Job title: Biological data analysis engineer (M/W)

Number of positions proposed: 1

Type of contract: Fixed-term contract – 36 months

Workplace: Roscoff Marine Station (CNRS, Sorbonne Université), France

Expected date of employment: 11 December 2023

Proportion of work: Full time

Remuneration: Between 2782,84€ and 2940,88€ gross salary per month depending on experience

Desired level of education: Master, engineer or higher degree

Application deadline: November 12th, 2023

As part of the BYTE-SEA project, which is dedicated to setting up the IT infrastructure for the PEPR ATLASEA, the candidate will be responsible for structuring the project data and will take part in supervising current developments to enable integration into the database, which he/she will be responsible for developing.

Working context:

ATLASea is a programme focusing on the genomics of marine biodiversity along the French coast. Led by the CNRS and the CEA, it includes a number of partner institutions in France and is part of a wider international context. ATLASea will sequence the genomes of 4,500 species along the French coast in mainland and overseas France. The 8-year programme will sample marine biodiversity under the coordination of the MNHN through expeditions and with the help of marine stations. Genomes will be sequenced and assembled at the Genoscope under the coordination of France Génomique, and the data will be managed and analysed under the coordination of the Institut Français de BioInformatique (as part of the BYTE-SEA project). Pilot projects coordinated by the ANR will enable the French scientific community to exploit this massive data in the context of the analysis and synthesis of marine molecules, the ecology of invasive species and innovation.

Tasks:

The BYTE-SEA Chief Data Scientist will be responsible for managing the multi-modal data collected (genomics, diversity, sampling, imaging, etc.), identifying it, integrating it into the analysis processes, making it interoperable with existing reference databases and making it available to the public (scientific or general).

Main activities:

  • Participate in defining the study and data collection plan best suited to the problem posed.
  • Designing and developing data management systems and information tools for collecting, structuring, storing and linking project data.
  • Study and implement the best technical solutions for managing large volumes of data in accordance with F.A.I.R. principles and institutional guidelines.
  • Independently evaluate, select, adapt and implement database management methods.
  • Acting as the team’s reference on DBMS (Database Management Systems) and the associated languages/tools (MySQL, phpMyAdmin).
  • Leading workshops to express the needs of the various PEPR stakeholders involved in the WHELL-SEA, DIVE-SEA, SEQ-SEA and BYTE-SEEA projects.
  • Communicate with the programme’s other database referenst within the WHEEL-SEA, DIVE-SEA and SEQ-SEA targeted projects.
  • Write the requirements specification.
  • Participate in the dissemination and promotion of technological results and achievements in the form of reports, publications and oral presentations.
  • Internal and external training on the tools and implementation of the interfacs developed.
  • Ensuring and organising scientific and technological monitoring in its field of activity.

Knowledge:

  • Data collection, analysis and processing (genomic and/or biodiversity and/or sampling).
  • Mastering the tools and concepts involved in the management, interoperability and opening up of multimodal data.
  • Proficiency in a programming or data processing language (Python, R) in a Unix/Linux environment.
  • Environment and professional networks.
  • English language: B2 to C1 (Common European Framework of Reference for Languages).

Operational skills:

  • Skills in DBMS (Database Management Systems) and associated database management languages/tools (MySQL, phpMyAdmin).
  • Guaranteeing the quality and relevance of analysis tools and results.
  • Implementing a quality approach.
  • Designing teaching and communication tools.
  • Scientific rigour, organisational skills.
  • Good interpersonal skills and a taste for teamwork.

Medium-term development factors:

  • Increasing complexity of data to be processed and analysis tools.
  • Development of means and methods for data access, presentation and visualisation.

Impact on job types:

  • Technical monitoring of developments in analysis tools
  • Diversification of the types of data collected and interoperated

Special conditions of exercise:

  • The position is based at the Roscoff Biological Station. The host team, the ABiMS platform (http://abims.sb-roscoff.fr), comprises 14 engineers. 
  • Full-time position.
  • Working hours adapted to the organisation of the work.
  • Possibility of teleworking days.
  • Essential interaction with all contacts located in different regions of France. The candidate will work closely with the BYTE-SEA project coordinator (Erwan CORRE , head of the ABiMS platform), and will interact with the platform engineers and with the partners involved in the programme (IFREMER-SeBiMer (PlouzanĂ©), GenOuest (Rennes) , IFBcore (Paris) , ENS Ulm (Paris) , MNHN (Paris) and Genoscope (Evry)).
  • Regular travel to the various sites of the project partners.

Regulatory diploma required:

  • PhD, engineering degree with 2 years’ experience
  • Desired area(s) of training: bioinformatics, biology, oceanography, ecology
ATLASea Recruitment: Biological data analysis engineer (M/W) [CLOSED]
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