chem-bla-ics

Critical mass for Open Notebook Science wikis by prepopulation with RDF data

2010-06-26T00:00:00+00:00

One of the problems with Open Data, - Source, and Standards (ODOSOS) is to get critical mass: for the project to move forward, you need both a good user community and an active developers community. The first is the crucial reward for the latter: people using your work is the incentive. Sometimes, a project does not succeed in doing that; Rich was questioning if his ChemPedia project built up enough mass.

This also applies to wikis. WikiPedia clearly has enough critical mass, but is struggling with scaling, which is another problem you can encounter. Building a dedicated, domain specific wiki allows you to do things the way you like. For example, the can be used to build up the knowledge base around a specific problem. For example, HIV drugs (see HIVdb as an example knowledge base). The wiki could contain information you need for your data analysis. The developers team will likely be small, but the data will be highly curated. You are basically both the developer and the user community. Hopefully, in good Open Notebook Science manner, things will grow, and others will join in on building the knowledge base.

Semantic MediaWiki bridges the human readable wiki content, with machine readable RDF content. This wiki does require some additional annotation, but at the same time makes important facts machine readable. The Bioclipse Wiki is using it, though we are not yet taking advantage of the RDF exposure.

Now, returning to the critical mass aspect we started with. Samuel, who did a project with me on reasoning with Prolog in Bioclipse, is now doing a Google Summer of Code project (is there any significance in the fact that three Bioclipse developers are student or have been mentor in the GSoC? :) within the Semantic MediaWiki project. In particular, one of the things he was just working on, is the import of RDF into a wiki.

Oh goodies! That is pretty cool, don’t you think? Just pull together RDF from your field of interest, drop it on the wiki, and you have your initial wiki the experts can continue to curate, add facts, etc. He already told me about his plans to add a SPARQL end point for the Semantic MediaWiki software.

Payed summer jobs in chemoinformatics

2007-06-16T00:00:00+00:00

Last year the Programmeerzomer.nl sponsored one summer student to work on Bioclipse (see the announcement). The Programmeerzomer is much like the Google Summer of Code where I mentor Alexandr. However, it is much smaller and oriented at just the NL area: both the student and the mentor needs to be Dutch, but the opensource project does not.

Rob worked last year on a Ghemical plugin for Bioclipse (see this interview in Dutch). The architecture for doing calculations (the Compute plugin) is still being used within several other plugins. This year I got assigned two students: one for Bioclipse and one for Jmol.

I have no idea at this moment what ideas the students picked from the lists in the wikis (see the Jmol project idea and Bioclipse idea lists). There is a meeting scheduled in the 25th.

The ideas include:

Jmol
- a SWT widget for Eclipse RCP-based application
- Pharmacophore rendering
- Support for PDB in XML
- Ajax-enabled JavaScript library (for the applet)
Bioclipse
- a validating CML editor
- a GROMACS plugin
- a sequence editor
- webservices over Jabber’s XMPP
- Beanshell and Jython scripting plugins

If you have a suggestion, it would be much appreciated if you can add that to the wiki pages linked above. Make sure to leave a comment to this blog item too, announcing the new idea!

Dutch Summer of Code sponsors a Bioclipse project

2006-06-20T00:00:00+00:00

The Dutch version of the Google Summer of Code, Programmeerzomer.nl, announced today the five students participating. I was happy to see that Rob Schellhorn was selected with his project proposal for a Ghemical plugin for Bioclipse. Like in the Google original, both the student and the mentoring organization are funded, 3600 and 400 euro respectively.