT list_biogps_pluginsresponseBody00net.sf.taverna.t2.activitiesrest-activity1.3net.sf.taverna.t2.activities.rest.RESTActivity GET http://biogps.org/plugin/all/?format=xml&size=1000 application/xml application/xml String false false true net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_pluginsxml_text0nodelistAsXML11net.sf.taverna.t2.activitiesxpath-activity1.3net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="ASCII"?> <biogps><data><item key="hits"><item key="hits"><item><item key="sort"><item>909.0</item></item><item key="_type">plugin</item><item key="_source"><item key="rating_data"><item key="avg_stars">10</item><item key="total">2</item><item key="avg">5</item></item><item key="name">Gene expression/activity chart</item><item key="created">2008-03-17 15:38:24</item><item key="url">http://plugins.biogps.org/data_chart/data_chart.cgi?id={{EntrezGene}}</item><item key="lastmodified">2011-08-30 16:10:20</item><item key="usage_data"><item key="layouts">909.0</item><item key="users">695</item></item><item key="popularity">909.0</item><item key="owner"><item key="username">jhuss</item><item key="url">/profile/349/jhuss</item><item key="name">Jon Huss</item></item><item key="species"><item>human</item><item>mouse</item><item>rat</item></item><item key="shortUrl">plugins.biogps.org</item><item key="id">9</item><item key="in">plugin</item><item key="short_description">This plugin displays reference gene expression data sets, including our popular "Gene Atlas" data set.</item><item key="role_permission"><item>biogpsusers</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="options"><item key="certified_owner">True</item><item key="mobile_url">http://plugins.biogps.org/data_chart/data_chart_mobile.cgi?id={{EntrezGene}}</item><item key="allowedSpecies"><item>human</item><item>mouse</item><item>rat</item></item><item key="securityAware">True</item></item><item key="tags"><item>chart</item><item>expression</item></item><item key="description">This plugin displays reference gene expression data sets, including our popular "Gene Atlas" data set.</item></item><item key="_score">None</item><item key="_index">biogps</item><item key="_id">9</item></item><item><item key="sort"><item>596.0</item></item><item key="_type">plugin</item><item key="_source"><item key="rating_data"><item key="avg_stars">10</item><item key="total">2</item><item key="avg">5</item></item><item key="name">Gene Identifiers</item><item key="created">2008-06-21 16:19:07</item><item key="url">/ext/symatlasbar/?geneid={{EntrezGene|EnsemblGene}}&amp;hidespecies=1</item><item key="lastmodified">2011-03-31 20:18:31</item><item key="usage_data"><item key="layouts">596.0</item><item key="users">474</item></item><item key="popularity">596.0</item><item key="owner"><item key="username">asu</item><item key="url">/profile/3/asu</item><item key="name">Andrew Su</item></item><item key="species"><item>human</item><item>mouse</item><item>rat</item><item>fruitfly</item><item>nematode</item><item>zebrafish</item><item>thale-cress</item><item>frog</item></item><item key="shortUrl">biogps.gnf.org</item><item key="id">73</item><item key="in">plugin</item><item key="short_description">Condensed view of many major gene identifiers (including Entrez Gene, Ensembl, Refseq, Interpro, GO, Affy reporters) with links out to...</item><item key="role_permission"><item>biogpsusers</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="options"><item key="certified_owner">True</item></item><item key="tags"><item>ensembl</item><item>entrez</item><item>identifier</item><item>interpro</item><item>refseq</item></item><item key="description">Condensed view of many major gene identifiers (including Entrez Gene, Ensembl, Refseq, Interpro, GO, Affy reporters) with links out to primary sources. 