A nice collaborative work highlighted on the INRAE website
Migale Bioinformatics Facility
We provide several services for scientists to deal with life sciences data
Our Services
Migale, one of the Collective Scientific Infrastructure of INRAE, is part of the BioinfOmics Research Infrastructure of INRAE for bioinformatics. It is also a member of IFB (Institut Français de Bioinformatique), the French bioinformatics infrastructure and associated facility of France Génomique, the French genomic infrastructure for which we contribute to support different developments in bioinformatics.
A free account gives you access to work and save directories for your data, and access to the computer farm for your analyses.
The cluster farm is composed of about a thousand cores organized in different queues. We use the Sun Grid Engine queuing system for managing jobs.
You have a free access to our Galaxy server. Galaxy allows non-bioinformaticians to easily run tools without technical knowledges.
Command line tools, R packages and Galaxy wrappers are available on request and accessible to all migale authenticated users.
We provide an access to a large set of public biological databanks including whole genomes, nucleic and proteic sequences and other resources. They are updated automatically with BioMaJ or upon request.
We write tutorials to help you get familiar with tools, best practices, languages, etc.
Each year, we offer our "Bioinformatics by practicing" cycle. This cycle covers a broad spectrum of bioinformatics. The modules mix theoretical part and practical work.
We answer to the most common questions regarding the technical difficulties you can go through on our infrastructure.
Find all the ways to contact us.
Planned shutdown of all services from September 27th to September 30th 2021
Access to the Migale bioinformatics facility will be unavailable from Monday, September 27th to Thursday, September 30th 2021.
Expected duration of interruption
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Start: 27/09/2021 8am
Unavailability: 27/09/2021 12pm
End (estimation) : 30/09/2021 6pm
Users affected by the incident
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Update R
R 4.1.0 is now the default version on migale
3.13
CHANGES IN R 4.1.0
FUTURE DIRECTIONS
-
It is planned that the 4.1.x series will be the last to support 32-bit Windows, with prod
Two engineering positions open to mobility
[English below]
Dans le cadre de la campagne de mobilité INRAE qui vient d’être ouverte, la plateforme de bioinformatique Migale affiche deux profils de postes pour renforcer l’équipe en charge du service d’analyse de données.
- Un•e ingénieur•e d’études bioinformaticien en méta-omiques [Profil complet]
Tutorial for an initiation to R
A new tutorial is available in our dedicated website: https://tutorials.migale.inra.fr/posts/initiation-r/
This post aims to help you start with R: data structures and their manipulation, the main features of the language and how to make very simple figures.Planned shutdown of Web service
Access to Migale web servers (Topaze, Tomcat server ...) will be unavailable on Thursday, July 15.
Expected duration of interruption
Start: 07/15/2021 8am
End (estimation) : 07/15/2021 1pm
Users affected by the incident
- All users of the platform.
Cause
Maintenance operations on the virtualization infrastructure.
Planned shutdown of Shiny apps
Access to the Shiny apps will not be possible on June 16th.
Expected duration of interruption
Start: 16/06/2021 2pm
End (estimation) : 16/06/2021 6pm
Users affected by the incident
- Users of the Shiny apps
Cause
Update ShinyProxy to version 2.5.0
Thank you for your understanding
FROGS 3.2 now available
The last available release has been installed on migale server and on Galaxy instance.
Major changes have been made since version 3.1. Some options have changed, and new tools are now available (details below).
SOP for 16S and ITS data anlysis are available at http://frogs.toulouse.inra.fr/
FROGS v3.1 is always available but is no more recommended. Galaxy users, be careful to choose the appropriate tools (section labels are named FROGS 3.2 or FROGS 3.1)
Tutorial for using FROGS on the command line
A tutorial dedicated to the use of FROGS using its command line interface on the migale server is proposed here : https://tutorials.migale.inrae.fr/posts/frogs-16s/. From a public dataset (Illumina 16S V3-V4), you will be able to run the full FROGS pipeline to create a BIOM file containing the OTUs, their abundances and their taxonomic affiliations.