2022-05066 - Building an open codebase of many pipelines for the analysis of a single neuroimaging dataset
Le descriptif de l’offre ci-dessous est en Anglais

Type de contrat : CDD

Niveau de diplôme exigé : Bac + 5 ou équivalent

Fonction : Ingénieur scientifique contractuel

Niveau d'expérience souhaité : De 5 à 12 ans

A propos du centre ou de la direction fonctionnelle

The Inria Rennes - Bretagne Atlantique Centre is one of Inria's eight centres and has more than thirty research teams. The Inria Center is a major and recognized player in the field of digital sciences. It is at the heart of a rich R&D and innovation ecosystem: highly innovative PMEs, large industrial groups, competitiveness clusters, research and higher education players, laboratories of excellence, technological research institute, etc.

Contexte et atouts du poste

Applications are invited for a research engineer position with Dr. Camille Maumet in the Empenn team at INRIA. This position is part of the exploratory action GRASP “Generalizing Results Across Scientific Pipelines”.

The fellow will join the Empenn team at INRIA Rennes, a group of circa 30 people working on neuroimaging applications and methods with a diverse set of expertise ranging from computer science and maths to medicine. The Empenn team is part of INRIA Rennes, a research centre of about 800 members focusing on all aspects of computer science research.

Mission confiée

With the development of data science, the different tools and approaches available to study a dataset have multiplied. With each pipeline providing its own version of the results, this multiplicity of approaches also leads to many possible results for a given problem, with sometimes conflicting conclusions. In recent years, the impact of pipeline choices on scientific findings has been demonstrated in a variety of scientific fields including psychology, medicine, climate science and also the field of brain imaging -- which will be the focus of this work. But to date, in neuroimaging, there is no open codebase that could be used to study this phenomenon. The successful applicant will implement and share such a codebase including multiple different treatments of the same neuroimaging study. The pipelines to implement will be selected from the NARPS project (Botvinik-Nezer et al., 2020). The research engineer will work closely with Dr. Camille Maumet and with the postdoctoral fellow that will also be recruited as part of the GRASP project. 

We are looking for excellent software engineers with a strong interest in working in neuroimaging research, and ideally with prior experience in a research environnement. The successful candidate must have a background in data science, computer science or a related field. Previous experience in open source and/or working with open communities will be highly valued.

Principales activités

Responsibilities/Duties

The goal of the research engineer is to make a public codebase that re-implements the 70 pipelines used in NARPS. To achieve this aim, the research engineer will:

  • Professionalise the existing codebase (circa 6 pipelines): containerize the code, add continuous integration, make the code compatible to run on an HPC cluster.
  • Make the code open to contributions: create an online contribution guide (+ code of conduct, README, communication channel) for the implementation of new pipelines.
  • Manage contributions from the research community, providing feedback, helping developing the code and merging the contributions.
  • Re-implement existing neuroimaging pipelines, validate those implementations (by comparing the new results with the results that were originally published) share those implementation openly as a resource for the scientific community.
  • Participate in the publicization of the project, e.g. by participating in Brainhack hackathons.

Compétences

Essential requirements

  • Master in computer science, data science or a related field.
  • Proficient in Python.
  • Prior experience working with Docker or Singularity.
  • In-depth experience of software project management including version control (git + GitHub/gitlab), continuous integration, roadmapping, managing issues, etc.
  • Well-organised.
  • Strong written communication skills in English.
  • Ability to work well in a team and exchange and share ideas with other members.
  • Strong enthusiasm to “work open”, i.e. adopt an agile approach in which the code is made available publicly from its inception and gradually improved. This approach also means working in collaboration with the community to take into account their feedback and intergate contributions.
  • Ability to work well with people from different fields (computer science, neuroimaging, medicine, etc.) and levels of seniority.

Desirable

  • Knowledge of how to build and manage inclusive online communities 
  • Prior experience working with HPC cluster
  • Prior participation in research projects.
  • Prior experience with processing of neuroimaging or medical data.
  • Prior experience working with a neuroimaging workflow engine, e.e. nipype or Pydra
  • Active in the open source community or with open communities

For more information

Informal inquiries can be sent to Dr. Camille Maumet (camille.maumet@inria.fr). 

General information on INRIA and on the Empenn team are available on the respective websites: https://www.inria.fr/fr https://team.inria.fr/empenn/ 

Salary will be commensurate with experience as per the INRIA salary grids. We are looking for experienced applicants (>5 years) but will consider applicants with less experience who are an excellent fit for the position.

 

Avantages

  • Subsidized meals
  • Partial reimbursement of public transport costs
  • Possibility of teleworking (90 days per year) and flexible organization of working hours
  • Partial payment of insurance costs

Rémunération

Monthly gross salary from 2 562 euros according to diploma and experience