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In addition to viewing the content shown in the page, you are welcome to add new contributions using the "edit" tab at the top of the page. References: http://dx.doi.org/10.1371/journal.pbio.0060175, http://dx.doi.org/10.1093/nar/gkp760</item></item><item key="_score">None</item><item key="_index">biogps</item><item key="_id">10</item></item><item><item key="sort"><item>417.0</item></item><item key="_type">plugin</item><item key="_source"><item key="rating_data"><item key="avg_stars">10</item><item key="total">1</item><item key="avg">5</item></item><item key="name">STRING - Proteins and their Interactions</item><item key="created">2008-05-01 07:46:20</item><item key="url">http://string-db.org/newstring_cgi/show_network_section.pl?targetmode=proteins&amp;caller_identity=gnf&amp;network_flavor=evidence&amp;identifier={{EnsemblGene}}</item><item key="lastmodified">2011-05-03 15:49:33</item><item key="usage_data"><item key="layouts">417.0</item><item key="users">352</item></item><item key="popularity">417.0</item><item key="owner"><item key="username">mering</item><item key="url">/profile/2727/mering</item><item 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net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_id_of_pluginxml_text0nodelist11net.sf.taverna.t2.activitiesxpath-activity1.3net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="UTF-8"?> <item><item key="sort"><item>909.0</item></item><item key="_type">plugin</item><item key="_source"><item key="rating_data"><item key="avg_stars">10</item><item key="total">2</item><item key="avg">5</item></item><item key="name">Gene expression/activity chart</item><item key="created">2008-03-17 15:38:24</item><item key="url">http://plugins.biogps.org/data_chart/data_chart.cgi?id={{EntrezGene}}</item><item key="lastmodified">2011-08-30 16:10:20</item><item key="usage_data"><item key="layouts">909.0</item><item key="users">695</item></item><item key="popularity">909.0</item><item key="owner"><item key="username">jhuss</item><item key="url">/profile/349/jhuss</item><item key="name">Jon Huss</item></item><item key="species"><item>human</item><item>mouse</item><item>rat</item></item><item key="shortUrl">plugins.biogps.org</item><item key="id">9</item><item key="in">plugin</item><item key="short_description">This plugin displays reference gene expression data sets, including our popular "Gene Atlas" data set.</item><item key="role_permission"><item>biogpsusers</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="options"><item key="certified_owner">True</item><item 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1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokechoose_plugin_by_nameselectionValues1answer00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity title 0 'text/plain' java.lang.String true message 0 'text/plain' java.lang.String true selectionValues 1 l('text/plain') java.lang.String true answer 0 0 workflow net.sourceforge.taverna.scuflworkers.ui.ChooseWorker UserNameHere 2012-02-15 21:09:29.239 GMT net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeflatten_name_listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_name_of_pluginxml_text0nodelist11net.sf.taverna.t2.activitiesxpath-activity1.3net.sf.taverna.t2.activities.xpath.XPathActivity <?xml version="1.0" encoding="UTF-8"?> <item><item key="sort"><item>909.0</item></item><item key="_type">plugin</item><item key="_source"><item key="rating_data"><item key="avg_stars">10</item><item key="total">2</item><item key="avg">5</item></item><item key="name">Gene expression/activity chart</item><item key="created">2008-03-17 15:38:24</item><item key="url">http://plugins.biogps.org/data_chart/data_chart.cgi?id={{EntrezGene}}</item><item key="lastmodified">2011-08-30 16:10:20</item><item key="usage_data"><item key="layouts">909.0</item><item key="users">695</item></item><item key="popularity">909.0</item><item key="owner"><item key="username">jhuss</item><item key="url">/profile/349/jhuss</item><item key="name">Jon Huss</item></item><item key="species"><item>human</item><item>mouse</item><item>rat</item></item><item key="shortUrl">plugins.biogps.org</item><item key="id">9</item><item key="in">plugin</item><item key="short_description">This plugin displays reference gene expression data sets, including our popular "Gene Atlas" data set.