[bip] Blog post on bioinformatics and Python

[Bruce Southey]

C. Titus Brown wrote:
> -> Exaggerating for emphasis - If you are developing a reusable library,  
> -> and don't yourself reuse components, then you will have problems  
> -> understanding the needs of your user base.  You are someone who wants  
> -> to write new code while your users are people who want to use  
> -> existing tools.
> -> 
> -> (Am I roiling the pot enough?)
>
> Andrew, you're missing the part where we're smarter than you.  That's
> why we'll do a better job of solving the problems!
>
> And I think the correct saying is 'tweaking the proboscis'.
>
> --t
>   
Also missing is the community because I tend to concur with Andrew, 
communications must to go both ways. Part of any project is foster a 
community as it changes and for the community to foster back.  The 
latter is hard in multiple ways especially the requirement to understand 
a person's coding style that is not your own. But I definitely agree 
that starting a new project or forking one (what happened to that other 
one) should be an option of last resort.

As previously been suggested on this list, what are the problems with 
BioPython and can these be fixed?

Also keep in mind that Python 3K is very near that will require 
extensive changes to any code base. So it is probably a good time to 
start addressing any issues as the developers are likely to be amenable 
to changes as the code has to change. Obviously there are dependencies 
on third-party modules that also have to change or these dependencies 
(e.g., Numeric) have to be removed in some way.

To start this, one issue for me is the use of the unmaintained Numeric 
but numarray (a fork of Numeric) was being maintained. Consequently, 
BioPython did not fit into my code. NumPy (yes, another fork of Numeric 
with some of the pieces of numarray) superseded both Numeric and 
numarray and version 1.2 is due very, very soon (that includes some of 
Andrew's fixes). Finally it would appear that BioPython will move to 
numpy although there is an mingw windows-64 bug affects the compilation 
on that platform that may delay things.

Just a few worthless cents (bailouts are welcome),
Bruce