[Bioperl-l] question about the nature of bioperl

[Brian Osborne]

Nathaniel,

>>but in browsing the hierarchy diagrams and reading the
>>emails, it sounds like a big confused mess that several(?) people are
trying
>>so hard to keep in order but the task is too big.

Hmm. I've been an "observer", and not an architect, in Bioperl for a number
of years and I think your first impression is partially mistaken. You're
correct in thinking that a number of key individuals make design decisions
and have implicitly and explicitly designed Bioperl. Anotherwords, when a
new proposal in comes the feedback comes back on how to integrate the new
code into the framework. And I've been continually impressed with how well
this "collective mind" works, given that Bioperl is a "side project" for
just about everyone who participates.

But "big confused mess" is an unfortunate choice of words. That it works is
sufficient counter-argument. Bugs? Of course! It's a body of work that's in
continual flux, sometimes great flux, as in the Blast parser -> Blast parser
case, sometimes minor. The best way to assess the state of the thing, messy
or not, is to use it, see if it works and if it's flexible and easy to use.
For someone with your technical background I maintain the answers will be
"yes", "yes", and "yes".

Your first question is a good one (by that I mean I asked it myself a while
ago ;-) What is this for and who is this for? It's to get work done, for
people doing real, heavy-duty bioinformatics, but in such a way that the
code fits with existing code and is extensible. This is where the
"collective mind" works, to make sure things fit. Unfortunately the intent
has veered a bit from the inception, when Bioperl was truly simple, but this
was inevitable, the simplicity simply couldn't keep up with the demands of
the work itself.

Brian O.


-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of nkuipers
Sent: Tuesday, August 20, 2002 3:38 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] question about the nature of bioperl

I mean no offense to anyone, especially being new to this mailing list, but
I
am starting to wonder just what people expect from this project.  Is this
supposed to be a do-it-all bioinformatics kit or a set of basic tools that
people are free to use, fleshing it out with their own code as per their
specific application?  It just seems to me that, if not already, the project
is on its way to being what is referred to as a "bloated monster" in
computer
science classes.  Everyone has their "bug" catches, specific formats, and
there are multiple versions flying around with varying degrees of
documentation and testedness.  Whoa horse.  Stop.  Trying to account for
every
single format or user-defined case is in my opinion folly and impossible,
especially given the nature of bioinformatics.  Define a broad but simple
suite that is flexible to specifics and leave the rest to the users.  That's
what Perl was made for by definition: TIMTOWTDI.  This was (is?) probably
the
idea with bioperl also, but in browsing the hierarchy diagrams and reading
the
emails, it sounds like a big confused mess that several(?) people are trying
so hard to keep in order but the task is too big.  Simplify simplify.  I
think
there comes a point where too many "bugs" (real or not) means more than
debugging.  Easier said than done I know.  Heh.  Pay me no mind.

Best regards,

Nathanael Kuipers

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