- Job area
- Research & Development
- Marcq-en-Barœul, France
- Contract type
- Permanent Contract
- 3 to 5 years
The Synthetic & Systems Biology team is part of the Bioengineering Center of Excellence and a core member of its Biofoundry. Our purpose is to design, build and learn from Lesaffre organisms, genes and genomes.
We have three core missions. First, we enable the large-scale, rational exploration of the strain design space by building arrayed strain libraries either for enzyme discovery, metabolic pathway optimization, hypothesis testing or gene target identification. Second, we combine high-content / genome-wide quantitative experiments and mathematical modeling to characterize and model strain (or strain consortium) behavior as a function of its genome (or their genomes). Finally, we provide access to a variety of full-stack NGS workflows tailored to needs of both the Lesaffre Institute of Science and Technology and Lesaffre Business Units.
Our team is already bringing together diverse expertises (in high-throughput synthetic biology and NGS, in computational biology and mathematical modeling…). We are now seeking a synthetic & systems biology scientist with computational skills to 1) contribute to our data analysis and experiment design efforts and 2) help us maintain and improve our data quality as we grow in scope and help us increase our throughput in both data generation and automated data analysis.
As a member of the Synthetic & Systems Biology team, your role will be to :
- Contribute to strain development as well as method development projects
- Analyse a diverse range of data (genomics, transcriptomics, physiological data from controlled fermentations, applicative performance data, other phenotypes from enzymatic, growth-based, cytometry-based assays…) to generate project-specific insights
- Make recommandations on informative experiments or new computational analyses to perform in order to fill project-critical gaps in knowledge
- Unlock operational excellence in data generation and automated data analysis
- Develop a detailed, structured understanding of all our processes and workflows both in terms of physical world operations (transformation and transfer of samples), of data flows (measurements, external information) and of their interdependence (sample tracking, quality control, decision branching points in protocols)
- Challenge our current data model and workflow automation procedures both using a bottom-up approach (i.e. starting from identified structured issues bottlenecks, cost-suboptimal steps, weaknesses in quality control…) and a top-down approach (i.e. starting from design principles identified in de-novo system design efforts)
- Participate in the implementation of the redesigned data model, processes and workflows by contributing to the associated codebase, re-configuring the LIMS (Laboratory Information Management System), and deploying necessary micro-services on our compute infrastructure
- Establish good practices leveraging the LIMS for tracking the quality, time and cost efficiency tracking of the all the team workflows. Perform accurate simulations of potential workflow variations to score their potential
- Grow and maintain knowledge and proficiency regarding relevant software programming and data engineering skills, by actively sharing your experiences within a community of Lesaffre developpers spanning a wide range of teams
- You must have :
- PhD in Computational Biology, Bioinformatics, Computational Systems Biology, Computational Synthetic Biology or Applied Mathematics / Computer Science on Biology-related topics
- Proficient use of Python for a variety of uses, including data analysis (data manipulation with pandas, plotting with plotly/bokeh/matplotlib…) and programmatic access to databases via APIs
- Experience with git and any of github/gitlab/bitbucket
- Fluency in English
- It’s nice to have:
- Hands-on experience with Benchling LIMS configuration as well as their Python SDK for API interactions
- Exposure to biology wet lab work
- Experience with model yeast and/or bacteria organisms
- Experience in running jobs on a cloud infrastructure / compute cluster
- Experience in writing SQL queries
- Knowledge of R in the context of bioinformatics
A key global player in fermentation for more than a century, Lesaffre, with a 2,2 billion euro turnover, and established on all continents, counts 11,000 employees and more than 90 nationalities. On the strength of this experience and diversity, we work with customers, partners and researchers to find ever more relevant answers to the needs of food, health, naturalness and respect for our environment. Thus, every day, we explore and reveal the infinite potential of microorganisms.
To nourish 9 billion people, in a healthy way, in 2050 by making the most of our planet’s resources is a major and unprecedented issue. We believe that fermentation is one of the most promising answers to this challenge.
Lesaffre – Working together to better nourish and protect the planet