Post-doctoral computer developer (F/H): Design and production of a multi-scale digital atlas of animal embryonic development

Posted on 4 August 2021

Context:

The CRBM team “Transcriptional control of chordate morphogenesis” combines advanced approaches in life microscopy, experimental embryology, genomics and computer science to decipher the logic that governs the embryonic development of a small marine animal, the ascidian Phallusia mammillata (recent references at the bottom of the page). The team is made up of biologists and computer scientists and has the necessary computer resources and collaborations to carry out the project.

Our recent results and the tools we developed (1, 2, 3) make it possible to envisage the construction of numerical models that combine the fundamental physical and chemical principles governing cell function with quantitative descriptions, at the scale of the single cell, of the biochemical and spatio-temporal characteristics of the system. The challenge is to identify the theoretical foundations of biological complexity.

Mission:

As part of a project funded by the University of Montpellier, we are seeking to recruit a post-doctoral fellow in computer science who will be responsible for the development of an atlas integrating molecular (multi-omics), anatomical (live cell imaging, connectomics) and mechanical (forces and tensions) descriptions of embryonic development. The atlas will provide both programmatic (APIs) and human (GUI) access to the data, and will be strongly interacting with the MorphoNet

skills and qualifications:

  • Knowledge of the Linux operating system
  • Advanced knowledge of programming and database query languages: PHP, Python, JavaScript, SQL, Cypher, … 
  • In-depth of XML, JSON, Owl formats
  • Knowledge of network protocols: Http/Https and APIs (REST, OpenAPI, Swagger)
  • Advanced knowledge of SQL (PostgreSQL, …) and NoSQL (Neo4J, …) databases
  • Knowledge of production methods, continuous integration and workflow management
  • Knowledge of application design, development and deployment tools
  • Routine use of versioning tools (Git)
  • Knowledge of FAIR principles
  • Strong motivation to apply IT skills to the investigation of the logic of life. Basic knowledge of biology would be appreciated, but is not a prerequisite.

Know-how :

  • Knowledge of good project management practices: needs analysis, writing technical specifications, conducting meetings, monitoring tasks and schedules
  • Ability to express yourself in English (written/oral)
  • Ability to communicate effectively in an international environment with a variety of interlocutors (biologists, IT developers, system administrators, bioinformaticians)

Soft skills :

  • Good team worker        
  • Good interpersonal skills
  • Personal commitment and work ethic
  • Ability to think ahead
  • Reactivity
  • Good organisational skills, autonomy and rigour 

Conditions:

The position is for an initial period of one year, which may be extended for a further year. The position will involve numerous interactions with computer scientist collaborators within the team, in France and abroad. A good command of English is essential.

Application: send a CV, a motivation letter, and the names of two academic referees to Patrick Lemaire (patrick.lemaire@crbm.cnrs.fr) and Christelle Dantec (christelle.dantec@crbm.cnrs.fr) before September 5th.

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