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Trying to squeeze sense out of chemical data

Archive for the ‘cinf’ tag

Another ACS Done

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Finally back home from another ACS National Meeting, this time in San Francisco. While the location is certainly an attraction, there was some pretty nice talks and symposia in the CINF division such as the Visualization of Chemical Data, Metabolomics and Materials Informatics. Credit for these (and all the other) symposia go to the organizers who put in a lot of effort to get an excellent line up of speakers – as evidenced by packed rooms. This time, I finally got round to visiting some of the other division – some excellent talks in MEDI.  As in the past, there was a Blue Obelisk dinner, this time at La Briciola (a fantastic recommendation from Moses Hohman and the CDD crowd) where there was much good discussion.  I got a Blue Obelisk Obelisk from PMR (Cameron Neylon and Alex Wade were also recipients this year).

CINF had some excellent receptions where I got to meet old faces and make some new friends – with many of whom I’ve actually had many virtual exchanges via email or Friendfeed. Here’s a picture of me and Wendy Warr from one of the receptions.

With the meeting over and most of the follow up now, I can take a bit of a break while the last few submissions for the Boston program come trickling in. And then I get down to finalizing the program for the Fall meeting. This fall, we have an excellent line up of symposia including “Data Intensive Drug Design“, “Semantic Chemistry and RDF” and “Structure Activity Landscapes“. At the Fall meeting, I’ll also be chairing a COMP symposium titled “HPC on the Cheap” where an excellent set of speakers will be focusing on various technologies that let users access high performance computing power at a fraction of the price of super computers – stuff like FPGA’s, GPU’s and distributed systems such as Hadoop. This is part of the “Scripting and Programming” series, so expect to see code on the slides!

I’d also like to let people know that in Boston, CINF will be running an experimental symposium consisting of several very short (5 minutes or 8 minutes) lightning talks. But unlike traditional ACS symposia, we’re going to open submissions to this symposia sometime in July and close about 3 or 2 weeks before the meeting itself. In other words, we’re going to be looking for recent and ongoing developments in chemical information and cheminformatics. The title and exact mechanics of this symposium – dates, submissions, reviews and the actual times, slide counts will be announced in the near future at various places. If you think the early ACS deadlines suck, consider submitting a short talk to this symposium.

Overall an excellent meeting in San Francisco and I’m already looking forward to Boston. But in the meantime, time to get back to chewing on data, and finishing up some papers, book chapters and talks.

Written by Rajarshi Guha

March 29th, 2010 at 12:23 am

Switching from the Chair to the Bed

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The Fall ACS meeting, held in Washington DC, is over and I can get back to breathing. The CINF program at the meeting was excellent (but I’m biased) with a variety of symposia. Notable amongst them was the Herman Skolnik symposium, honoring this years Herman Skolnik awardee, Yvonne Martin. Of all the talks, two that caught my eye. Jonathan Goodmans’ talk showed the first case of an InChI key collision, which appears to have been confirmed by ChemSpider and Symyx. The second talk was by Anthony Nicholls of OpenEye at the Herman Skolnik symposium. He discussed the issue of ‘hyperparametric modeling’, i.e., the fact that many types of models ranging from QSAR to molecular dynamics and ab initio methods are over paarmetrized. While this problem is very obvious in QSAR modeling (hence feature selection), the implicit parametrization in things like force fields, ab initio methods is not always obvious. He also discussed issues with model validation techniques such as cross-validation and y-scrambling and suggested techniques that might be better to assess a model. In essence he suggests that we will be more rigorous about model quality when we start assesing the “risk” of a bad model, rather than just how well the model fits the data (which can obviously be misleading). While these ideas are not brand new, the examples and the presentation were eye opening. The last talk in General Papers on Thursday was also quite interesting – B.-Y. Jin spoke about topological rules defining the structures of various nanotube and fullerene structures and how he had been constructing them as bead models. Examples of them can be found on his blog .

I was also involved in organizing a symposium on scripting and programming with COMP. We initially feared that the topic might be too geeky, but we were pleasntly surprised by the size of the audience. We had speakers talking about their favorite languages and how they do modeling and cheminformatics using them. I spoke about R and rcdk – which turned out to be so hot that we were interrupted by a fire alarm (three times!)

On the social events side of things, it was good to meet up with old friends and make new ones. CINF hosted a number of receptions, all excellent. A dinner for CINF functionaries was held at Zaytinya – a Mediterranean tapas restaurant. All I can say is: mindblowing! I had never realized that shrimp and dill could be such a killer combination. The Blue Obelisk dinner was held at PS7, serving eclectic American cuisine. The food was nice, though the service wasn’t too great.

But I have a few days to rest, after which I’ll get on to the San Francisco program (which I must say, is looking very cool)

Written by Rajarshi Guha

August 20th, 2009 at 11:51 pm

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