CoGe at PAGXXIII

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Published on: January 11, 2015

Happy New Year! We at GARNet enjoyed a long Christmas break and some of us have returned to work via California! Ruth, Jim and I are in San Diego this week for the Plant and Animal Genome Conference (PAG).

PAG is an enormous conference – take a look at the Twitter stream (PAGXXIII) for an idea of how many sessions run at any one time. Yesterday I went to sessions on Ontologies, Brassica and Tritaceae, and I thought I’d quickly update our blog readers about a workshop about the CoGe online tool. I mentioned CoGe in this post about the EPIC conference and it’s also featured in the June 2013 edition of GARNish.

Eric Lyons, one of the creators of CoGe, began the session by explaining that CoGe is a platform for managing, visualising, analysing and comparing genomes. It can deal with unlimited numbers of genomes of unlimited size—though there is a limit for the number of annotations per genome—and while there are tools set up for ease of use, users can perform custom, on-the-fly analysis too.

Throughout the session, Lyons was clear that CoGe is ‘Powered by iPlant.’ It uses iPlant middleware to enable data storage, universal log-in and much more functionality that the user might not be aware of but which makes their experience smooth and relatively stress-free.

Lyons and the other CoGe creators are keen to make sure CoGe is both open and accessible. So there are extensive tutorials, though if you’re like me you may have to dig a few pages deep before you find the detail you need. For example, I clicked through 1, 2, 3 to get to the step-by-step instructions for loading a genome on to CoGe. Documentation provides information on how the tools and platform work for anyone who’s interested; Lyons also encouraged anyone with questions to get in touch with the CoGe team directly.

In the PAG session we went through these tutorials. All the data needed to follow the tutorials are linked to from this guide, so you can do them yourself if you want. We learned how to find a genome of interest through OrganismView; how to compare different genomes via SynMap; and use GEvo to visualise and compare whole genomes. SynMap and GEvo both have very slick zoom and click functions, which let you find regions of interest and click through for more information and detail.

Lyons also took us through loading genomes, annotating them and changing privacy settings. You can keep data private, share it with specific people and assign different privileges to collaborators if you wish, or data can be completely public.

I’ll attending more workshops on online resources today and tomorrow so hopefully I’ll be back with a round-up of useful tips and new tools.



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  1. […] as the default genome browser and hosts datasets including the CoGe epigenomics resource, which I blogged about last […]

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