Mots-Clés

biomass, workflow, fair, galaxy, python

Description

Objective

The primary objective of this role is to design and implement workflows for laboratory protocols and integrate them into a centralized portal to design, execute, and monitor bioproduction projects.

Context

Despite the increasing adoption of the DBTL (Design-Build-Test-Learn) framework as a standard in bioengineering, biofoundries continue to face a significant lack of shared practices, with each developing its own pipeline. This fragmentation creates inefficiencies and limits reproducibility across the field. To address these issues, the GalaxyBioProd project funded by the France 2030 initiative under the B-BEST programme aims to develop a centralized portal, providing standardized digital tools and resources for designing, executing, and monitoring bioproduction projects. By adhering to the FAIR principles and utilizing the Galaxy workflow management system, the initiative seeks to create an accessible, unified platform that can serve diverse communities in synthetic biology, biocatalysis, and industrial biotechnology.

Engineer Mission

The mission of the engineer is to design and implement robust workflows that streamline laboratory protocols, integrating them into the centralized portal for managing bioproduction projects. A core responsibility will be ensuring that all workflows adhere to the FAIR principles (Findability, Accessibility, Interoperability, and Reusability) for data and resource management practices that maximize transparency, reproducibility, and long-term usability.

Requirements

Candidates should be completing a MSc in computer science, or engineering. Applicants should have strong skills in Python with knowledge of C++ considered a plus. Experience with package management tools, specifically Conda, is desirable, as well as experience in version control using GitLab. Candidates should also be comfortable documenting their work. Knowledge and/or interest in some topics related to biotechnology applied to biomass would be an asset. Communication and reporting skills are essential as the successful candidate will need to work in an interdisciplinary team and write up progress reports and make oral presentations.