[BioPython] Questions & suggestions

[Michiel Jan Laurens de Hoon]

Thomas Hamelryck wrote:
> We could make a list of modules that will be potentially removed, post it to 
> the biopython list, and then actually remove them when no-one objects. Is 
> anybody using the two HMMs (HMM and MarkovModel) for instance? Or the 
> support vector machine (SVM) and NeuralNetwork modules? The xKMeans, 
> KNN and KMeans clustering modules also seem to be obsolete in view of Michiel 
> de Hoons clustering module. 

The xKMeans and KMeans can be considered obsolete, as they are included in 
Bio.Cluster. The KNN and other modules under Bio/Tools/Classification are 
currently not obsolete, as they contain supervised learning methods, which are 
not included in Bio.Cluster.

I am not sure what the purpose is of the GA (Genetic Algorithm Neural Network) 
module and the NeuralNetwork module. Are they the same? Is their usage described 
somewhere?

After cleaning up the modules, it may be a good idea to set up some kind of 
unified way to deal with gene expression data in Biopython.

--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