</item><item key="role_permission"><item>biogpsusers</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="options"><item key="certified_owner">True</item><item key="mobile_url">http://plugins.biogps.org/data_chart/data_chart_mobile.cgi?id={{EntrezGene}}</item><item key="allowedSpecies"><item>human</item><item>mouse</item><item>rat</item></item><item key="securityAware">True</item></item><item key="tags"><item>chart</item><item>expression</item></item><item key="description">This plugin displays reference gene expression data sets, including our popular "Gene Atlas" data set.</item></item><item key="_score">None</item><item key="_index">biogps</item><item key="_id">9</item></item> /item/item/item[@key='name'] net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeflatten_id_listinputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity inputlist 2 l(l('')) [B true outputlist 1 l('') 1 workflow org.embl.ebi.escience.scuflworkers.java.FlattenList net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokefind_corresponding_idthe_index0the_list1the_element00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity the_list 1 text/plain java.lang.String true the_index 0 text/plain java.lang.String true the_element 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_render_urlgene_id0plugin_id0url00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity plugin_id 0 text/plain java.lang.String true gene_id 0 text/plain java.lang.String true url 0 0 workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeopen_render_urlthe_url0net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivity the_url 0 text/plain java.lang.String true workflow net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeextract_pluginsxml_textlist_biogps_pluginsresponseBodyextract_id_of_pluginxml_textextract_pluginsnodelistAsXMLchoose_plugin_by_nameselectionValuesflatten_name_listoutputlistflatten_name_listinputlistextract_name_of_pluginnodelistextract_name_of_pluginxml_textextract_pluginsnodelistAsXMLflatten_id_listinputlistextract_id_of_pluginnodelistfind_corresponding_idthe_indexchoose_plugin_by_nameanswerfind_corresponding_idthe_listflatten_id_listoutputlistcreate_render_urlgene_idgene_idcreate_render_urlplugin_idfind_corresponding_idthe_elementopen_render_urlthe_urlcreate_render_urlurl 231b716b-36c7-4b29-ad3b-fce25f95745e 2012-02-10 20:03:51.842 GMT a0feacb0-cc1c-4725-a5b4-d7c8a457685c 2012-02-10 19:52:11.441 GMT 40c5d083-c244-4b7d-afee-f7322968871e 2012-02-10 19:37:28.32 GMT 417c2bd0-c696-4b2e-b9f1-02bdc80e7ac8 2012-02-10 19:43:06.911 GMT 8c9cb861-20b9-4acd-aaaf-746f44f6852b 2012-02-15 21:08:46.610 GMT Alan R Williams 2012-02-10 19:57:54.450 GMT 4d95aa5e-c842-4ef5-9fde-5d56ce279b76 2012-02-10 19:32:30.519 GMT 3d2887c1-a8d5-4480-9a0d-c492f186ee17 2012-02-10 19:36:24.779 GMT 406a7efa-e0be-4b59-b963-53e8a943f114 2012-02-10 20:01:12.105 GMT 0f92f29a-38d3-4e27-8e56-c2519341f24a 2012-02-10 19:45:28.120 GMT 28b7012f-d38f-4969-b1df-fc3433c1161a 2012-02-15 21:03:27.541 GMT 568a8171-dc61-49cd-987a-a0cb4a38cd07 2012-02-10 19:46:31.305 GMT This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id 2012-02-10 19:59:06.394 GMT a0f61efb-60d0-4310-a394-75409d4ff2dd 2012-02-10 19:50:02.126 GMT e841a18b-6e97-4db9-bf5f-f8f8ef15a33f 2012-02-15 21:10:18.534 GMT 57dfda59-e1c9-4358-95c6-dbdedcda8aff 2012-02-10 19:40:41.716 GMT c919e31d-7caf-42bc-8fec-1018ab449d8a 2012-02-10 19:53:27.819 GMT 1cac8e08-227b-4e5b-9c4e-24fcfa7e3f7f 2012-02-15 21:01:49.564 GMT Render gene via BioGPS 2012-02-10 19:58:10.842 GMT 3135124b-0b94-4133-a134-99c641031c51 2012-02-15 21:09:35.470 GMT 9fbfef17-aecf-481d-b31c-430856c6ab66 2012-02-10 19:42:28.621 GMT 655ced0f-b659-498e-b6c9-2d24803472f3 2012-02-10 19:23:39.399 GMT 91ca66d5-09ea-4076-872a-8019aeafa2ee 2012-02-15 21:00:32.461 GMT