[BioPython] Some Biopython news, plans, and grants

[Peter Wilkinson]

I certainly would be interested in the documentation project, if you can 
find funding. I do like working on tutorials and documentation 
'solutions'... my own personal war on bad and thin documentation. Please 
add me to a list, and let me know what the time commitments would be.

With regards to numarray, i will be exploring this module for the use in 
microarray analysis as I need some structures (I think) that would be 
useful in  vectorising calculations. I am working on  some code that is 
structured after the RGlist and MAlist objects you find in Bioconductor's 
limma package. I am doing some large scale micrarra analysis (in the 
hundreds of arrays per project), and I find that R is not the tool for 
batch work, but it is a good tool for statistical analysis. Python + rpy or 
RSpython might = batch work. I am still exploring. It might turn out better 
to implement some new normalization algorithms directly in Python or in 
C++. R has memory management problems, and it is built for you to load all 
the data you want to work with at once ... this is limits batch processing.

I am hoping numarray can help.

Peter




At 04:41 PM 8/2/2004, Brad Chapman wrote:
>Hello everyone;
>As some of you may have noticed, I've been relatively absent from
>the Biopython lists over the last couple of months. This was due to
>the unfortunate arrival of dissertation and defense time for me;
>thankfully all of my painful finishing work is, well, finished and I
>am happily in PhD land as of this upcoming Saturday.
>
>What that means is that I'm going to make a concerted effort to go
>through the mailing list and try and sort out problems and bugs that
>have been posted that no one has been able to get to. I'd like this
>to lead up to a semi-soonish release, and then we'll worry about
>what goes from there.
>
>For the upcoming release, I'll stay simple. The main things I'd
>like to do before release are:
>
>-> Cleaning up bugs, problems from the mailing lists. This will take
>a bit; there are a lot of things that need attention.
>
>-> Move from using Numeric (Numpy, Numerical Python) to Numarray
>(http://www.stsci.edu/resources/software_hardware/numarray). Since
>development on this package is now entirely focused on Numarray, I
>think it makes the most sense for us to migrate over.
>
>That's it. Pretty simple. Besides a new release, another idea I'd
>like to toss out there is trying to write a grant for the Python
>Software Foundation to get money to "hire" someone to help with
>Biopython documentation. The PSF is accepting proposals up until
>October 1st:
>
>http://www.python.org/psf/call-2004.html
>
>Jeff pointed this out to me, and I think it is the perfect chance to
>try and find some individuals who might be motivated by supplemental
>financial gain to work on improving Biopython documentation. If
>there is anyone who has any interest in this, let me know, and I can
>start trying to imagine specifics for writing the proposal.
>
>Hope everyone is doing well. Boo dissertations. Yay Biopython.
>
>Brad
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