[Biopython-dev] Interested in a Phenotype Microarray parser?

[Marco Galardini]

Hi Peter,

yes, some feedback may be useful to point out any bug or (even better)  
some other addition. One way to asses the correctness of the module  
would be a comparison with the opm R package, which also reads/writes  
PM files and fits sigmoid curves (there's also ductape, but it's made  
by me). Maybe I can setup a small benchmark to show that the data is  
correctly handled.

I also have an uncommitted addition to plot the PM curves and their  
fit, using matplotlib, in a similar way as the Bio.Phylo module.  
Should it be added too?

Marco

----- Messaggio da p.j.a.cock at googlemail.com ---------
     Data: Tue, 3 Jun 2014 11:02:26 +0100
       Da: Peter Cock <p.j.a.cock at googlemail.com>
Rispondi-A:Peter Cock <p.j.a.cock at googlemail.com>
  Oggetto: Re: [Biopython-dev] Interested in a Phenotype Microarray parser?
        A: Marco Galardini <marco.galardini at unifi.it>
       Cc: Biopython-Dev Mailing List <biopython-dev at lists.open-bio.org>


> Hi Marco,
>
> This is definitely interesting - but as I don't do much with this area, I
> am really hoping one of the other Biopython developers (or active
> users) can give some feedback/comments.
>
> Peter
>
> On Tue, May 20, 2014 at 10:26 PM, Marco Galardini
> <marco.galardini at unifi.it> wrote:
>> Hi all,
>>
>> maybe not the best moment, as you are busy releasing the new version: just
>> wanted to inform you that the Bio.Phenotype module now supports sigmoid
>> curve fitting and parameters extraction, only if scipy is installed.
>>
>> The latest commits are here:
>> https://github.com/mgalardini/biopython/tree/phenomics
>>
>> The tests are working for either python2 and python3.
>>
>> Hope this is of interesting,
>>
>> Marco
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----- Fine del messaggio da p.j.a.cock at googlemail.com -----



Marco Galardini
Postdoctoral Fellow
EMBL-EBI - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Phone: +44 (0)1223 49 2547