Noel O'Blog celebrates one year at ACS New Orleans

To celebrate the first anniversary of Noel O'Blog, I'm going to be attending the ACS National Meeting in New Orleans, so say hi if you see me. I'll mostly be hanging around the CINF and COMP sessions, or at the CCDC (Cambridge Crystallographic Data Centre) stand in the Exposition Hall, and for sure, at the CINF reception on Tuesday evening.

If you're tired of hearing talks about how docking doesn't work, etc., etc., come along early on Monday and I'll explain one way to improve a scoring function (in the docking software GOLD) to pick out those pesky actives. Any other ideas people might have would be very welcome.

Molecular Modelling: Tools, GUIs and Visualisation

I've just been invited to speak at "Molecular Modelling: Tools, GUIs and Visualisation" (March 11-13, Runcorn, UK), a meeting organised by the CCP1 group of UK computational chemists. Come along if you can, as the meeting sounds very interesting. As you can see below, there are speakers from a number of chemistry projects, both open and closed: OpenBabel, Avogadro, Molekel, Molpro, cclib, GaussSum, the CCP1GUI, GAMESS, and GAMESS-UK.

Here's the announcement:

Meeting: Molecular Modelling: Tools, GUIs and Visualisation

11th - 13th March 2008

This is to announce a CCP1 meeting looking at graphical interfaces, visualisation and tools for molecular modelling in general, but with the focus towards electronic structure.

There are a large number of graphical interfaces and associated tools for working with electronic structure and molecular mechanics/dynamics codes in use in the computational chemistry community today. Many of these tools do similar jobs, but all have their own specialities, strengths and weaknesses.

The aim of this meeting is to bring together the developers and users of these tools to:

- raise awareness of the existing software tools and capabilities.
- allow users to give the developers feedback on what is needed and which areas are not being sufficiently covered.
- explore novel ways of visualising molecular data and other tasks.
- provide an opportunity to discuss collaborations.

We already have speakers confirmed from projects including OpenBabel, Avogadro, Molekel, Molpro, cclib, GaussSum, The CCP1GUI, GAMESS, and GAMESS-UK.

The meeting will be held at the Holiday Inn in Runcorn, Cheshire, from 11th-13th March (starting after lunch on the 11th and running through to lunch on the 13th). The afternoon of the 13th will be reserved for developers to run tutorials/practicals at Daresbury Laboratory.

We still have some slots available for speakers, so if you are a code developer or user, and would be interested in speaking, then please contact: j.m.h.thomas@dl.ac.uk

For registration information, please visit the meeting webpage at:

http://www.ccp1.ac.uk/chemtoolsmeet

We look forward to seeing you in March!

========================================
Jens Thomas,
STFC Daresbury Lab,
Warrington,
WA4 4AD, UK.
http://www.cse.scitech.ac.uk
========================================

4th Joint Sheffield Conference on Chemoinformatics

I recently attended the 4th Joint Sheffield Conference on Chemoinformatics, and enjoyed it a lot.

Some of the things I noted were:
(1) Industry talks have suddenly got more interesting (than they were, that is). After describing methods run on their own in-house data, they suddenly say "In order to compare with other methods, I ran this method on a publicly available dataset". Great. About time. The big free datasets are now so well established, they've even heard about them in industry. Thanks go to ZINC, DUD, PubChem, and the NIH guys who are even making available some HTS data (is this correct? I cannot easily find it on the web).

(2) In this postmodern age, it is now a requirement for all cheminformatics conferences to start with a talk that tells us we're wasting our time trying to dock anything, as it doesn't work. Full marks for shock value, but perhaps the more interesting content of Anthony Nicholls talk related to statistical comparisons of AUC (area under the ROC curve) for a published study of multiple docking problems (Warren et al.). Basically, the error bars are so large we cannot say that any program is significantly different from any other (according to him :-) [disclaimer, I'm developing GOLD]).

(3) Of course, no cheminformatics conference would be complete without dodgy statistics, and I'm as guilty of it (not knowingly, I hope) as anyone. Multiple tests on the same dataset require corrections for significance testing such as the Bonferroni statistic - "if it passes the Bonferroni it's probably true" was the quote from Martin Packer (AZ). Everyone wrote that one down when it was mentioned. But for the cheminformaticians who skipped Statistics 101, there was more extra homework. Jonathan Hirst directed us to read the appendix of one of his papers for some more light reading on hard-core statistics such as the Nemenyi test and the improved Friedman statistic.

(4) Open Source chemistry software got a mention by some of the academics speaking. Jonathan Hirst in particular gave Joelib2 a big thumbs up, and made it clear that his own software is Openly available from his web page (although no license is mentioned in the README there). The author of Joelib2 was in the audience, Joerg Kurt Wegner, and it would have been nice if the speaker had put Joerg's name on his slide along with the name of the program and the website. After all, it's nice to get some personal recognition if you put a lot of work into such a program and then make it Openly available. Jonathan had to skip his next-to-last slide promoting the Blue Obelisk group, but it was still good to see the reference flash by. Irilenia Nobeli used the CDK, as did David Wild who is very active in the development of Web services with open source software.

See you in Sheffield?

Conference season starts Monday for me. I'll be attending the Sheffield Conference on Cheminformatics on 18th June, and if you are too, be sure to say hi.