Your SlideShare is downloading. ×
Bioclipse
Upcoming SlideShare
Loading in...5
×

Thanks for flagging this SlideShare!

Oops! An error has occurred.

×
Saving this for later? Get the SlideShare app to save on your phone or tablet. Read anywhere, anytime – even offline.
Text the download link to your phone
Standard text messaging rates apply

Bioclipse

1,764

Published on

Published in: Technology
0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total Views
1,764
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
29
Comments
0
Likes
1
Embeds 0
No embeds

Report content
Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
No notes for slide

Transcript

  • 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

×