Migale Bioinformatics Facility
[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]
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.
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
Cause
Maintenance operations on the virtualization infrastructure.
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
Cause
Update ShinyProxy to version 2.5.0
Thank you for your understanding
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)
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.
Access to the Galaxy instance will be unavailable from January 29th to February 2nd 2021.
Expected duration of interruption
Start: 29/01/2021 6pm
End (estimation) : 03/02/2021 8am
Users affected by the incident
Cause
Update to version 20.09
Thank you for your understanding
The 2021 training cycle is openYou can consult the program and the schedule here: https://migale.inra.fr/trainings
A new tutorial (only in french for now) about Migale usage :
- Access
- Storage
- Databanks
- Cluster usage , R
- Galaxy portal
We welcome all comments, by mail or through our annual satisfaction survey
Translation coming soon !
The Migale bioinformatics facility give acces to its users to a R environment (version 4.02) with more than 1000 packages installed.
For your development and prototyping activities with R, we now give you access to the RStudio development environment through a web interface at this adress :
https://rstudio.migale.inrae.fr
This RStudio is configured to use the R from Migale. It is linked to your work directories on the platform.
Mahendra and Olivier were sollicited by Valérie Daugé at MICALIS institute to analyze feces microbiota (V3-V4 regions of the 16S rDNA gene): α- and β-diversities and differential abundance analyses of OTUs.
Biological results:
CHANGES IN R 4.0.2
UTILITIES:
* R CMD check skips vignette re-building (with a warning) if the VignetteBuilder package(s) are not available.
BUG FIXES:
* Paths with non-ASCII characters caused problems for package loading on Windows PR#17833.
* Using tcltk widgets no longer crashes R on Windows.
* source(*, echo=TRUE) no longer fails in some cases with empty lines; reported by Bill Dunlap in PR#17769.
* on.exit() now correctly matches named arguments, thanks to PR#1
Access to the Migale bioinformatics facility will be unavailable from September 29th to October 1st 2020.
Expected duration of interruption
Start: 29/09/2020 10am
End (estimation) : 01/10/2020 2pm
Users affected by the incident
A collaboration with Ecole Nationale Vétérinaire d’Alfort and INRAE teams led to the publication of this article. We showed that contaminant OTUs from sample laboratory processing steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples. You can access this article here.
From now on and as far as possible, we install our tools under the "conda" environment.
This allows us to avoid conflicts between the different dependencies of each tool.
We will gradually remove the "classic" "old" installations to keep only the "conda" versions. Beginning June 19th, all tools will be available only via Conda.
Help on how to use the tools under "conda" can be found here: https://migale.inra.fr/faq#migale-condalist
Due to recent developments in the COVID-19 epidemic, all facility staff is now teleworking. Some of us with children at home. We are commited to keep the platform running and answer to your requests as quickly as possible. Please excuse in advance any delay that may occur.
The facility shutdown initially planned at the end of the month (March 30th) is postponed at an unknown date.
A collaboration with the MICALIS institute and NBO team has led to the publication of an article entitled: "First step of odorant detection in the olfactory epithelium and olfactory preferences differ according to the microbiota profile in mice"
The highlights are:
You can consult the program and the schedule here: https://migale.inra.fr/trainings
From December 2 to 6, Mahendra Mariadassou, Cédric Midoux and Olivier Rué went to Roscoff to give a training course dedicated to the analysis of amplicon metagenomic data. This training was jointly organised by IFREMER and the ABIMS bioinformatics platform.
The 25 participants were trained in FROGS (bioinformatics and bistatistics) and dada2 under Galaxy environment.
Various presentations on metabarcoding were given by Olivier Chapleur (IRSTEA, Antony), Raffaele Siano (IFREMER, Brest), Marjorie Couton (Biological Station, Roscoff) and Angélique Gobet (IFREMER, Palavas).
A new article for the ProteoRE project (Proteomics Research Environment) with our colleagues from the EdyP laboratory in Grenoble and with an IFB funding.
In this work we propose a Galaxy workflow to select blood biomarkers for early cancer diagnosis in the case of pancreatic cancer.
Migale's 20th newsletter, Migazette, is now available.
The new Galaxy portal is now accessible at galaxy.migale.inra.fr. You can now connect to it with your migale account.
This migration allowed us to update the configuration of the portal and thus follow the new best practices recommended by the Galaxy community. This revision concerns the configuration of web services, the automatic installation of tools and their dependencies (via bioconda).
Mouhamadou Ba has just been recruited as a permanent engineer in the Migale platfom. He joined the team on October 2019 to develop text-mining services for bioinformatics.
A short self-introduction of Ba
Due to the current health crisis, the planned shutdown from 30 March to 2 April has been postponed indefinitely.
Thank you for your understanding,
Access to the Migale bioinformatics facility will be unavailable from Monday 30 March to Thursday 2 April 2020.
Expected duration of interruption
After more than 18 months without any system administrator, we are very pleased to welcome Damien Berry from January 2020. He was previously system administrator in the INRAE MIAT laboratory in Toulouse. His first task will consist in reorganizing the centralized storage of Migale.
Welcome Damien !
Migale members are involved in the DUbii!
Florilege is a database of habitats, phenotypes and uses of food microbe flora. It aims to gather, in a unified representation, public information on food microbes with a focus on positive flora (microorganisms involved in transformation, bioconservation or probiotics).
