Bioinformatics research engineer position within dry-lab group of the technological platform Biomics
data analyst, software development, Python
The Biomics technological platform
(Biomics hereafter) is the C2RT
structure at Institut Pasteur for Next Generation Sequencing
. Our mission is to facilitate scientific discoveries within the Pasteur Institute network with both service and collaborative projects.
We currently have 8 sequencers in the laboratories including a HiSeq2500, a NextSeq500, 2 MiSeqs, a ISeq100 for short reads
, a Pacbio Sequel and a Nanopore Minion for long reads
. Our current activities cover transcriptomics, genomics, genotyping, metagenomics including both short and long reads technologies.
The Biomics platform is currently composed of 14 members. It hosts a group of 3 bioinformaticians. This group is involved in Biomics projects
throughout their life cycle from conceptualization to closure including planning (experimental design), execution (bioinformatics and biostatistics analysis), and R&D. Due to an increase of activity, we wish to recruit a new collaborator to join the dry-lab group. The position is described here below. This is a great opportunity to work with researchers and engineers from many disciplines.
Description of the position
This is a position of bioinformatician within the Hub of bioinformatics and biostatistics
of Institut Pasteur. The successful candidate will be detached at 80% to the Biomics Platform to reinforce the existing group of bioinformaticians. Your main tasks will encompass (1) the management of NGS projects
in all its diversity (variant calling, genome assemblies, differential analysis, etc) from the design to final reporting and (2) the development of bioinformatics analysis software
, in particular within the sequana framework (https://sequana.readthedocs.io). Here is a non exhaustive list of tasks:
- Provide advice and support during kick-off meeting to plan the bioinformatics analysis ahead. This is essential to anticipate the needs in terms of experimental design for instance.
- Perform primary and secondary analysis (from experimental designs to final reporting of the bioinformatics analysis).
- Software development dedicated to the analysis of data generated within the platform.
- Participation to national and international conferences and working groups.
- Participation to publications with our collaborators or within the team as an active partner
- Quality control and data management
Like other detached member of the Hub, the successful candidate will also spend 20% of its time to activities dedicated to the Hub. He/she will participate to the Hub collaborative tasks such as trainings, help desk or team meetings.
Required skills / expected profile
Experience in a service facility is strongly advantageous. Experience in professional software engineering and development, as well as data analysis and data sharing strategies are beneficial.
- An excellent and enthusiastic Python developer. Indeed, most of our pipelines and software have been developed in Python and Snakemake framework.
- A good practice of software development is required for the position.
- Excellent communication skills to interact with computer scientists, biologists, bioinformaticians, etc
- Not essential but recommended for the position
- Enjoy software development
- Enjoy the diversity of projects that will be available in this position
- Good knowledge of english
- Knowledge and/or experience of reproducibility frameworks such as Docker and Singularity
- Statistical modelling, deep learning, machine learning, optimisation, etc
The types of data we currently foresee may include high-throughput sequencing data, epigenetics, genomics, metagenomics, etc. Your expertise will help shape the data sharing and dry-lab group and you will be able to learn from, as well as share your knowledge within the Biomics platform.
You have a Master’s degree or higher in bioinformatics, computational biology or data science.
You will have strong team-playing abilities and be able to interact with researchers from many fields, including biology, physics, mathematics and computer science. A friendly, outgoing personality and excellent communication skills are required, as is the ability to work independently.
For more information on this specific position and on the Biomics platform you can contact
- Thomas Cokelaer – thomas.cokelaer (at) pasteur.fr – Manager of the Dry lab group
- Marc Monot – marc.monot (at) pasteur.fr – Director of Biomics