[BioPython] Lisp in bioinformatics(!)

[Johann Visagie]

Ewan Birney on 2000-08-22 (Tue) at 03:58:28 +0100:
> 
> On Tue, 22 Aug 2000, Antoine van Gelder wrote:
> 
> > Was there, great sandwiches.

Ditto.  :-)

> > Overwhelming impression was that the lisp community feels a bit out in the
> > cold and disconnected.

... and nothing they said served to dispell the ivory tower mystique of Lisp.
Certainly, the speakers were all very experienced and accomplished software
engineers and bioinformaticians, but holding a Lisp BoF in a back room at
ISMB was _not_ the way to go!  It was merely preaching to the converted -
some old grey-haired fogies talking to their peers.  So to speak.  :-)

> > They should have been at BOSC, Lisp is a superb choice for some of the
> > problems.

Exactly!  After the two days of BOSC, the Lisp meeting was the first time in
days that I felt like one of the younger people present.  :-P

And what they said would've made so much sense to the people attending BOSC.
Peter Karp's presentation on his BioDB-Loader tookit clearly showed an
excellent application of Lisp in the field - had it been delivered at BOSC,
I'm sure many of the attendees would've felt motivated to go and learn more
about Lisp.  I did, and still do.

> Do they want to register biolisp and become one of hte bio* projects

Their reception to this idea was lukewarm (at best) when it was brought up.
Silly!  Seems that very smart people have a tendency to focus too closely on
the one field they know...  Many good programming languages have fallen into
disuse, and Lisp is heading the same way unless they can turn on a new
generation to its advantages.

</rant>

But as Antoine said to me afterwards, one of the reasons for using Python
would be to have access to some of the power of functional programming.

> (seriously - we would be open for this). Who s the main guys behind it.
> Tell them to get in touch with me ---

Larry Hunter, Peter Karp, Rich Latrhop.  Bigwigs all.

> I think lisp/prolog actually have alot to offer bioinformatics. Though I
> **detest** the ((())) thang in lisp. 

:-)  Some use parentheses, some use braces, some use whitespace.  I don't
think any method is inherently superior or inferior, as long as it works!
(OK, OK, I don't like "begin ... end".)

-- Johann