Bioclipse

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Bioclipse

  1. 1. Bioclipse -An open source workbench for chemo- and bioinformatics Ola Spjuth Dept. Pharmaceutical Biosciences Uppsala University Sweden
  2. 2. What is Bioclipse? <ul><li>Workbench for life-science </li></ul><ul><ul><li>Chemo- and bioinformatics </li></ul></ul><ul><li>Integration platform </li></ul><ul><ul><li>Easy to integrate/extend functionality using powerful plugin architecture </li></ul></ul><ul><li>Development environment </li></ul><ul><ul><li>Inherit existing functionality </li></ul></ul><ul><li>Deployment framework </li></ul><ul><ul><li>Spread your algorithms </li></ul></ul>
  3. 3. The Bioclipse project <ul><li>Objectives: </li></ul><ul><ul><li>Provide a free, open source platform for application development in life-science </li></ul></ul><ul><ul><li>Integrate as much functionality as possible into a user-friendly workbench </li></ul></ul>
  4. 4. Implementation <ul><li>Type of application: Rich client </li></ul><ul><ul><li>Responsive GUI </li></ul></ul><ul><ul><li>Make use of desktop computer </li></ul></ul><ul><li>Main programming language: Java </li></ul><ul><ul><li>Platform independence </li></ul></ul><ul><ul><li>Existing components in bioinformatics </li></ul></ul><ul><li>Release for Windows, Linux, and Mac OS X </li></ul>
  5. 5. Background: Eclipse <ul><li>Originally designed as an IDE </li></ul><ul><ul><li>Java </li></ul></ul><ul><ul><li>C++ </li></ul></ul><ul><ul><li>Web </li></ul></ul><ul><ul><li>etc… </li></ul></ul><ul><li>Today: Universal tool platform </li></ul><ul><ul><li>Plugin architecture </li></ul></ul><ul><ul><li>Everything is a plugin, even core modules </li></ul></ul>
  6. 6. Eclipse: screenshot
  7. 7. Bioclipse architecture <ul><li>Built on Eclipse Rich Client Platform (RCP) </li></ul><ul><ul><li>Minimal set of Eclipse plugins to develop a complete software application </li></ul></ul><ul><li>Powerful plugin-architecture </li></ul><ul><ul><li>Everything is a plugin </li></ul></ul><ul><li>Extension points </li></ul><ul><ul><li>Points that plugins can extend </li></ul></ul><ul><ul><li>Exist for almost anything </li></ul></ul><ul><ul><li>You can define new points </li></ul></ul>
  8. 8. Architecture <ul><li>Access data from a variety of sources </li></ul>
  9. 9. Basic features <ul><li>Load, retrieve, edit, convert, analyze, visualize, and save biological entities </li></ul><ul><ul><li>Small molecules </li></ul></ul><ul><ul><li>Proteins </li></ul></ul><ul><ul><li>Sequences </li></ul></ul><ul><ul><li>Spectra </li></ul></ul><ul><ul><li>Scripts </li></ul></ul><ul><ul><li>Reactions </li></ul></ul><ul><ul><li>Many more… </li></ul></ul>
  10. 10. Bioclipse basics View View Editor Console Properties
  11. 11. View <ul><li>Display information to user </li></ul><ul><li>User might interact </li></ul>
  12. 12. Editor <ul><li>Load/Save life cycle </li></ul><ul><li>Undo/redo </li></ul><ul><li>Cut and paste </li></ul><ul><li>Text-based </li></ul><ul><ul><li>Syntax highlighting </li></ul></ul><ul><ul><li>Code completion </li></ul></ul><ul><li>Graphical objects </li></ul>
  13. 13. PDB Editor
  14. 14. 2D Editor
  15. 15. Perspective <ul><li>Set of Views, menus, and editors with their relative position and sizes </li></ul><ul><li>Can be changed </li></ul><ul><li>Saved between sessions </li></ul><ul><li>Examples </li></ul><ul><ul><li>Chemoinformatics perspective </li></ul></ul><ul><ul><li>Bioinformatics perspective </li></ul></ul><ul><ul><li>Spectrum perspective </li></ul></ul>
  16. 16. Perspective
  17. 17. Wizard <ul><li>Ordered set of dialogs </li></ul>
  18. 18. Menus <ul><li>Menus </li></ul>Context menus
  19. 19. Work with molecules in 2D: JChemPaint plugin
  20. 20. Visualize molecules in 3D: Jmol plugin
  21. 21. Work with spectra: Spectrum plugin
  22. 22. Work with sequences: BioJava plugin
  23. 23. CMLRSS plugin: Chemistry on the web <ul><li>Reader for chemical information in feeds using CML (Chemical Markup Language) </li></ul><ul><li>Supports the formats: RSS 1.0, RSS 2.0, Atom 0.3, Atom 1.0 </li></ul><ul><li>Access structures/spectra/sequences published on the web </li></ul><ul><ul><li>Blogs, databases etc. </li></ul></ul>
  24. 24. CMLRSS plugin: Chemistry on the web
  25. 25. Web service support <ul><li>General Web service mechanism </li></ul><ul><li>Example of Web services </li></ul><ul><ul><li>WSDBFetch at EBI for retrieving proteins, sequences from various databases </li></ul></ul><ul><ul><li>SubLoc for subcellular predictions </li></ul></ul><ul><ul><li>Alignments (BLAST, ClustalW) </li></ul></ul>
  26. 26. The WSDbfetch Web Service in Bioclipse Supported Databases: embl emblsva emblcon emblanncon emblcds medline pdb refseq refseqp hgbase interpro uniprot uniparc uniref100 uniref90 uniref50 jpo_prt epo_prt uspto_prt ipi
