INFORMATICIAN/ BIOINFORMATICIAN

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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 TOXALIM unit, the research centre in food toxicology in Toulouse, which hosts the analytical facility AXIOM. AXIOM is part of METATOUL, the local platform, and METABOHUB (MTH), the National infrastructure of metabolomics and fluxomics. Launched in 2013, MTH is a leading international infrastructure serving more than 700 scientists worldwide. MetaboHUB gathers 6 regional facilities including more than 80 permanent staffs, 16 NMRs, 68 MS, robotic and computational platforms. MTH aims at pushing forward the field to develop metabolomics, lipidomics and fluxomics from single cell to population. Your contribution will serve a broad range of researchers in the fields of biotechnologies, Human health, nutrition and plant science. MetaToul, launched in 2007, is a multi-institutional platform uniting INRAE, CNRS, INSERM, INSA, the University of Toulouse, and Toulouse Hospitals. ISC- and IBiSA-labeled, and recognized by INRAE as a national strategic platform, MetaToul brings together about 50 staff members with expertise in biochemistry, chemistry, bioinformatics, biostatistics, automation, mass spectrometry, NMR, and chromatography. These complementary skills support the study of metabolism through metabolomics, lipidomics, and fluxomics workflows.

One objective of the MTH infrastructure is large-scale metabolomic studies. An automatic tool has been developed for preprocessing of 2D NMR spectra generated from these high-throughput studies. However, annotation is still a bottleneck in metabolomic studies. To streamline this step, the Peakforest spectral database and automatic annotation tools have been developed within MetaboHUB to share 1D and 2D NMR spectra as well as peak lists. But, populating this database is very time-consuming and false positive metabolites result from annotation tools. 

The first objective of this position is to develop an automated tool to populate the PeakForest database with NMR spectra of standard compounds, enabling the extraction of:

- Acquisition parameters from manufacturer files,

- Peak lists from one- and two-dimensional NMR sequences, obtained using automated tools such as the one developed.

The second objective is to combine for automatic annotation of complex NMR spectra from spectra of reference compounds available in the Peakforest database. Finally, the position includes training and supporting users in using these tools.

You will be more specifically in charge of:

1. The development of an automatic tool to implement the PeakForest database, with NMR data;
2. The combination of algorithms for the automatic annotation of one- and two-dimensional NMR spectra;
3. The training and supporting users in using both tools, as well the writing developer and user guides.

The successful candidate will travel to the MTH-PFEM site in Theix (63) to work on matters related to the PeakForest database.

Training and skills

Skills: Programming (R, Python); Forge (Gitlab, Github); Database management; English mandatory

Desired knowledge: Attraction for analytical chemistry and VIBE coding

Appreciated experience: Junior to mid-level developer (1+ years of experience preferred, but we are happy to train and mentor the right junior candidate)

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