Société Française de Bioinformatique

Mots-Clés

database variants web development human genome personalized medicine

Description

Position: Bioinformatic engineer

Location: Laboratory of Gael Cristofari, Institute for Research on Cancer and Aging of Nice (IRCAN) at the University Cote d’Azur (Nice, France)

Contract: 1-year contract with possibility of extension

Context

The position is funded by Inserm (French National Institute of Health and Medical Research) in frame of its cross-cutting program on Genomic Variability. Our team studies mobile element insertions, also known as transposable elements, and their role in generating genetic variations among humans. We developed an integrated database that provides a curated catalogue of such genetic variants, named euL1db, and accessible through a web interface. It plays an essential role to interpret whole genome sequencing experiments in the context of research or personalized medicine. Since its original design, massive amounts of new data sets have been publicly released and need to be curated and incorporated into the database. To achieve this, the infrastructure needs to be redesigned and optimized on both the server- and client-sides.

Related publication

Mir AA, Philippe C & Cristofari G. euL1db: the European database of L1HS retrotransposon insertions in humans. Nucleic Acids Res. 2015 Jan;43:D43-D47.

Main missions

• Optimization of database architecture
• Development of web applications and APIs (back-end and front-end)
• Evaluation of new data sources from published articles, data set collection and curation
• Generation of new data sets using existing tools
• Database update and maintenance

Skills & qualifications

• Master’s degree (MSc) in bioinformatics and/or database management and web development
• High proficiency in relational databases (MySQL) and Python development
• Experience in web application programming
• Experience in project management and documentation (versioning, bug tracking, Markdown, Jupyter Notebook, etc)
• Strong interest in and understanding of genomics concepts
• Ability to read and understand original scientific articles in English to identify useful data sets
• Ability to keep a high level of accuracy, attention to details and rigor
• English: Good