[Tutor] Re: Biology and introductory programming?

[Leighton Pritchard]

At 20:59 26/11/01, you wrote:
[Danny]
>Just out of curiosity, how many of us here have an interest in
>"bioinformatics"?

It's been my day-job for the last six years <grin>. As a word, it doesn't 
half cover a lot of ground, from designing algorithms, to performing 
web-based searches.

>Using molecular biology as a motivater for
>learning a programming language looks really exciting!

You'd be surprised how many molecular biologists are still put off by it, 
or the thought of anything maths-based :(. At our university we're trying 
to stress to the undergrads the mathematical aspects as much as possible in 
the courses, and the better students are 'getting it', but many still just 
moan.

On the other hand, the only reason I started to program was because no-one 
else had written the software I wanted. Bioinformatics was the only 
motivator for programming that I had :)

For motivated students, though, I think it's a very good idea. In order to 
represent the concepts of mutation or whatever in a program, they have to 
understand it enough to represent it in an abstract manner. If the language 
itself doesn't get in the way of this understanding, I can see it being 
very helpful.

Finding the staff to teach it might be difficult, mind...

>For example, we can start talking about a DNA fragment:
>[snip] and show how we can "mutate" such an example by zapping it:

As it happens, my current work involves simulating error-prone PCR, which 
does pretty much that - only in a slightly more complicated way :). There's 
a fair amount of (not great) code, so I'll not post it here. My boss might 
not be happy if I did that, either...

>Molecular biology is very much about structure and sequences, so this sort
>of stuff seems easy to approach from a programming standpoint.

Have you seen BioPython? http://biopython.org/ They've covered most of the 
routine ground, especially concerning BLAST searches and the like.

[Kirby]
>PMV is the program I was thinking of.  Anyone on here
>played with it?  Not me (yet), to the best of my
>recollection.

I've not played with it yet, but I'm off to the Scripps website to see what 
it's like...


-- 
Dr Leighton Pritchard AMRSC
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Institute of Biological Sciences
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