chem-bla-ics: June 2010

Program for the RDF symposium at the American Chemical Society fall meeting

It is my great pleasure to present the full symposium program for the RDF session at the American Chemical Society at the Boston meeting in August:

http://egonw.github.com/acsrdf2010/

I am excited that on Monday afternoon Eric Prud'hommeaux will present the work of the LODD working group to the chemistry community. The symposium contains three half day sessions with topics on computing, ontologies, and applications, all chemistry oriented. The goal of the meeting is to get together people using RDF technologies in chemistry, and the list of talks from around the world shows that this goal has been reached. The program is diverse and exciting, and I am very much looking forward to meeting all participants to discuss challenges and cool solutions.

Jun

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

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.

Jun

All CrystalEye data available as PDDL

I do not think I have seen this earlier, but I do not visit the

homepage regularly. But congratulations to the CrystalEye team for

releasing the data explicitly as PDDL! I cannot stress enough how useful it is if you add a statement like this to your public domain data.

Jun

Looking at your statistical models...

I do not think I have ever blogged the paper that played an important role in my thesis (doi:10.1021/ci990038z); research of one of the papers in my thesis, started with the hypothesis proposed therein. The paper had a really good idea; but, unfortunately, it did not contain the data to support the hypothesis. That gets me to one important lesson I learned: a QSAR data set of less than 100 molecules is not enough to make untargeted statistical models.

Jun

QSPR modeling with signatures

I had to dig deep to find posts on QSAR modeling. There are quite a few on QSAR in Bioclipse, but that focuses on the descriptor calculation. In a quick scan, I could only spot two modeling posts:

The CDK/Metabolomics/Chemometrics Unconference results When to stop including QSAR model variables... Given the prominent place QSAR has in my thesis, this is somewhat surprising. Anyway, here is some more QSAR modeling talk.

Jun

My OpenTox Workshop contribution: The Lost Slides

During the nice presentations at the recent OpenTox Workshop, I noted that My OpenTox Workshop contribution: Linking explicit and implicit knowledge was lacking two slides. The slides should have had screenshot of the excellent Bioclipse applications Ola Spjuth has written in the area of computational toxicology. But here they are.

Metabolic Fate

The metabolic fate of molecules can be predicted with the MetaPrint2D feature (see also the main MetaPrint2D page).

Jun

I’m just a sucker with no self esteem

Don't let anyone fool you: The Offspring is really just talking about Science:

When she’s saying that she wants only me

Then I wonder why she sleeps with my friends

When she’s saying that I’m like a disease

Then I wonder how much more I can spend

Well I guess I should speak up for myself

But I really think it’s better this way

The more you suffer

The more it shows you really care

Right? yeah yeah yeah

Really! Just read the whole text:

Late at night she knocks on my door

Drunk again a

Jun

CDK-JChemPaint #6: rendering atom numbers

I have made a few new CDK-JChemPaint patches in the past two days, the latest being patch 15. With the help from Gilleain, all rendering parameters are now using the new API, as explained earlier in this series.

Additionally, the API to work with rendering parameters is now much simpler. The previous posts did not really explain how to tune parameters, so here goes.

Jun

And now for something completely different...

A cake so good, you like to protect it with whatever force you have.