Wednesday, January 02, 2008

Collaborative work with Bioclipse

Ola blogged about something he is working on for Bioclipse2. The next major series of Bioclipse releases will use the RCP-based resource architecture, which allows better integrating with other RCP plugins, such as the Subclipse plugin which allows one to browse Subversion repositories directly in Bioclipse. That is cool! Check out the screenshot he posted in his blog.

Now, this kind of integration is important. Subversion is a tool to collaboratively work on data, which can be open source (e.g. the Bioclipse source code), open data (e.g. the Blue Obelisk Data Repository), or any other kind. However, unlike tools like Google Docs, Bioclipse with Subversion supports provides you with a rich client to process your data. No longer need for putting SMILES into a spreadsheet, just put the full 3D structure or NMR spectrum in your joint resource set. This is much more suited for Open Notebook Science, right Jean-Claude? Just put in the raw data as it came out of the spectrometer, and let Bioclipse deal with data extraction. Oh, did you that Bioclipse has Oscar3 integrated (which has not been updated to the latest release, though)?

Why bother with Wikis and Google Docs if you have Bioclipse? Why, even, bother with ICE?


  1. Are you saying that there is a built in viewer for JCAMP-DX files?

  2. Oh, it has indeed. Can't find a nice screenshot, but .dx files are supported. Roberts spectrum applet could be easily embedded too, if you'd prefer that.

  3. I don't think ICE and Bioclipse are comparable. ICE is about managing of large compound documents such as created in Open Office and Word. It's aimed at authoring in a general acdemic environment, with discpline-specific chunk where appropriate. Whereas Bioclipse is aimed at chemists and biologists.

    I don't think we will come up with a one-size-fits-all - at least for for some time.


  4. Sounds interesting. Now if it can be used to share a workspace, can you walk me through how you and I could share an NMR spectrum?