[BioPython] Questions & suggestions

[Michiel Jan Laurens de Hoon]

Jeffrey Chang wrote:
> kNN, LogisticRegression, MaxEntropy, and NaiveBayes are still useful, but
> need more documentation.  Also, another idea is that they could be donated to
> the pyml project.  Currently, no code in Biopython depends on them.  However,
> they might be useful for a microarray package, in which case donating them
> would introduce another dependency.

Biopython and pyml are likely to have different goals for these routines. In 
particular a routine as kNN is quite useful for microarray data analysis, and I 
expect that the routine will get updated over time to be better suited for 
biological (microarray or other) data analysis. So I would suggest to keep these 
routines in Biopython and to continue working on them. We can still donate these 
routines to pyml also, but I would expect that e.g. the Biopython-kNN and the 
pyml-kNN will diverge over time to be most suited for each package's requirements.

--Michiel.

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon