So much to do, so little time

Trying to squeeze sense out of chemical data

Archive for March, 2010

R-group support in the CDK

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Mark Rijnbeek recently implemented support for R-group queries and reading/writing of the MDL RGFile format. Egon just committed to master. Very cool functionality and now we (somebody?) can consider implementing support for Markush structure enumeration, filtering etc.

Written by Rajarshi Guha

March 30th, 2010 at 12:22 pm

Posted in cheminformatics,research

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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

Cheminformatics and R at the EBI

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Finally all the paper work is in place for me to visit the EBI in May to run a hands-on workshop on doing cheminformatics in R. This is part of a two day program. On May 17th I will be discussing the use of the rcdk and rpubchem packages, considering a variety of use cases such as QSAR modeling and fingerprint similarity. I’ll also be touching on the CDK, as that’s the underlying toolkit. The second day, May 18th, run by Stefan Neumann, Paul Benton and David Broadhurst will focus on handling and analyzing mass spectrometry data in R.

I’m really looking forward to this trip and the chance to discuss these packages as well as get feedback on what’s useful and what’s not. If any readers are attending and would like me to cover specific topics, feel free to drop me a line.

I’ll be reaching London on May 14th, visiting some friends and then heading to Hinxton on May 16th. Another reason I’m looking forward to the trip (in addition to some good fish and chips) is that I get to visit Harrogate, where I grew up.

Written by Rajarshi Guha

March 10th, 2010 at 2:11 am

Posted in cheminformatics,software

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