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Department of Bioinformatics - BiGCaT 1Bioclipse-OpenTox:Interactive PredictiveToxicologyEgon Willighagen, @egonwillighage...
Department of Bioinformatics - BiGCaT 2March 11 2013
Department of Bioinformatics - BiGCaT 3SEURAT-1 “...replacing animal testing”
Department of Bioinformatics - BiGCaT 4OpenTox / ToxBank
Department of Bioinformatics - BiGCaT 5ToxBankKohonen, P. et al. MolInf 2013 32(1):47-63.
Department of Bioinformatics - BiGCaT 6Alternative methods …
Department of Bioinformatics - BiGCaT 7Alternative methods …… computational.
Department of Bioinformatics - BiGCaT 8Alternative methods …… computational.“But they dont work, right?”
Department of Bioinformatics - BiGCaT 9How to integrate complementary info?• Experimental– Cell line– Rat models– Environm...
Department of Bioinformatics - BiGCaT 10Integration platform: BioclipseSpjuth, O et al. BMC bioinformatics 2007 8(1):59.
Department of Bioinformatics - BiGCaT 11Hanson, RM. Appl Cryst 2010 43(5):1250-1260.
Department of Bioinformatics - BiGCaT 12Why Bioclipse?O’Boyle, NM et al. JChemInf 2011 3(1):1-15.• Open Source eco-system–...
Department of Bioinformatics - BiGCaT 13Many extensions...Core bioclipse: latex, ui, bioclipse, xml, js, balloon, cdk, rdf...
Department of Bioinformatics - BiGCaT 14Decision Support (Ola Spjuth)Spjuth, O. et al. JCIM 2011 51(8):1840-1847.
Department of Bioinformatics - BiGCaT 15OpenToxHardy, B. et al. JChemInf 2010 2(1):1-29.Jeliazkova, N et al. JChemInf 2011...
Department of Bioinformatics - BiGCaT 16Thus: Bioclipse-OpenToxWillighagen, EL et al. BMC Res Notes 2011 4(1):487.
Department of Bioinformatics - BiGCaT 17Application #1: decision support
Department of Bioinformatics - BiGCaT 18Application #2: descriptor calculation
Department of Bioinformatics - BiGCaT 19Application #3: scripting
Department of Bioinformatics - BiGCaT 20Managers: the vital organs of BioclipseSome theory●Make sure that things happen●Th...
Department of Bioinformatics - BiGCaT 21Managers can be combined ...var alkanesIUPACNames = ["methane", "ethane","propane"...
Department of Bioinformatics - BiGCaT 22OpenTox: downloading data setsvar service = "http://apps.ideaconsult.net:8080/ambi...
Department of Bioinformatics - BiGCaT 23OpenTox: authenticationopentox.getToken(); // return a null// log in on the OpenTo...
Department of Bioinformatics - BiGCaT 24OpenTox: XLogP calculationmolecules = cdk.createMoleculeList();molecules.add(cdk.f...
Department of Bioinformatics - BiGCaT 25OpenTox: running modelsmodels = opentox.listModels(ontologyService);model = models...
Department of Bioinformatics - BiGCaT 26Conclusions & Outlook• InteractiveToxicityPrediction– Local andOpenTox services– S...
Department of Bioinformatics - BiGCaT 27Acknowledgements• Uppsala University– Ola Spjuth• Karolinska Institutet– Roland Gr...
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Bioclipse-OpenTox: interactive predictive toxicology

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Bioclipse-OpenTox is a platform developed for the interactive prediction of toxicity-related properties
or organic molecules. Integrating two independent projects, it enables toxicity prediction based
on the analysis of chemical structures, and visualization the substructure contributions to the
toxicity prediction. OpenTox is a semantic web framework, based on web services, which supports
open data exchange and toxicology model building and validation. Bioclipse is used to provide
user-friendly solution for graphical interaction and visualisations, as well
as scripting for workflow needs. It was recently extended to dynamically discover computational
algorithms exposed via the OpenTox servers, acting as a registry of available computational
toxicology services on the OpenTox network. We further show how predictions from multiple services
can be simultaneously evaluated while editing substructures new compounds.

