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The ARTbio bioinformatics platform at the Institut de Biologie Paris Seine

roadmap and settings

Galaxy Day

November 19th, 2015

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An Open Science bioinformatics facility at the IBPS

Goals

  • Involve Biologists in their analyses by providing them with [A]ccessible tools and workflows in Galaxy
  • GaaS - Galaxy as a Service

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  • Promote [R]eproducibility and [T]ransparency in Computational Biology
  • Give motivation for using workflows and recording all computational steps
  • Adapt or develop computational tools to the Galaxy framework

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  • Experiment AGILE organisation
  • Continuous Integration & automated testing
  • Minimal infrastructure
  • Containers & automatic deployment

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Analyses Services

Work Modes

  1. Autonomous Users, Free:
    • http://mississippi.fr
    • Maintenance of Galaxy, Tool installation bug fixes, usage advices
    • Through the Galaxy web interface and ARTbio trello connection
  2. Service (Acknowledgments in publications)

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  • Project accompaniment, collaboration mode (Authorship)
  • Specific expertise in Small RNA biology, epigenomics, virus genomics
  • ARTbio Hub for Users: http://artbio.fr
  • Galaxy infrastructure
  • Public instance: http://mississippi.fr
  • UPMC instance http://lbcd41.snv.jussieu.fr
  • On purpose Galaxy instance: ARTimed project with the Hopitâl Saint-Antoine

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Delivery

  • Personalized Trello Board for service or project management, shared with our users

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Delivery

  • Personalized Trello Board for service or project management, shared with our users
  • Galaxy Pages to summarize and report on performed analyses

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Delivery

  • Personalized Trello Board for service or project management
  • Galaxy Pages to summarize and report on performed analyses
  • Workflows and tools deposited in public repositories and/or Toolshed, to give visibility and accessibility to the analyses

Galaxy-Workflow-Workflow____Test_case_Noravirus_van_mierlo_et_al.ga

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Delivery

  • Personalized Trello Board for service or project management
  • Galaxy Pages
  • Workflows and tools deposited in public repositories and/or Toolshed
  • In development: Automatic deployment of the Galaxy environment used for the project (with input data, tools & workflows)

ansible-playbook -i "localhost," galaxy.yml -vvvv

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Tool development - Continuous integration

Local tool development

(Planemo Testing)

GitHub

https://github.com/ARTbio/tools-artbio

Private

Automatic Testing & Push

Pull Request

local toolshed

public toolsheds

Galaxy Server

(private)

Galaxy Server

(public)

Jenkins

Planemo

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Tool development - Example

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Tool development - Example

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Tool development - Example

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Automated deployment

  • to easily adapt to cloud / remote infrastructures
  • The long-term target is to have one Galaxy instance by Analysis Project
  • This is also the strategy we envision to preserve analyses

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The team

Marius van den Beek Fabio Rocha Jimenez Vieira Christophe Antoniewski

Thanks to François Delhommeau at the hôpital Saint-Antoine (IUIS ARTimed project)

PLASTiSiPi