Data engineer on workflows for genetic indicators

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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

◼ You will be welcomed in the Unit Biogeco, Biodiversity from genes to communities, a mixed research unit of INRAE and the University of Bordeaux, at the site “Domaine de l’Hermitage” located on 69 route d’Arcachon in Cestas, France. Biogeco comprises about 120 members, of which 75 permanent scientific and technical staff members, as well as numerous students, postdocs, collaborators and visitors. Its main research interest is in the biodiversity, function, evolution, adaptation, conservation and restoration of ecosystems, mainly forests, but also other natural and anthropized ecosystems. You can discover a presentation of the unit in a short video.

FR https://www.youtube.com/watch?v=HAyN9MM32dI

EN https://www.youtube.com/watch?v=q5TC9HuHvtI

◼ Your contract is funded by the Biodiversa+ project GINAMO, Genetic Indicators for Nature Monitoring, whose main objective is to facilitate the implementation of the Convention on Biological Diversity (CBD)’s Global Biodiversity Framework through improved calculation, operationalization and mainstreaming of genetic indicators.

You will be working within GINAMO’s work package 5, focussing on data management and the implementation of user-friendly workflows for the calculation of the CBD’s adopted genetic indicators for end users. You will be hosted by Myriam Heuertz and colleagues at Biogeco and work in close cooperation with the PNDB (Pôle National Données Biodiversité) and GBIF France (Yvan Le Bras and Anne-Sophie Archambeau), and communicate with a large international group of project members and stakeholders for the following specific tasks:

• Contribute to data management for the project
• Participate in project meetings and liaise with project members, discussing best practice recommendations for the calculation of genetic indicators and, more generally, Essential Biodiversity Variables (EBVs)
• Develop standardised workflows for genetic indicators and EBVs from DNA data, based on best practice recommendations from WP2, and building on the EBVOSC pilot project, comprising data integration, and workflow operationalization
• Develop standardised workflows for genetic indicators from proxy data, based on best practice recommendations from WP3 (handling proxies such as distribution data, density data, census sizes…), and WP4 (handling proxies derived from Earth observation data etc.), and building on the EBVOSC pilot project, comprising data integration, and workflow operationalization
  • Workflow operationalisation will consist of script customisation, managing, archiving and sharing of source code, user-friendly and reproducible interactive running of code, and formatting results and visualisations for publication, in line with the DataOne network of data catalogues
• Develop functionalities for customizable reports to meet management stakeholders’ needs for reporting on genetic indicators
• Contribute to project reporting, publication and valorization of results

Special conditions of activity: You will be required to travel occasionally, for project meetings, and to facilitate cooperation with the PNDB and GBIF.

Training and skills

◼ Recommended training: Master degree in bioinformatics with experience in conservation genetics, or similar

◼ Knowledge required (in order of priority):

• Knowledge of the Linux command-line environment,
• Proficiency in R and Python,
• Knowledge of software development platforms such as GitHub/GitLab,
• Knowledge in applying the FAIR Principles to computational workflows,
• Good operational English language knowledge (at least level B2),
• Experience with population genomics data analyses and/or genetic indicator estimation.

◼ Appreciated experience:

• Experience with the Galaxy environment and best practices for tool integration, particularly using Planemo,
• Experience with data management plans, Ecological Metadata Language, DarwinCore standard,
• Interest in applied conservation biology, and experience in data processing,
• Experience with Essential Biodiversity Variables,
• Interest in creating training materials would be a big plus,
• Interest in participating in training activities would also be a plus,
• French language knowledge.

◼ Skills sought: ability to communicate clearly with a large and dynamic international group of project members, team working skills, presentation skills

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.

How to apply

I send my CV and my motivation letter