[Biopython-dev] interaction networks in biopython

[Jason A. Hackney]

Hi All,

I'm also interested in an interaction network class for biopython.  
I'm willing to contribute to the effort with either code review or  
testing.

Cheers,

Jason


Jason A. Hackney

Postdoctoral Fellow
Department of Microbiology and Immunology
Stanford University

e-mail: jhackney at stanford.edu
lab phone: 650-724-3891
mobile: 650-283-6907



On May 16, 2007, at 10:25 AM, Jake Feala wrote:

> Thanks Ed and Yair, I'm really glad there's some interest in this!
> I'll get started on dusting off my code and adding more documentation.
>
> Steve - great suggestion.  I had already seen at NetworkX and was
> already thinking about switching over to this as the back-end graph
> representation.  Are there any issues that I should think about when
> creating these extra dependencies?
>
> Also, what is the next step in this process?  Should we agree on an
> API and class hierarchy before we start dumping code on each other?
> Which aspects can we make compatible with other Biopython objects? (I
> was thinking maybe parsers for the interaction datasets and the SQL
> interface)
>
> -Jake
>
>
> On 5/15/07, Steve Lianoglou <lists.steve at arachnedesign.net> wrote:
>> Hi,
>>
>> On May 15, 2007, at 3:25 PM, Yair Benita wrote:
>>
>>> I would be happy to contribute to this too.
>>> Currently I have a python script that uses HPRD to generate protein
>>> protein
>>> interaction maps. I have deferent filtering methods to display only
>>> classes
>>> of proteins or only links to a specific kegg pathway. It will need
>>> a bit of
>>> work before I can submit this to CVS. As for drawing the map, I am
>>> currently
>>> generating a dot file that can be converted to an image using
>>> GRAPHVIZ. If
>>> anyone wants to suggest anything else, please do.
>>
>> I've been using NetworkX[1] to play w/ networks/graphs interactively.
>> You can display them if you have matplotlib installed, and can save
>> the graphs to dot format as well.
>>
>> -steve
>>
>> [1] NetworkX: https://networkx.lanl.gov/wiki
>>
>>>
>>> Yair
>>>
>>>
>>> on 5/15/07 2:37 PM, Ed Schofield at edschofield at gmail.com wrote:
>>>
>>>> On 5/15/07, Jake Feala <jfeala at gmail.com> wrote:
>>>>> Hello Biopython people -
>>>>>
>>>>> With all the new research in genome-wide cellular interaction
>>>>> networks I was a little surprised not to see much support for  
>>>>> these
>>>>> type of data in Biopython.  I know that Bioperl has a networks
>>>>> package
>>>>> that looks like the kind of thing that I would love to also see in
>>>>> Python for all the obvious reasons.
>>>>>
>>>>> First - has this already been done and I missed it?  All I could
>>>>> find
>>>>> were a few scattered and application-specific scripts across the
>>>>> web,
>>>>> plus the Pathway package in BioPython.
>>>>>
>>>>> If not, then would there be any interest in development along  
>>>>> these
>>>>> lines?  A while back I wrote a few scripts that parse interaction
>>>>> datasets, stick them into a MySQL database, and retrieve the
>>>>> interactions into a Network object that can be used to analyze the
>>>>> graph of nodes and links.  I would be glad to update these to fit
>>>>> into
>>>>> the biopython framework, as it would be useful to my own research.
>>>>>
>>>>> One caveat is that I am an engineering PhD student and my
>>>>> programming
>>>>> skills are mostly self-taught beyond two Java courses, so I might
>>>>> need
>>>>> a little guidance in testing and preparing the code for
>>>>> distribution.
>>>>> I have only ever written code for my own personal research but I
>>>>> think
>>>>> my style is decent and I would love to get better.
>>>>>
>>>>> Any opinion or advice?
>>>>
>>>> This would interest me too; I'd be glad to have such  
>>>> functionality in
>>>> BioPython. I can offer you some guidance on Python, packaging and
>>>> testing, and (if you need it) use of external array packages.
>>>>
>>>> -- Ed
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>>>
>>>
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>>
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