1 year position Engineer : genome database developer

Friday, October 18, 2019


In the context of the Phaeoexplorer project (“France-Genomique” call) the ABiMS platform (http://abims.sb-roscoff.fr/), one of the bioinformatics platforms of the French Institute of Bioinformatics (IFB), is hiring a bioinformatician.

The aim of the Phaeoexplorer project is to sequence and annotate the complete genomes of 70 species of brown algae and sister species. This project is coordinated by the Roscoff Marine Station and involves the Genoscope Sequencing Center and an international consortium of laboratories.

The ABiMS platform has deployed the first genome databases for Phaeoexplorer algae using the Galaxy Genome Annotation project (GGA, https://github.com/galaxy-genome-annotation). This environment offers the possibility of making genomes and their annotations available to the community through user-friendly interfaces in an automated way. It uses lightweight virtualization technologies with Docker containers and is based on the GMOD suite and the Galaxy web portal.


Job outline:

The successful candidate will be in charge of integrating new genomic and transcriptomic data from the Phaeoexplorer project into the Phaeoexplorer GGA environment. He / she will also be involved in the development of the Phaeoexplorer GGA environment.


Main activities:

- Integrate new data (genomics, transcriptomics, annotations) into the Phaeoexplorer environment.

- Develop workflows for integrating functional data.

- Maintain/update the Phaoexplorer environment.

- Participation in the development of new features to improve data visualization and help data analysis.

- Develop and implement a web portal for Phaeoexplorer data.

- Interact with the contributing research groups and other ABiMS engineers to define and refine future needs.

- Liaise with partners at Roscoff and Genoscope concerning genomic and transcriptomic data.


Qualifications and experience:

  • Masters Level qualification or higher in a relevant discipline.
  • Familiarity with analysis methods for genomic and transcriptomic sequence data.
  • Interest in molecular, developmental and/or evolutionary biology.
  • Competence with Unix computer environments.
  • Proficiency in computer programming, ideally in Python.
  • Competence in web development with PHP5 and HTML/CSS.
  • Knowledge of Docker containers, the Drupal CMS and GMOD tools (JBrowse, Galaxy) would be an asset.
  • Good spoken and written English.
  • Collaborative and autonomous.

Start date: 1/01/2020; apply before 15 November 2019 to ensure consideration.

Activity rate: 100%.

Duration of contract: 1 year.

Salary on the CNRS « Ingénieur d’études » pay-scale: 2000 2300 (bruts) euros per month, depending on experience.

Link : http://bit.ly/2J24fbT