Software Engineer – 8 months contract – Institut Pasteur

EVENT : C3BI Available position

Software Engineer – 8 months contract – Institut Pasteur


We are hiring a software engineer for a 8 months period. This person will contribute to two different software development projects:

  • software development to enable the support of CWL [1] tools and workflows on the Galaxy platform
  • development of the next version of MacSyFinder [2], a software to model and search for macromolecular systems in bacterial genomes.
  • Masters degree in computer science, software engineering, or bioinformatics,
  • Good knowledge of the Python programming language and Object Oriented Programming,
  • Knowledge of data serialization formats such as XML, JSON and/or YAML,
  • Working knowledge of HTTP APIs (development and usage),
  • Familiarity with bioinformatics tools and data,
  • Familiarity with integrated environments such as Galaxy (
  • Familiarity with concurrent versioning system (git) would be a plus
The successful candidate will participate in two different projects:
  • a collaboration to unify the annotation of eukaryotic transcriptomes from MMETSP and Tara Oceans Project through interoperable workflows. The goal of this project will be to work on enabling the execution of CWL workflows in Galaxy, in close collaboration with international collaborators from ELIXIR and the Galaxy community.
  • the MacSyFinder project: MacSyFinder is an open source program to model and detect macromolecular systems and molecular pathways from protein sequence datasets ( MacsyFinder has now been used by bioinformaticians for several years and will be updated:
  • to ensure its technical sustainability
  • to make it more intuitive of use by biologists
  • to add new features

The new version of MacSyFinder is developed in collaboration by two research laboratories: the Microbial Evolutionary Genomics group at the Pasteur Institute ( and the GEM group at the TIMC-IMAG department (

On the first project, the main mission is to contribute to the development of the Galaxy platform to enable the direct execution of CWL tools and workflows. On the second project, the mission of the candidate will be to participate to the design and implementation of the new MacSyfinder version, through the implementation of new features, the creation of unit tests, the migration from python 2 to python 3, etc.

He/she will be affiliated to the “Bioinformatics Hub” and the “Microbial Evolutionary Genomics” research laboratory of the C3BI at the Institut Pasteur, and will work with the same core team of engineers that also works on both projects.

Please send your application (resume, supporting statement) by email to, and

[1] Amstutz P, Crusoe M R, Tijanić N, Chapman B, Chilton J, Heuer M, Kartashov A, Leehr D, Ménager H, Nedeljkovich M, Scales M, Soiland-Reyes S, Stojanovic L. Common Workflow Language v1.0. Figshare. 2016
[2] Abby, S. S., Neron, B., Menager, H., Touchon, M. & Rocha, E. P. MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems. PLoS ONE 9, e110726 (2014).