Bioclipse is an open source workbench for chemo- and bioinformatics that provides a platform for application development in life sciences. It integrates various functionality into a user-friendly workbench and is built on the Eclipse Rich Client Platform using a powerful plugin architecture. Bioclipse allows users to load, retrieve, edit, convert, analyze and visualize biological entities like small molecules, proteins and sequences.

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. Bioclipse basics View View Editor Console Properties

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. Menus Menus Context 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 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. 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. Acknowledgements 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

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