Orchestration of projects on a core bioinformatics facility

From primary to secondary data : analytics fluxes on Migale

Valentin Loux
valentin.loux@inrae.fr
Olivier Rué
olivier.rue@inrae.fr
Migale team
help-migale@inrae.fr

July 2, 2026

Migale team

Missions

The Migale Bioinformatics facility proposes different types of services and resources to its users:

  • Access to computing and storage resources
  • Access to training modules, tutorials, and user support
  • Access to informatics and bioinformatics development service
  • Access to data analysis service

A litlle bit of Migale history

Late 2015 … new kids arrives in town

Did this ever happen to you ?

How to Manage Project (and Data) Flows?

What We Wanted to Avoid:

  • Endless projects
  • Untracked data, metadata, and results (sent via email)
  • Tunnel effect on projects and endless review meetings

Our Principles:

  • Transparency
  • Traceability
  • Respecting deadlines to enable the management of multiple projects
  • Analysis projects and reports viewed as means for training and empowerment

Analysis process ISO9001 certification

Request and deadlines management:

  • A clear and formalized request (web form, feasability meeting)
  • A clear lifecycle for each project
    • Preparation: between request and collection of all useful data
    • Analysis: with a mutually agreed-upon time limit
    • Post-analysis: no time limit (beyond our control)

Organization :

  • A centralized workspace for reports : accessible to all team members, secure, with high availibility
    • Git Repositories: The ideal solution for secure, version-controlled collaboration
    • a project = a directory in a private repo for analysis
    • Resource centralization (bibliography, documentation, etc.)
    • Template system to streamline writing and code reuse
    • Template reports
      • Structured metatdata for project life : beginning, end, authors, contributors, status, directories, …
      • Data (raw, backup) and Metadata explictly linked in the report

Quarto + CI/CD

Quarto to build reports…

…hosted on a Gitlab repository…

…and easily published on the web!



Data management

Our project management solution

“Manage, publish, and track analysis projects in one place”

  • Quarto repository
  • Core entities and relationships
  • Python implementation for automating manual file entry

Reports & metrics

Conclusions

Quality driven organization to manage analysis projects :

  • A structured process with tooling to easily manage projects
  • Project metada structured allowing esay reports and follow-up
  • Modular , easy to install
  • Based on an easy to share and learn technology stack (Git, Gitlab pages, CI/CD, Quarto…)
  • From ~ one to 6 people using it in the team. Other teams or facility interested

First public release on Migale gitlab page

Perspectives

What’s next :

  • Ontologies & referentials everywhere:
    • ROR
    • PROV-O
    • EDAM
    • …
  • Experimental Metadata & Data:
    • Really collect , harmonize and submit early
    • 🎉 madbot 🎉