Using standards to gain interoperability: Bioclipse-OpenTox scripting  Egon Willighagen  BiGCaT - Maastricht University  1...
Managers: the vital organs of Bioclipse  Some theory  ●      Make sure that things happen  ●      They provide all domain-...
Many managers...  Core bioclipse: latex, ui, bioclipse, xml, js, balloon, cdk, rdf, inchi,  cml, moltable, jcp, jcpprops  ...
JavaScript ConsoleDepartment of Bioinformatics - BiGCaT   4
TAB TAB • Discover manager in the JavaScript   console with: 1) TAB TAB (auto-completion) 2) manDepartment of Bioinformati...
man <manager> • Discover what functionality a   manager hasDepartment of Bioinformatics - BiGCaT   6
Ctrl-N → JavaScript editor • Ctrl-N → JavaScript Wizard → Editor   → Save As …Department of Bioinformatics - BiGCaT    7
Running JavaScripts in the Editor • JavaScript Editor → Run → ActionDepartment of Bioinformatics - BiGCaT   8
Managers can be combined ...  var alkanesIUPACNames = ["methane", "ethane",  "propane", "butane"];  var alkanes = cdk.crea...
OpenTox: downloading data sets      var service = "http://apps.ideaconsult.net:8080/ambit2/";      var datasets = opentox....
OpenTox: download-ed data setsDepartment of Bioinformatics - BiGCaT   11
OpenTox: authentication     opentox.getToken(); // return a null     // log in on the OpenTox network     opentox.login("u...
OpenTox: XLogP calculation molecules = cdk.createMoleculeList(); molecules.add(cdk.fromSMILES("COC")); molecules.add(cdk.f...
OpenTox: running models models = opentox.listModels(ontologyService); model = models.get(3); // third model js.say(   open...
Under the hood... Internally, the opentox manager uses RDF and SPARQL for a lot of communication with the OpenTox network....
Where to get more scripts ...Department of Bioinformatics - BiGCaT   16
Future ... • Continued development • Computation without downloading data (pass by   reference) • More ontology developmen...
OpenTox: public, private, local!• AMBIT2 (IdeaConsult Ltd., Nina)   http://apps.ideaconsult.net:8080/ambit2/• localhost:80...
Delivering Bioclipse plugins...Department of Bioinformatics - BiGCaT   19
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Bioclipse-OpenTox demo

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Last week I demoed Bioclipse-OpenTox, and the scripting in Bioclipse in particular, and the semantic web foundations of Bioclipse-OpenTox.

