[Biopython-dev] Network analysis tool: PyPanda

D.G.P.van_Ijzendoorn at lumc.nl D.G.P.van_Ijzendoorn at lumc.nl
Mon Apr 25 16:45:27 UTC 2016

Hi Michael and Peter, 

I think the issues regarding licensing and python versions can be fixed quickly. Also concerning the dependencies, the only dependency that is really needed is numpy, the rest can be removed. 

Also our paper is now on arXiv: http://arxiv.org/abs/1604.06783

From: Peter Cock [p.j.a.cock at googlemail.com]
Sent: Friday, April 22, 2016 10:15 AM
To: Ijzendoorn, D.G.P. van (PATH); Michiel de Hoon
Cc: Biopython-Dev Mailing List
Subject: Re: [Biopython-dev] Network analysis tool: PyPanda

Thanks David,

I see you've also filed this on GtiHub as

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.



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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