CEA-Genoscope, a dynamic non-profit scientific research organization dedicated to environmental genomics science, is seeking a talented and highly motivated bioinformatics software engineer: Research Engineer, IR CNRS permanent position in the LABGeM team UMR8030.
About us / context
Rapid technological advances in genomics have transformed modern biology. From its inception, Genoscope has been at the forefront of large-scale sequence-based science. Today, our institute performs biological and bioengineering research with applications in environment, healthcare and alternative energy. The Genoscope department of CEA’s Genome Institute harbors a multidisciplinary team of approximately 120 staff, postdocs and technologists with expertise in genomics, bioinformatics, microbiology and biochemistry.
In this context, the Laboratory of Bioinformatics analyses in Genomics and Metabolism (LABGeM) develops and applies methods to infer genomic knowledge through computational analysis and integration of data generated by high-throughput projects. We are particularly interested in system biology through the exploration of microbial metabolism with applications in environmental biology and human health. Our research focuses on the development of original methods for the prediction of novel enzymatic activities and for the discovery of new metabolic pathways. The foundation of these methods relies on the quality of the annotation of gene functions. Since more than 10 years, our team is developing a deep expertise in annotation and comparative genomics of microbial genomes through the MicroScope platform. This system offers to the international community of microbiologists an integrated and collaborative environment for the annotation, exploration and expertise of genomic data (>3,300 users and 2,200 human-expertized annotations a month in 2016).
For some years now, the MicroScope platform is dealing with an increasing demand of genome integration (8 genomes a day in 2016), together with transcriptomics data and re-sequencing of evolved bacterial strains. Several important technological challenges should be addressed to efficiently annotate, compare, and manage this genomics data. The various MicroScope components (analysis workflows, database and graphical interfaces) are concerned by these evolutions and should be part of a strategy for opening up the platform, i.e., the deployment of MicroScope on different IT infrastructures, together with setting up an environment for collaborative developments.
Objectives
The recruited research engineer should:
- Drive and coordinate the technological developments of the MicroScope platform
- Propose and implement innovative solutions (data model, algorithms, workflows) to address the technological challenges raised by the annotation and comparison of thousand genomes
- Take part in the development of new bioinformatics methods in collaboration with researchers of the team
- Find and validate IT solutions in collaboration with the system and network team.
Medium-term objective: the recruited engineer will be responsible for the software developments of the MicroScope platform (team of ~5 bioinformatics engineers).
Qualification
Graduate Engineer or Ph.D. Degree in computer sciences/bio-informatics with skills in the following domains:
- Coordination and management of software developments
- Object-oriented programming and multitier architectures: databases, production system (workflows/HTC), Web GUI
- Linux/Unix OS and scripting language
- Knowledge in Cloud solutions (ideally)
- Knowledge in bioinformatics tools and algorithms in genomics (ideally)
Present MicroScope technologies: Linux, Python, Java (Spring, Hibernate), SGDB (MySQL), REST / WUI (HTML5, CSS3, jQuery, PHP)
Location
The Institute is located near Paris (France) on the stunning of Evry Genopole Campus, which is part of the Paris-Saclay federal research university. This growing and dynamic site is an excellent environment in which to work and collaborate with researchers on campus and around the world, and benefit from cross-fertilization of ideas.
Calendar for research engineer external competitions at CNRS:
- Application deadline: the 28th of June 2017
- Pre-selection (short-list of qualified candidates): summer 2017
- Interview of candidates: early in October 2017
- Selection results: November 2017
- Start: 1st December 2017
To apply: http://www.dgdr.cnrs.fr/drhita/concoursita
Competition n°42: job advertisement (in french)
For more information on the position: please contact Claudine Médigue (cmedigue@genoscope.cns.fr) and David Vallenet (vallenet@genoscope.cns.fr).