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Bioclipse-OpenTox demo

  1. 1. Using standards to gain interoperability: Bioclipse-OpenTox scripting Egon Willighagen BiGCaT - Maastricht University 17 May 2012Department of Bioinformatics - BiGCaT 1
  2. 2. Managers: the vital organs of Bioclipse Some theory ● Make sure that things happen ● They provide all domain-related functionality ● All Bioclipse GUI is using managers in the background ● Takes care of threading (background processes) ● They are plugged into the system ● Bioclipse dynamically discovers managers when booted ● Extend the JavaScript Console (also Groovy) Spjuth, O., Alvarsson, J., Berg, A., Eklund, M., Kuhn, S., Mäsak, C., Torrance, G., Wagener, J., Willighagen, E. L., Steinbeck, C., Wikberg, J. E., Dec. 2009. Bioclipse 2: A scriptable integration platform for the life sciences. BMC Bioinformatics 10 (1), 397+.Department of Bioinformatics - BiGCaT 2
  3. 3. Many managers... Core bioclipse: latex, ui, bioclipse, xml, js, balloon, cdk, rdf, inchi, cml, moltable, jcp, jcpprops Additional libraries: bridgedb, metfrag, metware, joelib, oscar, opsin, r, pellet, specmol, spectrum, bibtex, owl, ds, qsar, ambit, structuredb Online services: cir, opentox, google, gist, myexperiment, sadi, pubchem, pubmed, nmrshiftdb, twitter … and more.Department of Bioinformatics - BiGCaT 3
  4. 4. JavaScript ConsoleDepartment of Bioinformatics - BiGCaT 4
  5. 5. TAB TAB • Discover manager in the JavaScript console with: 1) TAB TAB (auto-completion) 2) manDepartment of Bioinformatics - BiGCaT 5
  6. 6. man <manager> • Discover what functionality a manager hasDepartment of Bioinformatics - BiGCaT 6
  7. 7. Ctrl-N → JavaScript editor • Ctrl-N → JavaScript Wizard → Editor → Save As …Department of Bioinformatics - BiGCaT 7
  8. 8. Running JavaScripts in the Editor • JavaScript Editor → Run → ActionDepartment of Bioinformatics - BiGCaT 8
  9. 9. Managers can be combined ... var alkanesIUPACNames = ["methane", "ethane", "propane", "butane"]; var alkanes = cdk.createMoleculeList() for (var i=0; i<alkanesIUPACNames.length; i++) { js.say("Adding: " + alkanesIUPACNames[i]); alkanes.add( opsin.parseIUPACName(alkanesIUPACNames[i]) ); } var filename = "/OpenTox/alkanes.sdf"; cdk.saveSDFile(filename, alkanes); ui.open(filename);Department of Bioinformatics - BiGCaT 9
  10. 10. OpenTox: downloading data sets var service = "http://apps.ideaconsult.net:8080/ambit2/"; var datasets = opentox.listDataSets(service); for (set=0; set<5; set++) { var dataset = datasets.get(set); js.say("Downloading set: " + dataset); ui.open( opentox.downloadDataSetAsMDLSDfile( service, dataset, "/OpenTox/ambit/" + set + ".sdf" ) ) }Department of Bioinformatics - BiGCaT 10
  11. 11. OpenTox: download-ed data setsDepartment of Bioinformatics - BiGCaT 11
  12. 12. OpenTox: authentication opentox.getToken(); // return a null // log in on the OpenTox network opentox.login("user", "password") opentox.getToken(); // returns the active token // log out again opentox.logout() opentox.getToken(); // return againDepartment of Bioinformatics - BiGCaT 12
  13. 13. OpenTox: XLogP calculation molecules = cdk.createMoleculeList(); molecules.add(cdk.fromSMILES("COC")); molecules.add(cdk.fromSMILES("CNC")); js.say(opentox.calculateDescriptor(service, descriptor, molecules)); js.say(opentox.calculateDescriptor( service, descriptor, cdk.fromSMILES("CCC") ));Department of Bioinformatics - BiGCaT 13
  14. 14. OpenTox: running models models = opentox.listModels(ontologyService); model = models.get(3); // third model js.say( opentox.predictWithModel( service, model, molecules ) );Department of Bioinformatics - BiGCaT 14
  15. 15. Under the hood... Internally, the opentox manager uses RDF and SPARQL for a lot of communication with the OpenTox network. For this, it uses the rdf manager. For example, directly to the ontology server: 1. rdf.sparqlRemote(String url, String SPARQL) Or to a REST service: 1. rdf.createInMemoryStore() 2. rdf.importFromStream(IRDFStore store, InputStream stream, String format) 3. rdf.sparql(IRDFStore store, String query)Department of Bioinformatics - BiGCaT 15
  16. 16. Where to get more scripts ...Department of Bioinformatics - BiGCaT 16
  17. 17. Future ... • Continued development • Computation without downloading data (pass by reference) • More ontology development for further standardization Pointers ● Bug tracker: http://bugs.bioclipse.net/ ● Feature requests: http://wishes.bioclipse.net/Department of Bioinformatics - BiGCaT 17
  18. 18. OpenTox: public, private, local!• AMBIT2 (IdeaConsult Ltd., Nina) http://apps.ideaconsult.net:8080/ambit2/• localhost:8080• ambitserverDepartment of Bioinformatics - BiGCaT 18
  19. 19. Delivering Bioclipse plugins...Department of Bioinformatics - BiGCaT 19
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