General service infrastructure in Bioclipse

The last week I have worked on a general service infrastructure for Bioclipse, or more specifically for Bioclipse2. the thought is to be able to easily add new services and service implementations via extension points in Bioclipse. The installed services can be displayed in the ServiceView (see figure to the right), and the aim is to add filters and hence only display the currently interesting services (based on user preference of course). Double-click the service to invoke it with a dialog or drag a resource (a sequence or a molecule) and drop it on a service to invoke it directly.


For a more detailed explanation about the extension points and examples for using it can be found on the Bioclipse wiki. Below is a sample screenshot for how this integrates into Bioclipse2.

A fully working use case with recording

Much hard work has finally paid off and now there is some cool recording features in bioclipse 2. Since I know how you all would love to try it out I am now gonna explain how you can do that. The plugins needed for this example is net.bioclipse.biojava.ui and all it's dependencies. First of all we need a sequence file containing a couple of sequences. I called my file "a.fasta". Something looking like this would suffice:

>a
ACT

>b
ACG

You can create such a file in Bioclipse by right clicking in a project and creating a new file.

Now for the interesting part. This sequence file contains two sequences. If we want to translate one of them we can open the children of the sequence file by clicking on the arrow in the left of it in the bioclipse explorer. Right clicking any of the sequences brings up a context menu where biojava.ui has contributed a few actions. We can for example translate our sequence to a protein sequence. After having done that, bring up the Action History view. It is under the Scripting category in the show view dialog.

The actions history view shows a view of the recording that has been taken place while we have clicked around in the gui. Select the actions you are intrested in, right click and choose Generate JavaScript. The JsScriptGenerator will now do it's best to build a javascript out how the selected actions. That isn't always so easy but I hope it performs quite good and I know that it succeeds with the sequence translation example I have described here. Try it out and please report any problems that you might find.

The 5000th commit to Bioclipse

The Bioclipse project team is delighted to announce the 5000th commit to Bioclipse made by Egon Willighagen when performing an SVN reorganization for Bioclipse2. Great job, Egon!

Swedish Bioinformatics Workshop

The Bioclipse team was present during the Swedish Bioinformatics Workshop in Uppsala on February 28th-29th. Ola Spjuth held a well-received talk about Bioclipse data integration in bioinformatics, and a poster detailing the workings of Bioclipse drew both interested parties in the hallway track, and a price for best poster. Overall, the reception of Bioclipse felt very positive, and many new contacts were made, possibly leading to further collaborations.