Monday, 13 September 2010

How to get into cheminformatics

A chemistry undergraduate from South America recently emailed me asking about how to get into cheminformatics:
My area is chemistry and I'm very interested about cheminformatics. Actualy, I'm using Python to develop a software to make some analysis (image analysis applied to chemistry). Here in ----, the college course of chemistry don't have disciplines of informatics related.

Because of this, I got some questions, if you can answer to me, I'll be very grateful:

Have you done chemistry college or some informatics college related?
If you have done the chemistry college, how you started to work with computation applied to chemistry?
Here, in ----, actualy I think that the cheminformatics is not very known, even in the scientific field. What about in other countrys? The most of people that are working with cheminformatics have done chemistry colleges or some computation college related?


I answered as follows:
My own background is a degree in Chemistry, followed by a PhD in Inorganic Computational Chemistry (DFT calculations). In the field most people have chemistry degrees, although there are also a few computer scientists. The types of problems the two work on are often different; the computer scientists may be more interested in developing methods, while the chemists may be more interested in applying and interpreting the results. I think that most chemists would not do any informatics or programming during their degree - they would just teach themselves at the start of their PhD - it sounds like you have already done this.

When I was 12 or 13, I started programming in BASIC on my home computer and got involved in programming competition for high school students. I didn't have a computer while in university, but during my PhD I started programming again, this time in Python. More recently, I've learnt C++ by working on Open Babel.

If you want to gain expertise in the field, I would very much encourage you to get involved in an open source cheminformatics project. You will learn a lot about programming, organising large projects, testing, how to work with other people, and so on. If you're interested in image analysis you could look at OSRA, etc. You may also want to subscribe to the blueobelisk mailing list or ask a question at blueobelisk.shapado.com.

Cheminformatics is not a very well known field - I didn't know what it was until I started doing it, even though I had done computational chemistry during my PhD. The main countries associated with cheminformatics are the UK, US and Germany, it seems to me; these are the countries where a lot of the pharmaceutical companies do drug design. But you can do cheminformatics anywhere - you just need a computer.


What advice would you give? I'm especially keen to hear from cheminformaticians from South America. (I'll point the student to this blog post)

Image credit: Duncan Hull

4 comments:

Rajarshi said...

While programming is a core cheminformatics skill, I'd also suggest that it's useful to get familiar with chemical applications - if possible browse JCIM, JMGM, JCAMD. And I definitely second getting involved in OSS cheminformatics projects.

baoilleach said...

See also comments on Friendfeed.

Anonymous said...

Hi,
I am currently doing a degree in Computer Science and Engineering and I do not have a degree in Chemistry. But I am interested in Cheminformatics and want to get into this field. Do you think that I would be able to do it with just my Computer Science background or will I need to follow another degree in Chemistry?
Thanks in advance!

baoilleach said...

@Anonymous: There are many computer scientists in the field particularly in the area of methods development or scientific software development. Of course, the more chemistry you know the better; even a familiarity with interpreting 2D chemical diagrams, and common functional groups in organic chemistry, will help a lot.