[GSoC] Possible project

[Rob Lanfear]

That's a great idea.

Is it possible to include functions from BioPython directly into the
program?

I would love to use the SeqIO modules and a few other things, but I haven't
done so to date because I need the program to be batteries included. I
would lose almost all of my users if I started asking them to install
Python dependencies.

Cheers,

Rob


On 27 February 2014 08:11, Hilmar Lapp <hlapp at drycafe.net> wrote:

> Perhaps such integration could even be the GSoC project idea.
>
>    -hilmar
>
>
> On Wed, Feb 26, 2014 at 1:33 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
>>
>> Peter and all;
>> Seconding Pjotr's comments, I think it would be a good challenge to try
>> and be more inclusive in projects we can work with. This is a good
>> chance to have OpenBio get more mentors and contributors. Conversely, this
>> is an opportunity for projects like Rob's to try and integrate better
>> with the OpenBio community and code. As a practical example, from quickly
>> scanning the source it looks like PartitionFinder has PhyML and RaXML
>> integration code that could benefit from using Biopython's support for
>> these tools, contributing back things that Biopython is missing.
>>
>> Peter, would adding contributions and Biopython integration along these
>> lines satisfy your concerns? Rob, would Biopython integration be
>> something you have interest in tackling along with your other goals for
>> the summer?
>>
>> Brad
>>
>>
>> > On Wed, Feb 26, 2014 at 7:29 AM, Rob Lanfear <rob.lanfear at gmail.com>
>> wrote:
>> >> Hi All,
>> >>
>> >> To clarify, I'm not a NESCent organiser, just a mentor who was hoping
>> to
>> >> put a specific project through NESCent. The link is for the project,
>> whose
>> >> title is "Automated partitioning for morphological phylogenetics":
>> >>
>> >>
>> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2014#Automated_partitioning_for_morphological_phylogenetics
>> >>
>> >> It's a Python (and some external C programs) project, which does not
>> use
>> >> any of the Bio* projects. So the questions are really specific to that
>> one
>> >> project - I'm interested to know if this is the kind of thing that OBF
>> >> might consider as a project.
>> >>
>> >> Cheers,
>> >>
>> >> Rob
>> >
>> > Given it doesn't use or extend any of the OBF's Bio* projects,
>> > as it stands, I don't see this as a obviously a good fit :(
>> >
>> > Perhaps there's a possible slant on this I've overlooked?
>> >
>> > Regards,
>> >
>> > Peter
>> > (OBF secretary, Biopython developer, etc)
>> > _______________________________________________
>> > GSoC mailing list
>> > GSoC at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/gsoc
>> _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>
>
>
>
> --
> Hilmar Lapp -:- lappland.io
>
>


-- 
Rob Lanfear
Research Fellow,
Ecology, Evolution, and Genetics,
Research School of Biology,
Australian National University

phone: +61 (0)2 6125 3611

www.robertlanfear.com