[GSoC] GSOC OBF & GMOD

[Robin Haw]

I don¡¯t think we have to have a perfect overlap but at least we should be comfortable with the projects that we propose. It¡¯s sematics. We use BioPerl in Reactome source code but for most of the time we call it Perl!

Robin

From: Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>
Date: Thursday, February 27, 2014 at 11:07 AM
To: Raoul Jean Pierre Bonnal <bonnal at ingm.org<mailto:bonnal at ingm.org>>
Cc: Robin Haw <robin.haw at oicr.on.ca<mailto:robin.haw at oicr.on.ca>>, Eric Talevich <eric.talevich at gmail.com<mailto:eric.talevich at gmail.com>>, "gsoc at lists.open-bio.org<mailto:gsoc at lists.open-bio.org>" <gsoc at lists.open-bio.org<mailto:gsoc at lists.open-bio.org>>
Subject: Re: GSOC OBF & GMOD

Hello all,

It might be better if Robin and I looked at the existing project list and tried to pick projects that would be more compatible with existing Bio* libraries. How tightly tied would you want them to be to existing Bio* libraries? For example, there's one project proposal that would involve writing server-side software to interact with a database to serve data to a genome browser (http://gmod.org/wiki/GSoC#JBrowse:_REST_daemon_for_Chado). The language used is currently up to the student, but we could specify that BioPerl (or BioJava?) is used for it.

There are also a few projects that require JavaScript, with the possibility of creating reusable libraries; presumably these would be more in the purview of the BioJavaScript group than the OBF?

Thanks,
Amelia.



On Thu, Feb 27, 2014 at 1:40 AM, Raoul Jean Pierre Bonnal <bonnal at ingm.org<mailto:bonnal at ingm.org>> wrote:
Dear All,
these are the projects selected by GMOD.
Next step is to "slightly" adapt then into obf and I am sure that we can fit them.

About firsr prj is it possible to have svg and make if something like D3 ? just a curuosity.

About the second projcet why just only drupal, would be possible to make it more genric?

Galaxy what about extract charts from galaxy and have a biopython module ?

ps : I am sorry because todat I am off  and I am using my mobile, internet is limited and i had no time dig into all the details but lets figure out.

Btw for this and other projects I would collect them in the cross project page by Friday so students have all the week end and we can advertise the initiative.

>From Robin (GMOD)
We have three projects that would like to propose as the ¡°Best of GMOD"

Reactome Pathway Comparison Widget: http://gmod.org/wiki/GSoC#Pathway_Comparison_Widget

Tripal pedigree viewer: http://gmod.org/wiki/GSoC#Tripal_Pedigree_Viewer

Galaxy Charts: http://gmod.org/wiki/GSoC#Galaxy_Charts_and_Open_Requests

What would be the next steps.
Thanks again for the offer of help.
Robin

From: Robin Haw <robin.haw at oicr.on.ca<mailto:robin.haw at oicr.on.ca>>
Date: Wednesday, February 26, 2014 at 11:49 AM
To: "ilpuccio.febo at gmail.com<mailto:ilpuccio.febo at gmail.com>" <ilpuccio.febo at gmail.com<mailto:ilpuccio.febo at gmail.com>>
Cc: Eric Talevich <eric.talevich at gmail.com<mailto:eric.talevich at gmail.com>>, Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>
Subject: Re: Adopting a project
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--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject