Under construction. The galaxy.prabi.fr service will be soon available.
Many "public" galaxy instances have been installed all around the world (>50). See here for an exhaustive list of registered instances.
The galaxy.prabi.fr is the PRABI’s galaxy local instance and will be soon available for registered users either for bioinformatic tools testing (open for all users with quota) or for small data analysis project (actually only for users belonging to the FRBioenvis, UCBL).
The aim of the galaxy.prabi.fr instance is to provide to the research teams (biologists and bioinformaticians) working within the perimeter of the PRABI a unique gateway for :
The PRABI will also provide access to its own toolshed repository : [toolshed.prabi.fr>toolshed.prabi.fr] - to share "home made" bioinformatics softwares with the galaxy users and developpers community.
The galaxy.prabi.fr is jointly funded by the PRABI/PRABI-AMSB(UCBL), the LBBE (UMR5558), the FR Bioenvis and the LECA(UMR5553).
A mailing list is also available forthe french users and developpers community : france-galaxy. The IFB-galaxy working group federates galaxy action launched by the french bioinformatics platforms and provides information concerning training courses, events and documentation for galaxy administrators and developpers.
Morning sessions – 9:00 to 12:30
Session I : Galaxy tour
In this session we will present some applications of the Galaxy workflow manager to analyse NGS data.
Tutor : Vincent Navratil (PRABI, Université Claude Bernard – Lyon 1).
Session II : KisSplice
The session will consist in a short tour of the possibilities of using KisSplice to analyse RNA-seq data with or without a reference genome. We will briefly explain what are the advantages of a local transcriptome assembler, w.r.t. both to global transcriptome assemblers (like Trinity or Oases), and to traditional mapping approaches (TopHat/Cufflinks...).
A hands-on session will then give details on how to analyse an RNA-seq dataset from the ENCODE project. We will focus on the SKNSH cell line, with and without retinoic acid stimulation. For practical reasons, we will restrict the analysis to only 10M reads in each replicate of each condition. Starting from the fastq files, we will use KisSplice to identify and quantify variants in both datasets. At the end of this step, a list of SNPs, indels and Alternative Splicing events is produced, with a quantification of each variant in each condition.
We will then use our newly developed R package KissDE to test if a variant is specific to a condition. Here we will focus on splice variants specific to the retinoic acid stimulation.
Finally, we will use our newly developed Python package KisSplice2RefGenome to annotate each event and assign a gene name to each candidate. This last step obviously cannot be used in the case of a non model species where no reference genome is available.
Tutor : Vincent Lacroix (LBBE, Université Claude Bernard – Lyon 1).
An .ova virtual machine is available to reproduce the kissplice and kissDE demo on galaxy.
Step 0 : Install the Oracle VirtualBox onto your OS.
Step 1 : Download the galaxy built-in VM file from the following URL galaxy-embnet.ova
Step 2 : Load the .ova format into VirtualBox by double click on the file and start the VM. Then use galaxy:galaxy123 as login:password to log into the linux system.
Step 3 : Start the galaxy server by double-clicking on the starting file on the desktop. The start iceweasle or firefox web navigator then enter the http://locahost:8080 URL to access to your own instance of galaxy running kissplice and kissDE.
Step 4 : Register the Login with your [login :password].
Acknowledgments : Stephane Delmotte, Dominique Guyot, Camille Marchet, Clothilde Deschamps, Christine Oger, Philippe Veber, Bruno Spataro.