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IJM
BioInfo Club

This club brings together scientists, from the Institut Jacques Monod and from neighboring research institutes, who want to develop their bioinformatics skills in analyzing high-troughput sequencing data. We generally meet every Friday between 10 and 11am.

Please bring your laptop. It can be Linux, Mac or Windows. There is no internet in the room so please download the required software before (if necessary). The instructor will provide all the required information.

If you want to be in the mailing list, please e-mail Virginie : orgogozo@ijm.univ-paris-diderot.....

Past courses:
2011-2012-2013 schedule past presentations

Useful links

Useful tips



2013 Schedule

Friday Jan 10, 10:00-11:00, room RB18B (course #47)
Introduction to statistics (1) (instructor = Gaëlle Lelandais, IJM)

Friday Jan 24, 10:00-11:00, room RB18B (course #47)
Introduction to statistics (2) (instructor = Gaëlle Lelandais, IJM)

Friday Jan 31, 10:00-11:00, room RB18B (course #47)
Introduction to statistics (3) (instructor = Gaëlle Lelandais, IJM)




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Planned courses:
Using BLAST in a correct manner (instructor = Virginie Orgogozo)
WormBase and FlyBase for every biologists (instructors = Lionel Pintard and Virginie Orgogozo)


We are looking for volunteers to present the following topics (in random order):
biopython, Ensembl, php and mysql, git, vim, cron, RNAseq, UCSC genome browser, IGV, RADseq and variants
or any paper that you would like to share

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MEMMO for Ubuntu users

In order to script with the shell and to programm, you need the following:
(a) your .bashrc file should contain a PATH to the scripts folder. For example:
export PATH="$PATH:${HOME}/scripts"
then launch a new terminal window and write:
echo $PATH
The scripts folder should be in the list.

(b) include a line such as:
#! /bin/bash
or:
#! /bin/env python
at the begining of the text file containing your script

(c) give permissions for the script file to be executed:
chmod u+x script-file-name.sh


Other interesting things to add in the .bashrc file:
alias cdp='cd ~/pcfd/sandbox'
alias cx='chmod u+x'
function premierepage() { pdftk $1 cat 2-end output $2 ;}
function trouve() { locate -i $1 | grep virginie | more ;}
set -o noclobber

or better: put them in a .bashrc_Virginie file and add the following line in the .bashrc file:
source /home/virginie/.bashrc_Virginie