Outcome of the Bioclipse autumn workshop 2006

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Group Photo


From the left: Johannes Wagener, Stefan Kuhn, Egon Willighagen, , Christoph Steinbeck, Tobias Helmus, Violetta, Miguel Rojas Cherto, Ola Spjuth.

Missing on the photo is Thomas Kuhn, who only was physically present on Tuesday.

Day 1

Egon's presentation: the ChildResourceExtractor extension point


The presentation will be available as XHTML shortly.

Egon demonstrated the bc_scixml plugin for visualizing SciXML in Bioclipse. SciXML is produced by Oscar from e. g. HTML, and Egon also demonstrated bc_oscar for doing this.

  • Save an article as HTML.
  • Right-click on html file in Bioclipse, select "Create SciXML".
  • Doubleclick the SciXML file or right-click -> open with browser


  • Clicking an HTML resource should open a HTML viewer as 'editor' (in core bioclipse)
  • Extract "appliesToBioResource" in the PLUGIN.XML
  • Oscar Web service
  • NewWizard 'From URL'

Stefan's presentation: NMRShiftDB functions in Bioclipse


Stefan demontrated the NMRShiftDB features of Bioclipse, e. g. for a given structure, predict NMR from NMRShiftDB

Stefan also demonstarted the use of CheatSheets in Bioclipse which looks excellent for tutorials and educational purposes.


  • Make a table view for quick browsing folders

Publication discussion

  • A new screenshot of the Chemoinformatics plugin was constructed on Windows. We should consider replacing it with a new screenshot with higher resolution.
  • The core object model image needs rewriting. Will be done by Ola
  • Ola and Tobias worked on a new image for showing the interconnectivity between plugins

QSAR functionality discussion

  • Will use IMatrixResource for output (see bc_statistical)
  • Need for a DescriptorProvider EP
  • Need for Wizard page for selection descriptors with an hierarchy

Hack Session

  • Added DescriptorProvider extension point
  • Added dummy CDK extension of the above EP


  • Finish implement CDK DescriptorProvider
  • Finish wizard

Day 2

Recap of Day 1


  • Make plugin identifiers fully qualified: prefix it with "net.bioclipse."
  • Put the DescriptorProvider into the bioclipse plugin

Ola's presentation: Bioclipse, present and future

  • 2045 downloads, 25% Linux
  • Focus afterwards on applications on top of Bioclipse
  • Need to decide on content of 1.1
  • IO support:
    • Fix on a few formats and support them fully
      • bc_spectrum: JCAMP-DX, CMLSpec
      • bc_cdk: MDL molfile, SMILES, XYZ
      • bc_biojava: fasta
  • Move from a library based resource to a concept based resource
    • e.g. PDBResource instead of CDKResource
  • webservices are hot, funding etc. Johannes will talk about this later
  • we have basic bioinfo functionality
    • PDB/CIF viewing (sequence, structure, using BioJava/Jmol)
    • access via webservices to EBI databases


  • setup wiki pages for IO support
  • implement basic bioinfo functionality
    • sequence alignment
    • ... (email us!)
  • finish update site (Ola)
  • finish database support

Johannes' presentation: web services in Bioclipse

  • bc_webservices using Axis 1.4 for EBI databases
    • problems include
      • blocking of thread by no HTTP server response
      • Axis 1.3/1.4, XFire, etc all imcompatible
      • HTTP is pull only
  • many, many other webservices
  • there is a strong need for a replacement of SOAP
  • Johannes demoed the XMPP (Jabber) protocol


  • It was decided that we should start a project for supporting XMPP web services in Bioclipse, and provide reference Web services in bio- and chemoinformatics. The project will be lead by Johannes.
  • The hacking session will be focused on hacking up Rhino support in Bioclipse

Scripting Discussion

  • Johannes introduces some engines, like Rhino, and how the work in Eclipse

Hacking Session

  • Rhine engine is embedded and simple sysout works

Day 3

Hack/Discussion Session

  • SWT/Swing problem on OS/X seems platform caused
    • BCJCPController is not being called, but stack trace shows that only RCP classes are called before that
  • Johannes got the scripting working: he showed opening a popup window in the Bioclipse classpath!
    • key: box = Packages.net.bla.bla

Miguel's presentation: Medea

  • he introduces mass spectrum prediction
  • he shows MS data visualization using bc_spectrum
  • and a MS fragmentation tree using a custom widget (screenshot please!)

Christoph's presentation: COSI

Discussion Session: database support

  • Egon introduces the code he wrote for Hibernate in Bioclipse
    • rather proof-of-principle
    • he's unsure it is the way to go
  • long discussion on what we really want to be able to do