Blog Moved to http://blog.rguha.net

Over the last few days I’ve started moving my web material to a new host. As a result I’ve decided to consolidate my blog there as well. So, I won’t be posting here anymore. The new blog is located at http://blog.rguha.net and carries over all the posts, tags and comments.

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Improved CDK Depiction Service

The folks at the EBI have been doing some great work on the CDK. A major effort is underway to revamp JChemPaint and part of this involves improving the rendering of 2D depictions. While not complete I rebuilt a version of the CDK 1.2.x branch with the latest rendering code from the jchempaint-primary branch and updated the CDK web service. The results are much nicer, though there’s scope for improvements. See for example

http://rguha.ath.cx/~rguha/cicc/rest/depict/c1ccccc1

http://rguha.ath.cx/~rguha/cicc/rest/depict/C1CCCCC12CCCCC2

http://rguha.ath.cx/~rguha/cicc/rest/depict/CC(=O)OC1=CC=CC=C1C(=O)O

http://rguha.ath.cx/~rguha/cicc/rest/depict/c1ccccc1CC=CC%23N

Thanks to Gilleain and Egon for pointing me in the right direction. Anybody using this service should see the new depictions automatically

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Spreading the Word on Open Source Cheminformatics

Over the last few years there has been a lot of activity in the area of Open Source cheminformatics software. Being a contributor to the CDK as well as a supporter of Open Source and Open Data efforts in general, I was delighted to be given the chance to talk about these topics at the BioIT World Conference & Expo. I’ll be talking about the state of art in Open Source cheminformatics, highlighting the advantages and pitfalls of using this type of software, using examples from toolkits, workbenches, pipelining tools and so on. In addition, I’ll be talking a little bit about Open Data and it’s importance and the possibilities that arise from combining Open Source software and Open Data.

Here’s the announcement of the actual meeting:

Join the life sciences community in Boston, MA next April 27-29, 2009 for the 7th Annual Bio-IT World Conference & Expo (www.bio-itworldexpo.com).  Since its debut in 2002, Bio-IT has established itself as a premier event showcasing the myriad applications of IT and informatics to biomedical research and the drug discovery enterprise.  The 2009 program will feature best practice case studies and joint partner presentations relevant to the technologies, research, and regulatory issues of life science, pharmaceutical, clinical, health, and IT professionals.

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A blog is born

I finally decided to get back into blogging – I’ve been doing it of and on (more off than on) and over time I’ve realized that updating static web pages are useful, but a blog lets me say things faster and (hopefully) get discussion going faster as well.

Since I spend most of time doing chemnformatics most of the posts will be related to that. However there will probably be posts relating to various topics such as academics, research, coding and cycling. I’m also quite attracted to shiny new things, so I hope to blog about experiences with new tools and techniques.

As to how often I’ll be posting, I hope to be regular but as always, real life (i.e. non-fun stuff) intrudes, so things may be slow.

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