[Biopython-dev] Network analysis tool: PyPanda

[Peter Cock]

Thanks David,

I see you've also filed this on GtiHub as
https://github.com/biopython/biopython/issues/814

There would be some practical questions for incorporating this into
Biopython (licensing, which versions of Python you support, adding
unit tests), but I think the main question is would this be a good fit?

I think Michael de Hoon would be a good person to comment here
as he's done a lot of related work with the Bio.Cluster module.

Regards,

Peter


On Thu, Apr 21, 2016 at 2:02 PM,  <D.G.P.van_Ijzendoorn at lumc.nl> wrote:
> Hi all,
>
> I work on network reconstruction of gene expression data using the PANDA algorithm (http://dx.doi.org/10.1371/journal.pone.0064832). PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of 'omics data.
>
> PANDA was first released in C++ but now we've created a python implementation of the PANDA algorithm that is both faster than the C++ version (because we now use matrix operations) and has more features.
>
> https://github.com/davidvi/pypanda
>
> We'll be adding a manuscript on pypanda to arxiv any day now.
>
> Would you be interested in adding pypanda to biopython? I would be willing to maintain the code. I'll also file an enhancement bug as stated in your contributing section.
>
> Regards,
> David
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