[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
▶ Mostra testo citato



--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject