Development of a plug-and-play platform for computer-automated experiments on microorganisms



November 13, 2022


2022-05348 - Development of a plug-and-play platform for computer-automated experiments on microorganisms

Contract type : Fixed-term contract

Level of qualifications required : Graduate degree or equivalent

Other valued qualifications : Master 2 / Engineering diploma

Fonction : Temporary scientific engineer

About the research centre or Inria department

The Inria Grenoble - Rhône-Alpes research center groups together almost 600 people in 22 research teams and 7 research support departments.

Staff is present on three campuses in Grenoble, in close collaboration with other research and higher education institutions (Université Grenoble Alpes, CNRS, CEA, INRAE, …), but also with key economic players in the area.

Inria Grenoble - Rhône-Alpes is active in the fields of high-performance computing, verification and embedded systems, modeling of the environment at multiple levels, and data science and artificial intelligence. The center is a top-level scientific institute with an extensive network of international collaborations in Europe and the rest of the world.


Project-Team MICROCOSME at Inria Grenoble - Rhône-Alpes is a highly interdisciplinary team working on the mathematical modelling, analysis, engineering and control of microorganisms. In collaboration with the experimental biology group BIOP at LIPhy (Laboratoire Interdisciplinaire de Physique, Université Grenoble-Alpes), we have developed a computer-automated lab-scale platform for microbial growth and control experiments in a system of mini-bioreactors. Already operational, the platform is at the center of several current and future projects of the team ranging from fundamental research on microorganisms to the engineering of microbial consortia for biotechnological applications. Objective of the project is to turn the current hardware and software setup into a plug-and-play system for simulation, execution and replay of microbial control experiments.


The current physical setup comprises a fluidic system actuated by pumps for the transfer of liquids and samples and the control of bioreactors, an optical system for spectrometric measurements and light-based control, and several measurement instruments (spectrometers, cytometer). Co-developed with the BIOCORE group of Inria Sophia-Antipolis, the platform software is a web-based, modular system for platform operation and implementation of control algorithms.

Goal of this project is to develop:

- Software modules for the monitoring of all platform devices (connection, activity status, ... ) - User interface for the management of the current device operation scheduler - A plug-and-play mechanism for the addition of new devices - Modules for the virtualization of devices and simulation/replay of experiments

Part of the above developments will be conducted in collaboration with BIOCORE, including possible participation in coding sessions at Inria Sophia- Antipolis.

Main activities

The core activity of the project is software development. The project may include developments of the hardware/software communication system with the platform devices, with possible interventions on platform electronics. The activity is co-localized at the Inria site in Montbonnot and at LIPhy (Grenoble campus), where the platform is installed. The project is supervised by Eugenio Cinquemani in collaboration with the SED (Experiment and Development Service) of Inria Grenoble - Rhône-Alpes, and experimentalists at LIPhy. Progress meetings will be held at least on a weekly basis. Development sessions with the BIOCORE (Inria Sophia-Antipolis) collaborators will take place twice per year. Development will be based on Git. Documentation and reporting are part of the project.


- Required: Python, C++, Linux environment, Git, Embedded systems (Modbus, Serial communication, Microcontrollers) - Desired: MQTT broker, SQL, Docker - Appreciated: Java and/or Erlang, continuous integration

Working knowledge of English is expected.

Previous experience in team projects is a plus but young engineer applications will equally be evaluated.

Benefits package
  • 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 and flexible organization of working hours
  • Professional equipment available (videoconferencing, loan of computer equipment, etc.)
  • Social, cultural and sports events and activities
  • Access to vocational training
  • Social security coverage
  • General Information
  • Theme/Domain : Modeling and Control for Life Sciences Software Experimental platforms (BAP E)

  • Town/city : Montbonnot

  • Inria Center : CRI Grenoble - Rhône-Alpes
  • Starting date : 2022-12-01
  • Duration of contract : 1 year, 8 months
  • Deadline to apply : 2022-11-13
  • Contacts
  • Inria Team : MICROCOSME
  • Recruiter : Cinquemani Eugenio /
  • The keys to success

    The project takes place in a highly interdisciplinary and international environment. The candidate is thus expected to be a person open to collaboration and exchange, with interest for scientific experiments and research, and ready to integrate a team with diverse competences and backgrounds.

    She/he should be rigorous, autonomous and proactive, open to discussion and respectful of priorities and time planning. She/he should be at ease with co- localized work / videoconferencing if needed, and ready for a couple of worktrips (France) per year.

    About Inria

    Inria is the French national research institute dedicated to digital science and technology. It employs 2,600 people. Its 200 agile project teams, generally run jointly with academic partners, include more than 3,500 scientists and engineers working to meet the challenges of digital technology, often at the interface with other disciplines. The Institute also employs numerous talents in over forty different professions. 900 research support staff contribute to the preparation and development of scientific and entrepreneurial projects that have a worldwide impact.

    Instruction to apply

    Defence Security : This position is likely to be situated in a restricted area (ZRR), as defined in Decree No. 2011-1425 relating to the protection of national scientific and technical potential (PPST).Authorisation to enter an area is granted by the director of the unit, following a favourable Ministerial decision, as defined in the decree of 3 July 2012 relating to the PPST. An unfavourable Ministerial decision in respect of a position situated in a ZRR would result in the cancellation of the appointment.

    Recruitment Policy : As part of its diversity policy, all Inria positions are accessible to people with disabilities.

    Warning : you must enter your e-mail address in order to save your application to Inria. Applications must be submitted online on the Inria website. Processing of applications sent from other channels is not guaranteed.

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