Research engineer position in numerical methods

The Inria research centre in Lyon is the 9th Inria research centre, formally created in January 2022.  It brings together approximately 300 people in 17 research teams and research support services.

Its staff are distributed in Villeurbanne, Lyon Gerland, and Saint-Etienne.

The Lyon centre is active in the fields of software, distributed and high-performance computing, embedded systems, quantum computing and privacy in the digital world, but also in digital health and computational biology.

The position is open in the Inria team MOSAIC. The team scientific activity revolves around mathematical modeling and digital simulation in the field of plant developmental biology. The main task of the sought engineer will be to extend an existing python library (BVPy) and provide a set of tools to implement simulations of plant tissue morphogenesis within the framework of Finite Element Methods (FEM). The goal is to enable the implementation of Initial and Boundary Value Problems (BVP & IBVP) on dynamical strucutres, generated from 3D acquisitions of living tissues. This mission will be carried in collaboration with researchers and engineers of the team as well as close biologist collaborators.

Missions:

Supervised by Olivier Ali (researcher at Inria), Julien Derr (full professor at ENS Lyon) and Manuel Petit (research engineer at Inria), the sought engineer will extend the existing library BVPy, initially developped within the team to solve BVP and IBVP on static domains. The following upgrades are expected:

1. Handeling of complex meshes extracted from 3D fluorescent microscopy acquisitions.
2. Implementation of a remeshing module to edit these meshes, to enable the simulation of tissular growth.
3. Code optimization through parallelization in order to address complex "multi-physics" scenarios. 

For more context and details:

• Team website: MOSAIC and the hosting biology lab website: RDP.
• Librarie BVPy V1.0: publication in Journal of Open Source Software  and gitlab repository.
• Published proove of concept: Boudon, Ali, Chopard et al PLoS Comp Biol 2015

Collaboration :

The succesful candidate will be supervised by  Olivier Ali  and  Julien Derr , in close interaction with the engineer staff of the team.

Responsabilities:

The succesful candidate will be in charge of the technological development of the library. He/She will also help the team members (scientists, students) in their usage of the new library to address their specific scientific questions. He/She could also supervised studients and interns that will eventually join the project in the future. 

Main activities:

• Desing and develop the architecture and the new components of the BVPy library.
• Implement a dynamic remeshing module (based on GMSH and/or CGal).
• Optimize the library performances through parallelization.

Side acitivites:

• Promotion of the library towards internal and external partners through scientific and technical presentations.
• Realization of training materials (tutorials, notebooks) and training sessions to sustain this promotion.

Technical skills:

• Expertise in numerical methods for scientific computing.
• Theoretical knowledge and practical experience in Finite Element Methods.
• Knowledge in python and experience with standard modern programming tools (IDEs, versionin...)

Language:

• English
• French (Optional but could be useful for daily and informal interactions)

Other skils:

• Scientific meeting chaimanship.

• Subsidized meals
• Partial reimbursement of public transport costs
• Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
• Possibility of teleworking (90 days / year) and flexible organization of working hours Social, cultural and sports events and activities
• Access to vocational training
• Social security coverage under conditions

From 2692 € (depending on experience and qualifications).