chem-bla-ics: November 2010

Adding a new dictionary to Oscar

Say, you have your own dictionary of chemical compounds. For example, like your companies list of yet-unpublished internal research codes. Still, you want to index your local listserv to make it easier for your employees to search for particular chemistry you are working on and perhaps related to something done at other company sites. This is what Oscar is for.

But, it will need to understand things like UK-92,480. This is made possible with the Oscar4 refactorings we are currently working on. You only need to register a dedicated dictionary. Oscar4 has a default dictionary which corresponds to the dictionary used by Oscar3, and a dictionary based on ChEBI (an old version) (see this folder in the source code repository).

Nov

Uppsala Status Report

As you know, my post-doc in Uppsala ended. It was a good time, and it was great collaborating on Bioclipse with Ola, Jonathan, Arvid, and Carl. I would have loved tighter integration with the work of Maris and Martin, but that was limited to one joined paper (in press). I thank Professors Jarl Wikberg and Eva Brittebo for allowing me to continue my research at their department, and hope this is not the end of the collaboration yet.

Nov

Installing Oscar

About half-way my Oscar project now. I blogged about the Oscar Java API, the command line utility, and the Taverna plugin (all in development). Also, David Jessop joined in, boosting the refactoring. The meeting with the ChEBI team last week was great too. We worked out details for the use cases, involving Oscar and Lezan's ChemicalTagger.

Here follow some install instructions to get going. Please give things a try, even though we are under heavy development.

Nov

More fails... (aka: no VR grant awarded)

I failed to get a VR grant in 2010. The arguments are interesting:

My competence

The applicant had published 15 papers in mostly low impact journals.

True, the top journals in my field (chemometrics, cheminformatics) do not have very high impact factor, because the field is less eager to add 100+ citations to each journal paper, nor is the field know to be popular enough for Nature, Science, etc.

Two of these are highly cited.

Indeed. I recently blogged about that.

Nov

Why you have not heard me much about chemometrics recently...

A casual reader my not know the background of the title of my blog. A bit over five years ago, when I started this blog, I defined chemblaics:Chemblaics (pronounced chem-bla-ics) is the science that uses computers to address and possibly solve problems in the area of chemistry, biochemistry and related fields. The general denomiter seems to be molecules, but I might be wrong there.

Nov

Oscar4 command line utilities

One goal of my three month project is to take Oscar4 to the community. We want to get it used more, and we need a larger development community. Oscar4 and the related technologies do a good, sometimes excellent, job, but have to be maintained, just like any other piece of code. To make using it easier, we are developing new APIs, as well as two user-oriented applications: a Taverna 2 plugin, and command line utilities.

Nov

TTT it is

The fact that Piet Hein said it, gives it an extra (fourth) dimension. Things Take Time.

But, as Peter indicated, we are getting there in cheminformatics. We see the commercial entities experimenting and contributing to Open Source cheminformatics and the Blue Obelisk has reached critical mass a few years ago. Next year is the year of Open Source cheminformatics on the desktop ;)

We are not their yet, and Piet Hein makes a truely wise choice here.