Volume 14 Nr. 3
EMBnet
35
Abstract 10 - METAGENOME ANNOTATION: AN OPPORTUNITY FOR UNDERGRADUATE BIOINFORMATICS TEACHING Hingamp Pascal*[1], Brochier Céline[2], Talla Emmanuel[1], Gautheret Daniel[3], Thieffry Denis[1], Herrmann Carl[1] - [1]Biology Department, Mediterranean University ~ Marseille ~ France - [2]Biology Department, Provence University ~ Marseille ~ France - [3]Université Paris Sud ~ Paris ~ France # 2B) Education and Training: Instruments, cooperation and collaboration
Motivation: The bottleneck in genomics is shifting from sequencing to annotating, increasing the demand for expert annotators. It is in the interest of research and future job seekers that graduate training anticipates this trend by introducing students to the art of raw sequence annotation. Methods: 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”. This internet teaching platform, called “Annotathon”, 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 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. Communication relies on classical internal forums and chats, but more importantly on an iterative evaluation cycle which allows students to respond to constructive criticism and produce enhanced versions of their annotations. Results: The 720 students that have taken part in the Annotathon over the past three years have analyzed a total of 23 Mb of ocean microbial DNA, representing 9500 hours of cumulative annotation. The following aspects of the approach appear to significantly contribute to its success: a) learning by doing: bioinformatics is best introduced by first hand experience; theoretical considerations are easier to grasp once truly familiar with the tools. b) learning by repetition: repeating the analyses on several sequences gives the students the opportunity to experience a wide range of situations, e.g. BLAST report for widespread proteins versus ORFans etc. c) learning by excitement: according to students, exploring yet unannotated sequences is a major incentive. d) learning from constructive criticism: giving students the opportunity to correct themselves results in noticeable progression over time. The Annotathon environment is available as an open source software, but teams are also welcome to join us on our public server http://biologie.univ-mrs.fr/annotathon/. Ideally as more teams join in, this could lead to an educative distributed annotation jamboree with room for modest scientific contribution.