Hingamp Pascal

Search As part of the pan-oceanic expedition Tara OceansI have worked to make the genomics data produced available to the scientific community. Given the sheer volume of genomic datasets generated by the project (Tara Ocean consists of more than 600 evolutionary terabases), transforming this raw data into knowledge is proving difficult for biologists without know-how and high-performance computing equipment. So, with my colleagues at the Institut Méditerranéen d'Océanologie, we developed the Ocean Gene Atlas (OGA), an online metagenome exploration tool that enables data mining armed with a single web browser. What's more, handling this heterogeneous dataset (which combines biological sequences, abundance estimates from raw reads, and environmental metadata) is also complex for bioinformatics experts, so we have also set up an API for programmed access complete with OGA data and analysis tools. Read more about the data, methods and visualisations in the paper NAR "The Ocean Gene Atlas: exploring the biogeography of plankton genes online"..

The Ocean Gene Atlas is the culmination of a nearly decade-long project that began with a sampling campaign at sea, followed by half a dozen more years of data acquisition (DNA/RNA extraction, sequencing), primary analysis of the raw data (assembly, annotation), and finally integration into usable final products (analyses, publication, datasets, tools). I had the privilege of taking part in all the stages, including two embarkations as a member of the scientific crew (Mediterranean Sea, South Atlantic) in charge of bacterial and viral sampling, and one embarkation as mission leader (Arctic Ocean along the Siberian coast). Just goes to show that being a bioinformatician isn't all about sitting at your computer screen... Teaching With 25 years' hindsight on teaching bioinformatics at university, I've migrated most of my courses to a 'hands-on' format, centred on the analysis of real data from research. In support of such an approach, which poses challenges in the case of large cohorts of students, I have developed theAnnotathona web-based environment for learning bioinformatics methods for sequence analysis. In this flipped classroom strategy, participants add environmental genomic DNA fragments (for example from different oceans of the Tara Oceans project or sites of the human body of the Human Microbiome Projectand, in 2021, coronavirus genomes) and then annotate them. Analyses include the detection of coding regions, the search for homologous sequences in sequence banks, the identification of conserved protein domains and the construction of phylogenetic trees. Designed to manage large cohorts of participants (known as teams, e.g. classes of students), the investigations are supervised by teachers. Each sequence annotated by each participant is examined, commented on and assessed twice by the teachers, enabling participants to correct themselves and improve the quality of their analyses. At the end of a session, participants can receive a quantitative assessment of all their annotations. More than 200 cohorts of learners have been trained via Annotathon since it was first delivered in 2005, with teams joining us from all continents after Annotathon was described in the November 2008 issue of PLoS Biology".Metagenome Annotation Using a Distributed Grid of Undergraduate Students". . I have also had the pleasure of teaching bioinformatics face-to-face using the Annotathon infrastructure in Brazzaville (Congo in 2009, 2011, 2012, 2013 & 2014), Hanoi (Vietnam in 2015 & 2018) and Kuwait (2009).