Biology and introductory programming?
Author Message
Biology and introductory programming?

Quote:
> > Danny,

> > Could I post this message to another programming language email list,
> > as an example of the kind of synergy I would like that language to
> > have? The programming languajes is Logo.

> Sure, no problem!
> Date: Mon, 26 Nov 2001 17:02:22 -0800 (PST)

> Subject: [Tutor] Biology and introductory programming?

> Hi everyone,

> Just out of curiosity, how many of us here have an interest in
> "bioinformatics"?  I've just bought the book "Beginning Perl for
> Bioinformatics", and it appears to be an introductory test for biologists
> who are trying to smash their brains against Perl.  *grin*

> In all seriousness though, it looks like a great book for people who
> haven't programmed before.  Kirby has mentioned using python to play
> around with mathematical ideas; the same synergy would probably work with
> molecular biology too.  Using molecular biology as a motivater for
> learning a programming language looks really exciting!

> For example, we can start talking about a DNA fragment:

> ###
> dna = "ATTAAGCATTAAA"
> ###

> and show how we can "mutate" such an example by zapping it:

> ###
> def mutate(dna):
>     """Introduce a single point mutation into a sequence of dna."""
>     bases = ['A', 'T', 'G', 'C']
>     position_of_mutation = random.randrange(len(dna))
>     original_nucleotide = dna[position_of_mutation]
>     bases.remove(original_nucleotide)
>     return (dna[:position_of_mutation]
>             + random.choice(bases)
>             + dna[position_of_mutation + 1:])
> ###

> Here's an test of the DNA mutation:

> ###
> >>> mutate('AAAAA')                             ## Zap!
> 'AAACA'
> >>> mutate(mutate('AAAAA'))
> 'AATCA'
> >>> mutate(mutate(mutate('AAAAA')))
> 'ATAGG'
> ###

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

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Sun, 16 May 2004 22:07:57 GMT

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