  27. 27. Scripting capabilities <ul><li>Javascript-based (Mozilla Rhino) </li></ul><ul><li>Write scripts for anything! </li></ul><ul><ul><li>Open wizards </li></ul></ul><ul><ul><li>Calculations </li></ul></ul><ul><ul><li>Pipelining tasks </li></ul></ul><ul><ul><li>Web services </li></ul></ul>
  28. 28. Scripting capabilities
  29. 29. Plugging into Bioclipse <ul><li>Add functionality via plugins </li></ul><ul><ul><li>Visualizations </li></ul></ul><ul><ul><li>Algorithms </li></ul></ul><ul><ul><li>Interfaces </li></ul></ul><ul><li>Plugins can interact! </li></ul><ul><li>User may select what plugins to install </li></ul>
  30. 30. Plugin dependencies
  31. 31. Current development <ul><li>Maintain and develop Bioclipse core </li></ul><ul><li>Increase basic features </li></ul><ul><li>Support more file formats </li></ul><ul><li>Online update function </li></ul>
  32. 32. Ongoing projects <ul><li>Structure-activity analysis </li></ul><ul><ul><li>Descriptor calculation </li></ul></ul><ul><ul><li>Dataset/matrix editing </li></ul></ul><ul><ul><li>Interface with R for analysis </li></ul></ul><ul><li>Taverna interoperability </li></ul><ul><ul><li>Run workflows from within Bioclipse </li></ul></ul><ul><ul><li>Visualize results from Taverna </li></ul></ul><ul><li>Computer aided structure elucidation </li></ul>
  33. 33. Ongoing projects <ul><li>Local database persistence </li></ul><ul><ul><li>Molecular libraries </li></ul></ul><ul><ul><li>Substructure searching </li></ul></ul><ul><ul><li>Virtual screening </li></ul></ul><ul><ul><li>Pharmacology </li></ul></ul><ul><ul><li>Drug screening data management </li></ul></ul><ul><ul><li>Interaction modeling </li></ul></ul><ul><li>New asynchronous Web services (XMPP) </li></ul><ul><li>Microarrays (Base 2.0) </li></ul>
  34. 34. Ongoing projects <ul><li>Molecular dynamics (Ghemical, using JNI) </li></ul><ul><li>Systems biology (SBML) </li></ul><ul><li>Text mining (Oscar3) </li></ul><ul><li>Mass spectrometry (Mascot, other) </li></ul><ul><li>Reaction modeling </li></ul><ul><li>Semantic publishing (SciML) </li></ul><ul><li>Data analysis (R, Matlab, Java, 3’rd party) </li></ul><ul><li>More Web services </li></ul>
  35. 35. Future projects <ul><li>Integrate more tools and features! </li></ul><ul><li>Find areas where plugin interaction lead to new possibilities </li></ul><ul><li>Connect to GRID services </li></ul>
  36. 36. Major back-ends <ul><li>Chemoinformatics: Chemistry Development Kit (CDK) </li></ul><ul><li>Bioinformatics: BioJava </li></ul>
  37. 37. Licensing <ul><li>Bioclipse: EPL - Eclipse public license </li></ul><ul><ul><li>Flexible open source license </li></ul></ul><ul><li>Plugins: Any license, even commercial </li></ul><ul><ul><li>All plugins packaged with Bioclipse are free and open source </li></ul></ul>
  38. 38. Bioclipse Workshop 2007 <ul><li>May 23-25, 2007, BMC, Uppsala </li></ul><ul><li>Lectures and hands-on labs to demonstrate the features of Bioclipse, the power of the plugin architecture, and how to integrate new features into the framework. </li></ul><ul><li>Participation in the workshop is free of charge. </li></ul><ul><li>Workshop homepage: </li></ul><ul><ul><li>http://teacher. bmc . uu .se/BioclipseWS07 </li></ul></ul>
  39. 39. Acknowledgements <ul><li>Dept. Pharmaceutical Biosciences, Uppsala University, Sweden </li></ul><ul><li>Prof. Jarl E. S. Wikberg </li></ul><ul><li>Martin Eklund </li></ul><ul><li>Jonathan Alvarsson </li></ul><ul><li>Dept of Chemistry, Molecular Informatics, Cambridge University </li></ul><ul><li>Prof. Peter Murray-Rust et al (CML) </li></ul><ul><li>Linnaeus Centre for Bioinformatics, Uppsala University and SLU, Sweden </li></ul><ul><ul><li>Dr. Eric Bongcam-Rudloff </li></ul></ul><ul><ul><li>Sofia Burvall </li></ul></ul><ul><li>Cologne University Bioinformatics Centre </li></ul><ul><li>(CUBIC), Germany </li></ul><ul><li>Prof. Christoph Steinbeck </li></ul><ul><li>Egon Willighagen </li></ul><ul><li>Tobias Helmus </li></ul><ul><li>Stefan Kuhn </li></ul><ul><li>Miguel Rojas </li></ul><ul><li>Thomas Kuhn </li></ul><ul><li>Others </li></ul><ul><li>Johannes Wagener (Web services, scripting) </li></ul><ul><li>Jerome Pansanel (Chemical structures) </li></ul><ul><li>Rob Schellhorn (Ghemical) </li></ul><ul><li>… and all others for contributing code, feature requests, bug reports, proposals, and comments </li></ul>
  40. 40. Bioclipse <ul><li>www.bioclipse.net </li></ul>Bioclipse: An open source workbench for chemo- and bioinformatics Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E.S. Wikberg BMC Bioinformatics 2007, 8:59

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