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Bioclipse

Bioclipse. -An open source workbench for chemo- and bioinformatics. Ola Spjuth Dept. Pharmaceutical Biosciences Uppsala University Sweden. What is Bioclipse?. Workbench for life-science Chemo- and bioinformatics Integration platform

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Bioclipse

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  1. Bioclipse -An open source workbench for chemo- and bioinformatics Ola Spjuth Dept. Pharmaceutical Biosciences Uppsala University Sweden

  2. What is Bioclipse? • Workbench for life-science • Chemo- and bioinformatics • Integration platform • Easy to integrate/extend functionality using powerful plugin architecture • Development environment • Inherit existing functionality • Deployment framework • Spread your algorithms

  3. The Bioclipse project • Objectives: • Provide a free, open source platform for application development in life-science • Integrate as much functionality as possible into a user-friendly workbench

  4. Implementation • Type of application: Rich client • Responsive GUI • Make use of desktop computer • Main programming language: Java • Platform independence • Existing components in bioinformatics • Release for Windows, Linux, and Mac OS X

  5. Background: Eclipse • Originally designed as an IDE • Java • C++ • Web • etc… • Today: Universal tool platform • Plugin architecture • Everything is a plugin, even core modules

  6. Eclipse: screenshot

  7. Bioclipse architecture • Built on Eclipse Rich Client Platform (RCP) • Minimal set of Eclipse plugins to develop a complete software application • Powerful plugin-architecture • Everything is a plugin • Extension points • Points that plugins can extend • Exist for almost anything • You can define new points

  8. Architecture • Access data from a variety of sources

  9. Basic features • Load, retrieve, edit, convert, analyze, visualize, and save biological entities • Small molecules • Proteins • Sequences • Spectra • Scripts • Reactions • Many more…

  10. Editor View View Console Properties Bioclipse basics

  11. View • Display information to user • User might interact

  12. Editor • Load/Save life cycle • Undo/redo • Cut and paste • Text-based • Syntax highlighting • Code completion • Graphical objects

  13. PDB Editor

  14. 2D Editor

  15. Perspective • Set of Views, menus, and editors with their relative position and sizes • Can be changed • Saved between sessions • Examples • Chemoinformatics perspective • Bioinformatics perspective • Spectrum perspective

  16. Perspective

  17. Wizard • Ordered set of dialogs

  18. Context menus Menus Menus

  19. Work with molecules in 2D:JChemPaint plugin

  20. Visualize molecules in 3D: Jmol plugin

  21. Work with spectra: Spectrum plugin

  22. Work with sequences: BioJava plugin

  23. CMLRSS plugin: Chemistry on the web • Reader for chemical information in feeds using CML (Chemical Markup Language) • Supports the formats: RSS 1.0, RSS 2.0, Atom 0.3, Atom 1.0 • Access structures/spectra/sequences published on the web • Blogs, databases etc.

  24. CMLRSS plugin: Chemistry on the web

  25. Web service support • General Web service mechanism • Example of Web services • WSDBFetch at EBI for retrieving proteins, sequences from various databases • SubLoc for subcellular predictions • Alignments (BLAST, ClustalW)

  26. The WSDbfetch Web Servicein 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. Scripting capabilities • Javascript-based (Mozilla Rhino) • Write scripts for anything! • Open wizards • Calculations • Pipelining tasks • Web services

  28. Scripting capabilities

  29. Plugging into Bioclipse • Add functionality via plugins • Visualizations • Algorithms • Interfaces • Plugins can interact! • User may select what plugins to install

  30. Plugin dependencies

  31. Current development • Maintain and develop Bioclipse core • Increase basic features • Support more file formats • Online update function

  32. Ongoing projects • Structure-activity analysis • Descriptor calculation • Dataset/matrix editing • Interface with R for analysis • Taverna interoperability • Run workflows from within Bioclipse • Visualize results from Taverna • Computer aided structure elucidation

  33. Ongoing projects • Local database persistence • Molecular libraries • Substructure searching • Virtual screening • Pharmacology • Drug screening data management • Interaction modeling • New asynchronous Web services (XMPP) • Microarrays (Base 2.0)

  34. Ongoing projects • Molecular dynamics (Ghemical, using JNI) • Systems biology (SBML) • Text mining (Oscar3) • Mass spectrometry (Mascot, other) • Reaction modeling • Semantic publishing (SciML) • Data analysis (R, Matlab, Java, 3’rd party) • More Web services

  35. Future projects • Integrate more tools and features! • Find areas where plugin interaction lead to new possibilities • Connect to GRID services

  36. Major back-ends • Chemoinformatics: Chemistry Development Kit (CDK) • Bioinformatics: BioJava

  37. Licensing • Bioclipse: EPL - Eclipse public license • Flexible open source license • Plugins: Any license, even commercial • All plugins packaged with Bioclipse are free and open source

  38. Bioclipse Workshop 2007 • May 23-25, 2007, BMC, Uppsala • 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. • Participation in the workshop is free of charge. • Workshop homepage: • http://teacher.bmc.uu.se/BioclipseWS07

  39. Dept. Pharmaceutical Biosciences, Uppsala University, Sweden Prof. Jarl E. S. Wikberg Martin Eklund Jonathan Alvarsson Dept of Chemistry, Molecular Informatics, Cambridge University Prof. Peter Murray-Rust et al (CML) Linnaeus Centre for Bioinformatics, Uppsala University and SLU, Sweden Dr. Eric Bongcam-Rudloff Sofia Burvall Cologne University Bioinformatics Centre (CUBIC), Germany Prof. Christoph Steinbeck Egon Willighagen Tobias Helmus Stefan Kuhn Miguel Rojas Thomas Kuhn Others Johannes Wagener (Web services, scripting) Jerome Pansanel (Chemical structures) Rob Schellhorn (Ghemical) … and all others for contributing code, feature requests, bug reports, proposals, and comments Acknowledgements

  40. Bioclipse www.bioclipse.net 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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