[bip] Blog post on bioinformatics and Python

[Andrew Dalke]

On Sep 17, 2008, at 5:57 PM, Ryan Raaum wrote:
> 1. It is monolithic. It is like one of those honking huge Swiss Army
> knives. It has a big knife, a small knife, a saw, a scissor, a fork, a
> spoon, a magnifying glass, a toothpick, a small shovel, a beach
> umbrella, and more!

How come with Python "batteries included" is a good thing,
but with Biopython it's not?

Is the solution like what Zope's been doing - split itself
into many smaller packages, and distribute them as eggs?

(Ahh, you answered elsewhere that this is a deployment matter,
which is not something I've had to worry much about.)

> 2. It is not pure python. I recognize the need for Numeric and C for
> speed in many circumstances, but having those in the core framework
> limits where and how it can be used.

Just a history note here.  My memory is hazy, but Jeff Change
wrote some code which use a C extension if it was available
or in pure Python if it wasn't.  Some people complained about
how slow it was, and it turns out it was a misconfiguration
that caused only the Python code to be installed.

We decided it was better to get complaints about "it doesn't
work" than deal with unvoiced "Python is so slow" complaints.

>  because I could not get a functional mxTextTools installation

That's my fault.  An exciting idea that didn't pan out, and
with consequences that lasted for years.  :(

> And, to add some kudos, I think the BioPython people have made some
> very good choices in the past few years.
>
> 1. Changing from GPL to the BioPython license significantly expanded
> the number of people who could contribute and use the project
> (especially among those in industry).

Since I was the one that wrote the Biopython license I
can say for certain it was never GPL.  I have a strong
preference for BSD-like licenses over GPL, precisely so
that people can grab parts of the code and not worry
about license effects.

				Andrew
				dalke at dalkescientific.com