BAZOO

So much to do, so little time

Trying to squeeze sense out of chemical data

Change – Yes, I Did

with 12 comments

I’ve been at IU for 3 years now, the last two as a visiting faculty member. However the time has come for a change. I have accepted a position at the NIH Chemical Genomics Center working in the informatics group and will start there in mid-May.

I’m pretty excited about this move, as the group is doing some pretty cool stuff with cheminformatics and high-throughput assays. The group releases their code into the public domain and you can see some of their stuff here. From a scientific point of view, this is an excellent place to do cheminformatics (as well as informatics and computation in general) because the biologists and chemists are right next door. This means access to fresh, raw data as well as the possibility of working with wet chemistry and biology to test out in silico analyses and predictions. (They also have a neat robotics set up, also next door).

As part of the informatics group, I will have fingers in many pies – modeling and computation, developing software, data management and project support. I’m particularly excited about the forthcoming RNAi screening infrastructure that is being set up at the Center.

What happens to the web services?

All services are currently running, but will not be available at the rguha.ath.cx URL’s after mid May. The services have been transferred to David Wild and I will try and redirect URL’s before I leave – if you find that a service you are using is not working, get in touch with David. However, the source code for the SOAP services are freely available on SourceForge, so you can always deploy them into your local Tomcat container. However, I do not plan on supporting these services any longer.

As I have described previously, I am shifting to REST based services. Thus all the CDK based cheminformatics services are converted to REST forms and are currently hosted of rguha.ath.cx, but after I move, this URL will no longer be available. However, running these services is very easy and is described here. If anybody is interested in hosting these REST services, please get in touch with me. In terms of future support, I plan to work on these REST services in my spare time. Note that these services replace a number of my mod_python based REST services (see the GitHub repository which I will updated shortly to remove deprecated services). In general, I plan to maintain the Python REST services. In particular, some of these  services are still front-ends to SOAP services. Where possible, I will reomove the dependency on the SOAP service. The prediction service is something I plan to work on as it is a very light weight way to deploy predictive models built using R (and less hassle than going via the SOAP based R infrastructure). Unfortunately, until I work out some server solution, the predictive model service will likely not be publicly accessible (as a service, that is).

Databases

Over the last three years I’ve been maintaining a partial mirror of PubChem and the Pub3D database. After my move I will no longer be handling these, so questions should be sent to David. A number of services that I provide make use of these databases. Examples include, 3D structure search, InChI/InChI key¬† resolution, synonyms and so on. These services will continue to run, though the URL’s will likely change. – as before, if you see something is down, David should be able to point you in the right direction. I will likely continue work on the 3D database (especially the similarity search aspects, which is currently flawed), but at this point I don’t know when or how new results will be posted.

I should point out that future work on the projects described here are spare-time projects and not part of my official duties at NCGC. So progress on these is not going to be particularly fast.

Finally, my website has moved to http://rguha.net and the old one should automatically redirect you to the new one.

Written by Rajarshi Guha

March 13th, 2009 at 1:10 pm

Posted in Uncategorized

12 Responses to 'Change – Yes, I Did'

Subscribe to comments with RSS or TrackBack to 'Change – Yes, I Did'.

  1. Congratulations!

    Egon Willighagen

    13 Mar 09 at 1:24 pm

  2. Thanks everybody!

    Rajarshi Guha

    13 Mar 09 at 1:43 pm

  3. All the best!

    baoilleach

    13 Mar 09 at 2:12 pm

  4. Congratulations, Guha!

    Duan Lian

    13 Mar 09 at 2:42 pm

  5. That’s great – congratulations!

    Steve W

    14 Mar 09 at 1:12 am

  6. Rajarshi..Great stuff. I’m 4 hours south of Washington and get up there quite regularly for InChI meetings and to give talks etc. Will ping you when I am up there so I can take you to dinner and say thanks for all the work you’ve helped us with.

    ChemSpiderMan

    14 Mar 09 at 3:09 am

  7. Tony, thanks! Yes, it be good to meet up sometime. (of course I’ll see you in SLC)

    Rajarshi Guha

    14 Mar 09 at 1:28 pm

  8. Hi Rajarshi,
    Congratulations! Landing a joyfull job during those bailout times is always nice. Thanks for the link to the software, I did not know they have some interesting code. Especially the JAVA PubChem fingerprint code; I needed that some months ago, when the PubChem Score Matrix wasn’t out yet :-( or :-)

    PubChem Score Matrix
    http://pubchem.ncbi.nlm.nih.gov/score_matrix/score_matrix.cgi

    I hope you keep up blogging (using a large disclaimer) and publishing (public domain) code. Good luck.
    Tobias

    Tobias Kind

    16 Mar 09 at 1:52 am

  9. Thanks Tobias! I certainly hope to keep on blogging and one of the nice things about the NCGC, is that they they are open to releaseing code publicly. BTW I ported the Pubchem FP code to the CDK

    Rajarshi Guha

    16 Mar 09 at 8:21 pm

  10. Congrats! Come by and see us! (@PubChem)

    Paul Thiessen

    19 Mar 09 at 6:09 pm

  11. @Steve – thanks! (BTW I didn’t realize it was you blogging)

    @Paul – thanks. I’d love to drop by and meet the faces behind the DB

    Rajarshi Guha

    19 Mar 09 at 10:36 pm

  12. Excellent! Hope new work will be as OPEN as it was before!

    Vladimir Chupakhin

    9 Apr 09 at 1:04 pm

Leave a Reply