New Google+ communities: Bioclipse, Cheminformatics, Semantic MediaWiki

After spending countless hours on Google+, I have realized how useful their new group feature is, for sharing/finding interesting stuff happening around different technologies. It's nice handling of previews of movies, images, webpages etc makes it so much easier to spot interesting stuff. IMO it works FAR better than e.g. twitter, for this.

E.g. by subscribing to groups for the topics you are interested in (I have over 50...), I get tons of interesting stuff on your Google+ home page all the time.

While Google+ groups definitely don't replace mailing lists and IRC, which are superior for discussions, it is a great complement for sharing interesting stuff happening around a technology.

With this in mind, during the last week or so, I've tried to make sure that a few of my favourite softwares and topics have groups, which resulted in a few new ones:

... so make sure to join those of these that you like, and post some interesting stuff there! :)

How to force update of the layout of a Eclipse JFace Wizard?

Add this to it's onEnterPage() method:

getShell().layout(true, true);

For more info, see this StackOverflow question:

My SMWCon Fall 2011 Talk now on YouTube

I blogged it earlier, but better to get everything in one post, so taking the summary again:

After doing my GSoC project for Wikimedia foundation / Semantic MediaWiki in 2010, resulting in the RDFIO Extension, I finally could make it to the Semantic MediaWiki Conference, which was in Berlin in September.

Now, the video of my talk, "hooking up Semantic MediaWiki with external tools via SPARQL" (such as Bioclipse and R), is out on YouTube, so please find it below. For your convenience, you can find the slides below the video, as well as the relevant links to the different stuff shown (click "read more" to see it all on same page).

My SMWCon Fall 2011 Talk

After doing my GSoC project for Wikimedia foundation / Semantic MediaWiki in 2010, resulting in the RDFIO Extension, I finally could make it to the Semantic MediaWiki Conference, which was in Berlin this week.

While I write up a longer review of the many interesting talks, you can in the meantime find the slides from my talk below, on "hooking up Semantic MediaWiki with external tools" (such as Bioclipse and R):


  • For the SMW/Bioclipse Hookup there is a status update on my blog.
  • ... with a demo screencast.
  • More info on the RDFIO extension available on the Extension page
  • Code for the Bioclipse SMW module is available at github
  • Bioclipse website is at
  • ... and the (SMW) Bioclipse wiki
  • The SMW/R hookup is not yet published in any journal, but this is what is available:
    • Egon Willighagen, who did it, has blogged it.
    • Also, the rrdf package he wrote, is is available in the CRAN, and there's a PDF available, describing it.

HPC Client Screencast: Experimental Job Config Wizard

My work at UPPMAX, on the Bioclipse based HPC Client i is progressing, slowly but steadily. I just screencasted an experimental version of the job configuration wizard, which loads command line tool definitions from the Galaxy workbench, and use them to generate a GUI for configuring the parameters to the command line tool in question, as well as the parameters for the Slurm Resource manager (used at UPPMAX). Have a look if you want :) :

The Wizard obviously has quite some rough edges still. My current TODO is as follows:

  • Set sensible default values i widgets (i.e. when there is just 1 alt)
  • Use checkboxes and radiobuttons for select fields with few options
  • Use progress bar between wizard pages that takes time to load
  • Decide how to take care of the cheetah #if#lse#endif syntax, available in some galaxy tool config files.
  • Add validation
  • Use a time widget for the job time
  • Add a custom view with just a "connect" button, and showing only remote files for the configured host.
  • More modular loading of modules (hierarchical etc.)
  • More advanced parsing of options (i.e. allowing to omit params, rather than just saying "no" on them).

Etc ... More suggestions? :)

A graphical client for running bioinformatics tools on HPC clusters

This blog has been silent for a while and someone might wonder what I've been doing.

One answer is: Developing a graphical client for non-linux-experienced users to connect securely to a computer cluster and configure batch jobs for common bioinformatics software. The project is financed within the UPPNEX project, and so the focus is foremost analysis of Next Generation Sequencing data, but the client will be fully capable to use for any software installed on the cluster.

The client meets a rising need in the next generation sequencing community, since biologists generally have far less experience with *nix systems and programming, than, say physicists, while the vast amounts of sequencing data increases the need to use large scale computing resources such as the ones provided in the UPPNEX project.

I demonstrated a proof-of-concept version at the UPPNEX-SciLifeLab bioinformatics forum on Feb 22nd, and the slides are now available:

As can be seen in the slides, the client is based on the very capable Bioclipse platform.

Looping over a List<String> in Bioclipse's JS console

I had some trouble finding out how to loop over the results of a manager method in Bioclipse, which returns a List<String> to Bioclipse's javascript console. Since I didn't find it documented anywhere (probably it is, somewhere?), I wanted to ducument the snippet here:

var strings = myManager.methodReturningListOfStrings(someParams);
for (var i=0; i<strings.size(); i++) {

Editing Semantic MediaWiki from Bioclipse (with Screencast)

The original use case behind the RDFIO Semantic MediaWiki Extension which I developed as part of "Google Summer of Code 2010", and which was to hook up SMW with Bioclipse, is now concretizising. By using the new Bioclipse SMW Module (code here) it is now for the first time possible to add and remove SMW facts from inside Bioclipse, using a little Bioclipse JS Script:

var wikiURL = "";
smw.addTriple( "w:Caffeine", "w:is_a", "w:Molecule", wikiURL );

Removing triples is similar:

var wikiURL = "";
smw.removeTriple( "w:Caffeine", "w:is_a", "w:Molecule", wikiURL );

Well, you can use full URI:s also, but using the "w" prefix references wiki article titles directly. Thus you can view the result of the addition at

What does this mean? Well, one thing is that with Bioclipse you can edit facts in SMW with the ease and power of javascript! This could enable scenarios where an SMW gets prepopulated with data for subsequent community editing, whereafter data can be transferred back to Bioclipse again, (as blogged about by Egon Willighagen already), possibly making community editing of scientific data mainstream!

There's a little convenience method for getting all RDF data from the SMW too:

rdfStore = rdf.createInMemoryStore();
rdfStore = smw.getRDF( "" );

... which you can then query locally with SPARQL, using the rdf manager:

result = rdf.sparql( rdfStore, 
                     "SELECT DISTINCT ?p WHERE { ?s ?p ?o } LIMIT 10" )
js.print( result );

...getting some output like so:


That's it! Oh, well, I demonstrated the same thing with a screencast as well:

Yay! :) As getting this to work, we ran into a number of bugs in RDFIO, so that also resulted in a new release

Autumn is here - new projects starting

Now that the autumn is here I have some new projects starting, and running for approximately this month (before jumping out into the real world and trying to get a real job :) ). Good thing is, it all builds upon previous work.

First thing is, I'll work with Egon Willighagen to hook up Bioclipse with Semantic MediaWiki, via the RDFIO extension, which I developed as part of GSoC this year, mentored by Denny Vrandecic. I'm excited about putting RDFIO into some real world usage!

Second thing is I'll work part time at the Bioclipse group to improve the ways user documentation for plugins is authored and published, enabling some automation of publishing content to the Bioclipse website as well as the wiki etc. This will hopefully make it a lot easier for end users to find their desired extra functionality, and make more users see the value of a research platform with an open and modular structure, as is Bioclipse!

New release of Bioclipse (2.4)

Bioclipse, the open source chemoinformatics and bioinformatics workbench, which was the context for my thesis project, just released a new major version, 2.4:

Also, the site got a major overhaul just a few days ago, so why don't you have a look! :)