Operational Engineer for Tara-Pacific Data
The Université Côte d’Azur (UCA) is a Community of Universities and Higher Education Institutions (ComUE) created in 2015 with a research mission and consists of 13 members and more than 30,000 students. The UCA unites the University of Nice Sophia Antipolis, public scientific and technological institutions, and other organizations contributing to higher education and research in the Alpes-Maritimes department. A winner of a grant from the French Initiative of Excellence (IDEX) program with its UCAJEDI project, the UCA aims to increase its visibility and national and international stature. The long-term goal is to be counted among the top ten French universities comparable to the best in the world.
The UCAJEDI project is steered by a committee consisting of the President of the UCA and four Program Directors (Education, Research, Innovation, and International). The President is supported with UCAJEDI by an executive assistant (DEA), and each Program Director has an Operational Program Director (DOP).
To encourage and structure transdisciplinary exchanges in research, UCAJEDI relies on the Center of Modeling, Simulation, and Interactions (MSI), which provides both a forum for as well as related scientific and technical expertise in modeling and simulation in various scientific areas.
The MSI is recruiting an Engineer with expertise in the processing of big data in support of a project led by the Institute of Research on Cancer and Aging in Nice (IRCAN, Pasteur medical campus) as part of the Tara-Pacific expedition and its collaboration with the Tara Foundation. Reporting to the head of the MSI, the Engineer will work under the direction of the head of IRCAN and perform analyses of complex data (eco/morpho/genomic) from the Tara-Pacific expedition. To accomplish this, he/she will establish and develop collaborations between UCA researchers in data science and automatic image recognition as well as teams from IRCAN’s Tara-Pacific Consortium, the Scientific Center of Monaco (CSM), and the Villefranche Oceanographic Observatory.
The work on the Tara-Pacific project developed at the MSI is part of the UCA’s wish to provide its expertise in data science, biology, oceanography, and genomics to support the Tara-Pacific expedition, which is governed by the consortium
agreement signed by all of its partner institutions. Specifically, the work involves the automatic acquisition of morphological data from approximately 10,000 photographs of samples of coral colonies taken during the expedition. It further entails extracting and compiling environmental data from the expedition and linking them with the molecular (stress markers and telomeres) and multi-omic (genomic, transcriptomic, metabolic, and taxonomic) data generated by the Consortium. In particular, the development of state-of-the-art techniques to recognize a region of interest, process an image with a complex background, and handle big data will be required. The Engineer will coordinate his/her methodology and objectives with all partner institutions of the Tara Consortium and should also share his/her expertise with both MSI engineers and the UCA’s scientific community. For these tasks, like all MSI engineers, 20% of the Engineer’s time will be spent at the MSI in Sophia Antipolis for training programs and gatherings.
Main duties By consulting with MSI engineers and cooperating on research projects, the Engineer will: 1. Develop techniques for both the automatic processing (recognition of regions of interest, extraction of various data from those regions) and automatic annotation of images of coral colonies generated during the Tara-Pacific expedition;2. Help researchers of the Tara Consortium analyze and interpret the information extracted from these images and make all data available to the Consortium; 3. Extract, aggregate, and compile the environmental data from the sampling sites of the Tara-Pacific expedition and make them available to the Tara Consortium; 4. Develop tools to facilitate the linking of all data generated by the Tara Consortium; 5. Integrate the various data generated by the Consortium’s member institutions so as to find correlations and establish biological models; 6. Regularly interact with the main institutions of the Tara Consortium. These discussions will aim to: (1) coordinate the objectives and technical solutions and (2) share expertise and help Consortium members solve their problems with the analysis of big data; 7. Present results during the biannual meetings of the Tara Consortium; 8. Participate in and provide training sessions to maintain the MSI’s advanced expertise in data science for biology, multi-omic data, environmental science, and image recognition.
Candidate profile/Required qualifications
• Ph.D.-level data scientist; • Required knowledge (master’s level or equivalent) of: o information systems and databases (mining and management), o object-oriented programming (Java, C++, or Scala), o Python and/or R;
• Experience and deep understanding of at least three of the following areas: o information systems and databases, data mining, o image analysis, recognition of a region of interest, and automatic image processing, o bioinformatics, o data science and learning;
• General knowledge of: o biology, marine biology, o genomics, o software development (architecture, compilation, etc.);
• Interest in marine biology research; • Interpersonal skills and adaptability; • Project management; • English proficiency.
Job location and hours
80 % at IRCAN (Faculty of Medicine, Pasteur campus, Nice) and 20 % at the MSI (Sophia Antipolis) – 35 hr/week
Applicants should send a motivation letter and CV before the end of July 2018 to: Prof. Eric Gilson, Eric.Gilson@unice.fr, Director of IRCAN, Anne Khoury, email@example.com, Deputy Executive Director, Université Côte d’Azur, Prof. Elisabeth Pecou, Elisabeth.Pecou@unice.fr, Laboratoire Jean-Alexandre Dieudonné and MSI.
Renewable, fixed-term contract (CDD) of 1 year or on secondment. Provisional start date: from 1 September 2018