chem-bla-ics: March 2012

BiGCaT: Protein Structure

The last two weeks I have been busy with a course I gave last week (2x two hours lectures, 2x three hours practical) on Protein Structure. I had slides from last year at my disposal, but added some stuff, including a pointer to Google Play's page for the Jmol Android App (cool stuff!). The content involved the basic links between primary, secondary, tertiary, and quarternary structure.

At Maastricht University we use problem-based learning, and the topics for the students of this block (two bachelor studies) were aging and immunology. Interesting, because as a chemist I have limited background in these fields. Other content in this bioinformatics course done by our BiGCaT group involved SNPs, and I found a few interesting examples.

Mar

CDK 1.4.8: the changes, the authors, and the reviewers

Mmmm... when I pasted the list of changes in the CDK 1.4.8 release (download it here), I was surprised by the length. Then again, the 1.4.7 release was almost three months ago.

However, a careful look at the list shows that quite a few are JavaDoc fixes, additional unit testing in the inchi module, and other small tuning. Of more much more interest are the fix in the SDF parser, which failed to continue reading when it encountered a broken molfile entry in the SD file.

Mar

Visualizing metabolite fluxes on WikiPathways pathways using a PathVisio plugin

Visualizing metabolite fluxes on WikiPathways pathways using a PathVisio plugin

Presenters: Anwesha Dutta (student in our group)

Date: Thursday March 29th 2012

Description: Biological pathways provide intuitive frameworks to integrate and co-analyze different kinds of biological data, such as system-wide transcriptomic, proteomic, and metabolomic measurements.

Mar

Google Summer of Code 2012: CDK and Bioclipse project ideas

The NRNB +Google Summer of Code is primarily about +Cytoscape and Wikipathways / PathVisio (the latter two are co-developed in our BiGCaT group in Maastricht), but involves a few project ideas where the +Chemistry Development Kit and Bioclipse have an important role too:

IDEA 27: Extend PathVisio with a Plugin for Metabolomics-related Properties

IDEA 33: Substructure search and small molecule lookups within Cytoscape network

For Bioclipse, I wrote up these two project ideas:

IDEA 28: Integra

Mar

666

Well, another milestone, I guess...

Mar

Dutch government threatens with censorship: publishing needs export permit

De Volkskrant reported this morning very worrying news. Dutch minister Bleker threatens Dutch researchers to censor them, based on the idea that publishing is exporting knowledge, and therefore needs a permit from his department. One has to realize this is in the context of the flu mutation research in Rotterdam (see H5N1, and this Nature item), but such censorship threat is unacceptable, and is a direct attack on science.

Bleker (@HenkBleker) is the Dutch underminister for economics.

Mar

Bioclipse and SADI

I do have to apologize to the Dumontier Lab... Michel visited us when I was still in Uppsala University (so, that's way too long ago), and we spoke about SADI, a really interesting framework for semantic computing. At thought that at the time, and I still do. But, I never got around to playing with it... but this week was so weird, I had to get my mind off... so, time for some random hacking...

Thus, a SADI manager (client) for Bioclipse. Why? Because I can.

Mar

Visualization of Life Science data with Java (Apache 2.0)

Daniel Swan pointed me to this blog post with a rather interesting title: Exploring multiple cancer genomics alterations with Gitools. The Gitools is more than a library, but just the visualization seems interesting already.

(The image comes from their website, and is licensed CC-BY.)

Gitools itself is licensed Apache 2.0 and I am wondering if we can reuse this in other projects, e.g. Bioclipse.

Mar

ChEMBL 13 as RDF

Update: this work is now described in this paper. Last week, ChEMBL 13 was released, with even more data, data fixes, etc. Since my RDF for ChEMBL 09 my workflow has become more solid and uses more common ontologies, started using more common ontologies and ontologies I just like, such as CHEMINF and CiTO. Below is an overview of the resource types present in the RDF: activities (almost 7M now), chemical entities, assays, targets, and documents.

Mar

Call for Input: a "Schema.org" for the (Life) Sciences

Task

define at most five diverse concepts by which triple sets can be summarized for the (life) sciences.

Background

The website schema.org is used by various big web players to define a small set of entities omnipresent on the web. Talis' Kasabi uses this to summarize the triple data sets hosted, and uses the few entities for graphical icons combined with the number of resources of that type.

Now, schema.org defines types like Person, Organization, Event, and Product.