Streamlining open medical data sharing and reuse in Europe
Inria
Rennes
Streamlining open medical data sharing and reuse in Europe
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 3 à 5 ans
A propos du centre ou de la direction fonctionnelle
The Inria Centre at Rennes University is one of Inria's eight centres and has more than thirty research teams. The Inria Centre 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 FLI-IAM, i.e. the “Information Analysis and Management” (IAM) node of the national infrastructure “France Life Imaging (FLI)”.
Open science practices are being increasingly supported by a variety of stakeholders in scientific research. UNESCO defines open science around 3 key features including: "Encourage collaboration and information-sharing to benefit science and society". In particular, opening up scientific data is very central to open science as it makes it possible to reuse dataset within scientific communities effectively leading to larger sample sizes and the possibility to build more generalizable discoveries. In the European landscape, a number of initiatives have emerged to streamline sharing of medical image datasets. The focus of this work will be to interoperate the FLI-IAM infrastructure — and specifically the Shanoir imaging data management system — to other European open science efforts towards building integrated easy-to-use databases and tools for open data sharing and reuse.
Mission confiée
The successful applicant will work with European initiatives to interconnect infrastructure and tools for open medical imaging data in order to streamline the process of accessing, analysing and publishing results on public medical imaging datasets. To get started, the goal will be to work closely with datalad (distributed data management – https://www.datalad.org/) and Openneuro-PET (EU-GDPR compliant PET data sharing https://openneuropet.github.io/) and connect those to the Shanoir imaging data management system (https://shanoir.irisa.fr/shanoir-ng/welcome). The research engineer will work closely with Michael Kain who is the technical lead of the FLI-IAM infrastructure.
We are looking for an excellent software engineer with a strong interest in working in medical imaging research, and ideally with prior experience in a research setting. The successful candidate must have a background in computer science or a related field. Previous experience in open source and/or working with open communities will be highly valued.
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.
Principales activités
The goal of the research engineer will be to develop new tools to interconnect existing European infrastructure. To achieve this aim, the engineer will:
- Learn about European medical data sharing tools and infrastructure such as Shanoir, datalad and Openneuro-PET
- Learn about existing standards to share and exchange medical imaging data
- Develop tools to interconnect platforms in order to make sharing and reusing datasets more efficient
- Contribute to the Shanoir codebase to share those tools
- Exchange with users to learn about their needs in terms of data reuse
- Participate in the publicization of the project, e.g. by participating in Brainhack hackathons.
Compétences
Essential requirements
- Master/Engineering degree in computer science, data science or a related field.
- Proficient in software development.
- 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, medical imaging experts, etc.) and levels of seniority.
Different levels of experience can be considered for this position. Salary will be commensurate with experience as per the INRIA salary grids. Ideally, we are looking for experienced applicants (>5 years) but will consider applicants with less experience if they are an excellent fit for the position.
Desirable
- Prior participation in research projects.
- Prior experience with processing of neuroimaging or medical data.
- Active in the open source community or with open communities
For more information
Informal inquiries can be sent to Dr. Camille Maumet ([email protected]).
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/
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 2 695 euros according to diploma and experience