Tuesday, November 25, 2008

Open Metagenomics Highlight - Metagenome Annotation using massively parallel undergrads.

Another fun metagenomics related paper in PLoS Biology. In it Pascal Hingamp et al discuss an Open Source, Open Science system for metagenome annotation (see PLoS Biology - Metagenome Annotation Using a Distributed Grid of Undergraduate Students).

They do this as part of a course on metagenome annotation. And the software for running this is all Open Source and available. They say
"Teachers wishing to use the Annotathon for their courses are invited to create new teams on the public server at http://annotathon.univ-mrs.fr/ (course logistics and team management are detailed in the instructor manual:http://annotathon.univ-mrs.fr/Metagenes/index.php/Instructor_Manual). The underlying open-source software (PHP and MySQL scripts, under a General Public License) is also available for local installation (https://launchpad.net/annotathon/). In addition, a special “Open Access” team is available for freelance students (volunteer instructors are most welcome to help oversee the Open Access team)."
IN a way this is a metagenomics version of the Undergraduate Genomics Research Initiative (UGRI) which was described in a PLoS Biology paper previously.

Well, this is really the end all be all for me combining so many things I like - genomics, metagenomics, annotation, OA publishing, open source software, etc. Nice job Pascal et al ...

1 comment:

  1. Inspired by Sandra Porter i skimmed through the paper, very impressive. Amazing work Pascal et al ...

    Talking about annotation Here is a web 2.0 based free service helps discovering newer scientific relations across abstracts. it provides manually curated and annotated sentences for the keywords of your choice. Its free, check it out http://www.xtractor.in


Storify of Day 1 of "An open digital global south meeting" at #UCDavis

I made a Storify of Tweets and some pictures from the "An open digital Global South" meeting that I am a co-organizer of. This was...