Re: [apollo-dev] Collaborative avian annotation project

[Ed Lee]

Hi Rob,

GMOD in the Cloud will remove a lot of the sys-admin required, since all applications supported will already be installed, along with any pre-requirements.  That being said, you'll still need to know a bit of Linux sys-admin and getting around the shell (Bash by default).

Speaking from the engineering side, since most of the sys-admin stuff is already taken care of, I believe one of the bigger challenges will be configuring all the tools to work the way you want (how things are displayed, what's displayed, etc).  This requires some effort to familiarize yourself with the different tools and what configuration options they each have.  Luckily getting the different tools to share data isn't too difficult since they support shared formats (Chado, GFF3).

I'm sure others can give some feedback on challenges with getting a community up and running and working harmoniously together.

Cheers,

Ed

On Fri, Apr 11, 2014 at 4:30 AM, Robert Lachlan <[hidden email]> wrote:

Hello,

We are in the early stages of developing a collaborative site for the annotation of songbird genomes. Our plan is to focus on one model species, the zebra finch, on which the vast majority of genomic and neurogenomic work has been carried out, and integrate it with comparative data from other oscine passerine species which tend to be studied from an ecological and evolutionary perspective. At present, there appears to be no resources to combine transcriptomic and manual annotation work with the assembled genome data.

To accomplish this, we are thinking of combining a Tripal/Chado/JBrowse site to serve curated data, with a WebApollo system to allow a moderate-sized (<50 research groups), worldwide community of researchers to collaboratively annotate zebra finch genomes. ‘GMOD in the cloud’ seems like a straightforward way to proceed. “We” - at the moment - consists of three researchers with a combination of expertise in computational and zebra finch genome biology. We are currently running WebApollo within the lab for our own annotation efforts.

We are looking for advice from anyone who has organised such a project. Especially:  how much time investment, and sys-admin expertise is required to design, set-up, curate and maintain such a project? We know this is an annoyingly open-ended question, but we would really like to hear of others’ experiences so that we can gauge the requirements of our own project.

Regards,

Rob Lachlan

[girlwithglasses]

Hello Rob,

You could get in touch with the Banana Genome Hub team -- they have created a fantastic resource using GMOD tools with Tripal as the backbone that holds everything together. I believe they are also in the process of creating a similar resource for coffea.

Website: http://banana-genome.cirad.fr/

The contact details are at the bottom of the front page.

You may also be interested in attending the GMOD Online Training, which covers the tools that you're interested plus others that you might want to include. There's more information at http://gmod.org/wiki/GMOD_Online_Training_2014

Thanks,

Amelia.

GMOD Community Support

On Mon, Apr 14, 2014 at 2:48 PM, Ed Lee <[hidden email]> wrote:

Hi Rob,

GMOD in the Cloud will remove a lot of the sys-admin required, since all applications supported will already be installed, along with any pre-requirements.  That being said, you'll still need to know a bit of Linux sys-admin and getting around the shell (Bash by default).

Speaking from the engineering side, since most of the sys-admin stuff is already taken care of, I believe one of the bigger challenges will be configuring all the tools to work the way you want (how things are displayed, what's displayed, etc).  This requires some effort to familiarize yourself with the different tools and what configuration options they each have.  Luckily getting the different tools to share data isn't too difficult since they support shared formats (Chado, GFF3).

I'm sure others can give some feedback on challenges with getting a community up and running and working harmoniously together.

Cheers,

Ed

On Fri, Apr 11, 2014 at 4:30 AM, Robert Lachlan <[hidden email]> wrote:

Hello,

We are in the early stages of developing a collaborative site for the annotation of songbird genomes. Our plan is to focus on one model species, the zebra finch, on which the vast majority of genomic and neurogenomic work has been carried out, and integrate it with comparative data from other oscine passerine species which tend to be studied from an ecological and evolutionary perspective. At present, there appears to be no resources to combine transcriptomic and manual annotation work with the assembled genome data.

To accomplish this, we are thinking of combining a Tripal/Chado/JBrowse site to serve curated data, with a WebApollo system to allow a moderate-sized (<50 research groups), worldwide community of researchers to collaboratively annotate zebra finch genomes. ‘GMOD in the cloud’ seems like a straightforward way to proceed. “We” - at the moment - consists of three researchers with a combination of expertise in computational and zebra finch genome biology. We are currently running WebApollo within the lab for our own annotation efforts.

We are looking for advice from anyone who has organised such a project. Especially:  how much time investment, and sys-admin expertise is required to design, set-up, curate and maintain such a project? We know this is an annoyingly open-ended question, but we would really like to hear of others’ experiences so that we can gauge the requirements of our own project.

Regards,

Rob Lachlan

--

Amelia Ireland
GMOD Community Support

Generic Model Organism Database project

http://gmod.org || @gmodproject