Migale Bioinformatics Facility
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).