Bioinformatics training through metagenomic sequence annotation

Registered 2008-07-07 by hingamp

The Annotathon is an Internet teaching environment for university students following a basic bioinformatics course. An online server implementing the Annotathon is available at: http://annotathon.univ-mrs.fr/

We have taken advantage of the increasing amount of metagenomic data
publicly available to develop a teaching environment in which undergraduate
students are given the opportunity to “turn data into knowledge”. Called
Annotathon, this internet teaching platform fosters team work and guides
apprentice annotators through each step of in silico analyses, from ORF
identification to functional and phylogenetic classification. Generating raw
results is an integral part of the exercise, but heavy emphasis is put on
their interpretation and critical assessment. The online format is ideally
suited for student involvement outside class, whilst allowing instructors to
provide annotators with continuous feedback. An iterative evaluation cycle
allows students to respond to constructive criticism and produce enhanced
versions of their annotations. A student exit survey shows that, although
challenging, the study of as yet non-annotated sequences is a major incentive
for 75% of participants. The success of this approach relies on the following:
i) Learning by doing: bioinformatics is best introduced by first hand
experience; theoretical considerations are easier to grasp once truly familiar
with the tools. ii) Learning by repetition: successively analysing several
sequences gives the students the opportunity to experience a wide range of
situations, e.g. “twilight zone” similarities, or “garbage in, garbage
out” phylogenetic tree reconstructions.
iii) Learning from constructive criticism: giving students the opportunity to
correct themselves results in noticeable progression over time. 502 students
have taken part in the Annotathon over the past three years, analysing a total
2.3 Mb of ocean microbial DNA, representing 9500 hours of cumulative
annotation. Interestingly, student hand crafted annotations are in very close
agreement with those obtained by automatic annotation pipelines.
Based on these observations, we call on our colleagues to consider joining an
initiative to create a worldwide “grid of undergraduate annotators”.
Tentatively, as more teams join in, this could lead to an educative annotation
community with room for scientific contribution. The open source online
Annotathon environment (http://annotathon.univ-mrs.fr) is offered as a basis
for this collaborative initiative.

Project information

Maintainer:
hingamp
Driver:
hingamp
Development focus:

trunk series 

lp:annotathon 
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Programming Languages:
PHP MySQL
Licences:
GNU GPL v3
(Dependancies: PHP Mail/mime, Net/GeoIP, Math/Stats PEAR libraries: BSD Style, LGPL 2.1 & PHP licences http://pear.php.net/ MySQL GPL License http://www.mysql.com/about/legal/licensing/ JpGraph: released under a dual license. QPL 1.0 (Qt Free Licensee) For non-commercial, open-source or educational use http://www.aditus.nu/jpgraph/jpdownload.php )

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