[bip] Future of bioinformatics in python..?

[Andrew Dalke]

On Aug 2, 2007, at 12:24 PM, Peter Clarke wrote:
> I think that the python bioinformatics community needs to come
> together to form a project that can deliver something directly to the
> end users (that caters for everyone from computationally naive
> biologists to experienced programmers).

That's what Biopython was supposed to do.  Well, it depends
on what you call "everyone."

> I think this would only really work (and could work really well) if we
> could make it a completely collaborative effort with everyone involved
> in Python bioinformatics.

Why didn't Biopython become that project?

Doing what you outline is very hard.  Designing reusable systems
is (roughly) three times harder than designing single use systems.
Who has the resources to devote to that?

Developing for a diverse set of skills is also hard.  One technique
in HCI is persona development, and in business there's the related
idea of market segmentation.  Different people have different needs,
and it's very hard to be everything to everyone.  (Neat example
of that in the video of Malcolm Gladwell at
   http://www.ted.com/index.php/talks/view/id/20 )

One limitation in Biopython is that no one really has the
ability to say "please change your code to make it fit in
better with the rest of Biopython."  Partially because no one
wants that job enough, and partially because there's no existing
sense of unity, and partially because it would/may/might reduce
yet further the number of people willing to contribute code.

Another is that there weren't enough people involved in Biopython,
and I don't think any were working on the same research project.
I previously on this list compared Biopython to Bioperl, which
I think became much better because of the EBI/Sanger efforts
in the 1990s using bioperl.  There were many people, in the
same spot, using bioperl for different but related work.

I think that needs to happen for this sort of infrastructure
Python project.  Or at least a large number of sprints where
everyone got together at the same physical location.


On the plus side, this field is small enough that if there
were a dozen or so good programmers who worked together on
a project then it could do amazing things.

I just don't know what that project is.  Of the ones I
thought up, I couldn't get sales numbers to work out right.
And I'm biased enough that I want my end-users to be the
ones paying me directly, and not indirectly through grants.



				Andrew
				dalke at dalkescientific.com