The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community.

International audienceWe report the development of the ReproGenomics Viewer (RGV), a multi-and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org

Colib'read on galaxy : a tools suite dedicated to biological information extraction from raw NGS reads

Background: With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools. Findings: Dedicated to 'whole-genome assembly-free' treatments, the Colib'read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories. Conclusions: With the Colib'read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.Peer reviewe

A Standardized Workflow Based on the STAVIRO Unbaited Underwater Video System for Monitoring Fish and Habitat Essential Biodiversity Variables in Coastal Areas

Essential Biodiversity Variables (EBV) related to benthic habitats and high trophic levels such as fish communities must be measured at fine scale but monitored and assessed at spatial scales that are relevant for policy and management actions. Local scales are important for assessing anthropogenic impacts, and conservation-related and fisheries management actions, while reporting on the conservation status of biodiversity to formulate national and international policies requires much broader scales. Measurements must account for the fact that coastal habitats and fish communities are heterogeneously distributed locally and at larger scales. Assessments based on in situ monitoring generally suffer from poor spatial replication and limited geographical coverage, which is challenging for area-wide assessments. Requirements for appropriate monitoring comprise cost-efficient and standardized observation protocols and data formats, spatially scalable and versatile data workflows, data that comply with the FAIR (Findable, Accessible, Interoperable, and Reusable) principles, while minimizing the environmental impact of measurements. This paper describes a standardized workflow based on remote underwater video that aims to assess fishes (at species and community levels) and habitat-related EBVs in coastal areas. This panoramic unbaited video technique was developed in 2007 to survey both fishes and benthic habitats in a cost-efficient manner, and with minimal effect on biodiversity. It can be deployed in areas where low underwater visibility is not a permanent or major limitation. The technique was consolidated and standardized and has been successfully used in varied settings over the last 12 years. We operationalized the EBV workflow by documenting the field protocol, survey design, image post-processing, EBV production and data curation. Applications of the workflow are illustrated here based on some 4,500 observations (fishes and benthic habitats) in the Pacific, Indian and Atlantic Oceans, and Mediterranean Sea. The STAVIRO’s proven track-record of utility and cost-effectiveness indicates that it should be considered by other researchers for future applications.publishedVersio

Galaxy Training: A powerful framework for teaching!

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments

QTL/eQTL identification for osmoregulation capacities in rainbow trout

National audienc

Étude génétique et génomique de la réponse à un changement de salinité chez la truite arc-en-ciel Oncorhynchus mykiss

Diplôme : Dr. d'UniversitéEuryhalin teleosts can live in freshwater as well as in seawater. The success of their survival depends then on their osmotic acclimation capacities. The objective of my work is to describe acclimation processes in the salted water at the rainbow trout by a study coupling functional genomic and genetic approaches. From a first differential gill transcriptomic kinetic study, a list of candidates genes was established and the physiological answer of the fish sudied. Main results reveal good euryhalinity capacities a maximum trasncriptomic answer 24 h after the seawater transfer. Biological processes implicated in the acclimation mechanisms are also proposed. A second part of this work consisted of the characterisation of the genetic control of processes linked to seawater acclimation in rainbow trout. Using as characters, a two times repeated 24h post seawater transfer plasma sodium and chloride levels, as well as gill weight, unitrait and multitrait analyses allowed to reveal 18 QTL among whom 9 are qualified as robust. A last approach of eQTL detection then allowed, based on a gill transcriptomic analysis and on the results of the first two approaches, to offer 69 exclusive candidates genes. If the majority of these genes are offered as acting at functional level, some are suggested as positional candidates. It is the first time that a blending transcriptomie differential approach coupled to a QTL / eQTL study is led to a non-sequenced genome aquacole interest teleost for the acclimation capacity to different osmotic environments. These results lay the road with cobblestones for a definite investigation of the genetic bases of seawater acclimation processes in teleosts.Les téléostéens euryhalins peuvent vivre dans des milieux à salinité très différentes. L'objectif de mon travail est de décrire les processus d'acclimatation à l'eau salée chez la truite arc-en-ciel par une étude couplant approches de génomique fonctionnelle et génétique. A partir d'une première approche cinétique de transcriptomie différentielle menée sur la branchie, une liste de gènes candidats a été établie et la réponse physiologique des poissons étudiée. Les principaux résultats révèlent de bonnes capacités d'euryhalinité et une réponse transcriptomique maximum 24h après le transfert en eau de mer. Des processus biologiques impliqués dans les mécanismes d'acclimatation sont également proposés. Une seconde partie de ce travail consistait en la caractérisation d'un contrôle génétique des processus liés à l'acclimatation à l'eau de mer chez la truite. Utilisant comme caractères, les teneurs plasmatiques en sodium et en chlore mesurées 24h après un transfert d'eau douce en eau salée répété à 2 reprises, ainsi que le poids branchial, des analyses univariées et multivariées ont permis de détecter 18 QTL dont 9 sont qualifiés de robustes. Une dernière étape de détection de QTL d'expression a alors permis de proposer 69 gènes candidats de premier choix. C'est la première fois qu'une approche mêlant transcriptomie différentielle et approche QTL / eQTL est menée chez une espèce d'intérêt aquacole au génome non séquencé pour la capacité d'acclimatation à un milieu osmotique différent. Ces résultats pavent la route pour une investigation précise des bases génétiques des processus d'acclimatation à l'eau de mer chez les téléostéens

Linux/Unix: A short introduction

A very short introduction to Unix/Linu

Tutorial : Initiation à la plateforme web Galaxy

Support de formation présentant la plateforme web d'analyse de données NGS Galax