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Transcript of "Bioclipse-OpenTox: interactive predictive toxicology"

  1. 1. Department of Bioinformatics - BiGCaT 1Bioclipse-OpenTox:Interactive PredictiveToxicologyEgon Willighagen, @egonwillighagenDept. of Bioinformatics - BiGCaT - Maastricht Universityorcid.org/0000-0001-7542-0286ACS New Orleans, 9 April 2013, #ACSNola #DrugDisco
  2. 2. Department of Bioinformatics - BiGCaT 2March 11 2013
  3. 3. Department of Bioinformatics - BiGCaT 3SEURAT-1 “...replacing animal testing”
  4. 4. Department of Bioinformatics - BiGCaT 4OpenTox / ToxBank
  5. 5. Department of Bioinformatics - BiGCaT 5ToxBankKohonen, P. et al. MolInf 2013 32(1):47-63.
  6. 6. Department of Bioinformatics - BiGCaT 6Alternative methods …
  7. 7. Department of Bioinformatics - BiGCaT 7Alternative methods …… computational.
  8. 8. Department of Bioinformatics - BiGCaT 8Alternative methods …… computational.“But they dont work, right?”
  9. 9. Department of Bioinformatics - BiGCaT 9How to integrate complementary info?• Experimental– Cell line– Rat models– Environmetal data– ...• Computational– “COMP” stuff– “CINF” stuff– Systems biologyNeeds: integrate, visualize, analyze.
  10. 10. Department of Bioinformatics - BiGCaT 10Integration platform: BioclipseSpjuth, O et al. BMC bioinformatics 2007 8(1):59.
  11. 11. Department of Bioinformatics - BiGCaT 11Hanson, RM. Appl Cryst 2010 43(5):1250-1260.
  12. 12. Department of Bioinformatics - BiGCaT 12Why Bioclipse?O’Boyle, NM et al. JChemInf 2011 3(1):1-15.• Open Source eco-system– Jmol, CDK, OPSIN, ...
  13. 13. Department of Bioinformatics - BiGCaT 13Many extensions...Core bioclipse: latex, ui, bioclipse, xml, js, balloon, cdk, rdf, inchi,cml, moltable, jcp, jcppropsAdditional libraries: bridgedb, metfrag, metware, joelib, oscar,opsin, r, pellet, specmol, spectrum, bibtex, owl, ds, qsar, ambit,structuredbOnline services: cir, opentox, google, gist, myexperiment, sadi,pubchem, pubmed, nmrshiftdb, twitter… and more.
  14. 14. Department of Bioinformatics - BiGCaT 14Decision Support (Ola Spjuth)Spjuth, O. et al. JCIM 2011 51(8):1840-1847.
  15. 15. Department of Bioinformatics - BiGCaT 15OpenToxHardy, B. et al. JChemInf 2010 2(1):1-29.Jeliazkova, N et al. JChemInf 2011 3:18.
  16. 16. Department of Bioinformatics - BiGCaT 16Thus: Bioclipse-OpenToxWillighagen, EL et al. BMC Res Notes 2011 4(1):487.
  17. 17. Department of Bioinformatics - BiGCaT 17Application #1: decision support
  18. 18. Department of Bioinformatics - BiGCaT 18Application #2: descriptor calculation
  19. 19. Department of Bioinformatics - BiGCaT 19Application #3: scripting
  20. 20. Department of Bioinformatics - BiGCaT 20Managers: the vital organs of BioclipseSome 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. BMCBioinformatics 10 (1), 397+.
  21. 21. Department of Bioinformatics - BiGCaT 21Managers 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);
  22. 22. Department of Bioinformatics - BiGCaT 22OpenTox: downloading data setsvar 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"))}
  23. 23. Department of Bioinformatics - BiGCaT 23OpenTox: authenticationopentox.getToken(); // return a null// log in on the OpenTox networkopentox.login("user", "password")opentox.getToken(); // returns the active token// log out againopentox.logout()opentox.getToken(); // return again
  24. 24. Department of Bioinformatics - BiGCaT 24OpenTox: XLogP calculationmolecules = 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")));
  25. 25. Department of Bioinformatics - BiGCaT 25OpenTox: running modelsmodels = opentox.listModels(ontologyService);model = models.get(3); // third modeljs.say(opentox.predictWithModel(service,model,molecules));
  26. 26. Department of Bioinformatics - BiGCaT 26Conclusions & Outlook• InteractiveToxicityPrediction– Local andOpenTox services– Scriptable– Mixable– Extensible• Ontologies– Detail exchange• Virtual Machine– Inside firewall
  27. 27. Department of Bioinformatics - BiGCaT 27Acknowledgements• Uppsala University– Ola Spjuth• Karolinska Institutet– Roland Grafström• IdeaConsult Ltd.– Nina Jeliazkova• DouglasConnect– Barry Hardy– Roman Affentranger• http://bioclipse.netMentioned EU projects• http://opentox.org• http://toxbank.net• http://dixa-fp7.eu
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