Multiple alignments in Bioclipse

I have talked a lot about about integrating Jalview into Bioclipse for visualization and editing of multiple sequence alignments. I spent some hours on the problem and it was not too hard to get things going. It's now possible to double-click an alignment in any of the formats supported by Jalview (fasta, msf, clustalw, pileup, pir, blc, pfam) and Bioclipse opens an Alignment Editor with Jalview on one tab and the source file on the second.

It is currently not possible to interact with Jalview via the mouse, this needs some wrapping of functionality into SWT actions and menus. But it's a good start :-). See the wiki page net.bioclipse.jalview for progress.



Go to the Javascript Console, type rhi and press <Tab>. The command line now says rhino.

If you now type a . (after the rhino) and then <Tab> twice. The first time around, there'll be a beep, and the second time, there'll be a list of possible completions.

People seem happy about this feature when I show it to them. Myself, I'm even happier because I got to implement the (top secret) mechanism that does this under the hood. I could tell you more, but I would have to kill you.

Update: I forgot to say that this goes for Bioclipse 2 only, but I've now backported the feature to Bioclipse 1 too.

Update2: Tab completion now in the Ruby Console, too.


Subversion in Bioclipse2

Since Bioclipse2 is more Eclipse-like, it is quite easy to make use of external Eclipse plugins. Here I demonstrate this by adding the Subclipse plugin for Subversion and making use of it from the Bioclipse2 workbench.

Figure: A local project shared on a Subversion repository. The editor shows compare of the local and remote version of the same document with changes highlighted.

Having version control inside the Bioclispe workbench opens up many new possibilities for collaborative work. It allows e.g. for shared editing of chemical and biological files, to resolve conflicts, and rollback any undesired changes.

The current solution requires some editing in the Subclipse source due to unresolved dependencies, but I will contact the Subclipse team and try to resolve this.

Links: Bioclipse wiki page