In 2011 and 2012, we followed the chapters from the book Practical computings for biologists and manipulated a set of real Chip-seq data.


2011

1rst course = Friday Oct 14, 15:30-16:30, room RB18B
Manipulating text files with regular expressions (1) (instructor = Virginie Orgogozo)

2nd course = Friday Oct 21, 15:30-16:30, room RB18B
Manipulating text files with regular expressions (2) (instructor = Virginie Orgogozo)

3rd course = Friday Oct 28, 15:30-16:30, room RB18B
The shell and command-line operations (instructor = Michael Lang)

4th course = Friday Nov 4, 15:30-16:30, room RB18B
Handling text in the shell (instructor = Amir Yassin)

5th course = Friday Nov 18, 15:30-16:30, room RB18B
Scripting with the shell (instructor = Guillaume Balavoine, no summary available yet)

6th course = Friday Nov 25, 10:00-11:00, room RB18B
Elements for Programming - chapter 7 (instructor = Michael Lang)

7th course = Friday Dec 2, 10:00-11:00, room RB18B
Begining Python programming (instructor = Peter Brooks)

8th course = Friday Dec 9, 10:00-11:00, room RB18B
Decisions and Loops (instructor = Virginie Orgogozo)

9th course = Friday Dec 16, 10:00-11:00, room RB18B
Lists revisited  (instructor = Fabien Duveau) = end of chapter 9 (p159-172)



2012

10th course = Friday Jan 6, 10:00-11:00, room RB18B
Reading and writing files (1) (instructor = Virginie Orgogozo)

11th course = Friday Jan 13, 10:00-11:00, room RB18B
Reading and writing files (2) (instructor = Peter Brooks) = end of chapter 10 (p184-199)

12th course = Friday Jan 20, 10:00-11:00, room RB18B
Processing files (instructor = Peter Brooks) = chapter 11

13th course = Friday Jan 27, 10:00-11:00, room RB18B
Exercices on processing files (instructors = Peter Brooks and Virginie Orgogozo)

14th course = Friday Feb 3, 10:00-11:00, room RB18B
Modules  (instructor = Lydia Danglot) = chapter 12

15th course = Friday Feb 10, 10:00-11:00, room RB18B
Debugging strategies  (instructor = Michael Lang) = chapter 13

16th course = Friday Feb 17, 10:00-11:00, room RB18B
Exercice  (instructor = Fabien Duveau) = making an Excel file containing all the primers that a Sigma user has ordered (please download oligoexos.tar in Past courses)

17th course = Friday Feb 24, 10:00-11:00, room RB18B
Exercice  (instructor = Fabien Duveau) = making an Excel file containing all the primers that a Sigma user has ordered (continued)

18th course = Friday March 2, 10:00-11:00, room RB18B
Selecting and cobining tools (regular expressions, shell commands, shell scripts, python scripts) to do the job you want  (instructor = Fabien Duveau) = chapter 14

19th course = Friday March 9, 10:00-11:00, room RB18B
Relational databases (1) (instructor = Ataaillah Benhaddou) = begining of chapter 15

20th course = Friday March 16, 10:00-11:00, room RB18B
Useful shell commands (instructor = Virginie Orgogozo) = beginning of chapter 16

21rst course = Friday March 23, 10:00-11:00, room RB18B
Useful shell commands - exercice (instructor = Virginie Orgogozo) = beginning of chapter 16

22nd course = Friday March 30, 10:00-11:00, room RB18B
Relational databases (2) (instructor = Ataaillah Benhaddou) = end of chapter 15

23rd course = Friday April 6, 10:00-11:00, room RB18B
Alias, Function, Wrapper and pipelines (instructor = Virginie Orgogozo) = end of chapter 16

24th course = Friday April 13, 10:00-11:00, room RB18B
Graphical concepts  (instructor = Lydia Danglot) = chapter 17

25th course = Friday April 20, 10:00-11:00, room RB18B
Vector art  (instructor = Lydia Danglot) = chapter 18

26th course = Friday April 27, 10:00-11:00, room RB18B
Pixel images  (instructor = Vincent Contremoulins) = chapter 19

27th course = Friday May 4, 10:00-11:00, room RB18B
Analyzing Chip-seq data (1) (instructor = Ataaillah Benhaddou)

28th course = Friday May 11, 10:00-11:00, room RB18B
Analyzing Chip-seq data (2) (instructor = Ataaillah Benhaddou)

29th course = Friday June 1rst, 10:00-11:00, room RB18B
Working with remote computers (instructor = Pedro Henriques)

Friday Sept 14, 10:00-11:00, room RB18B (course #30)
R - part 1 - Reading files with R (instructor = Gaelle Lelandais and Leslie Regad)

Friday Sept 21, 10:00-11:00, room RB18B (course #31)
R - part 2 - Manipulating data with R (instructor = Gaelle Lelandais and Leslie Regad)

Friday Sept 28, 10:00-11:00, room RB18B (course #32)
R - part 3 - Statistical tests with R (instructor = Gaelle Lelandais and Leslie Regad)

Friday Oct 5, 10:00-11:00, room RB18B
R - please come with your questions, exercice session (instructor = Gaelle Lelandais and Leslie Regad)

Friday Oct 12, 10:00-11:00, room RB18B
Geneious - part 1 - Analyzing DNA sequences with Geneious (instructor = Thierry Grange)

Friday Oct 19, 10:00-11:00, room RB18B
Geneious - part 2 - Making phylogenetic trees with Geneious (instructor = Thierry Grange)

Friday Oct 26, 10:00-11:00, room RB18B
Presentation of Galaxy - part 1 (instructor = Jean-Charles Cadoret)

Friday Nov 2, 10:00-11:00, room RB18B (course #34)
I sequenced my small RNAs, what's next? (instructor = Christophe Antoniewsky)

Friday Nov 9, 10:00-11:00, room RB18B
Presentation of Galaxy - part 2 (instructor = Jean-Charles Cadoret)

Friday Nov 16, 10:00-11:00, room RB18B
No BioInfo Club

Friday Nov 23, 10:00-11:00, room RB18B (course #35)
Identification of a new class of non-coding RNA in yeast by RNA-Seq and ChIP-Seq (instructor = Chunlong Chen)

Friday Nov 30, 10:00-11:00, room RB18B (course #36)
Sophisticated manipulation of data with Excel  (instructor = Lydia Danglot)

Friday Dec 7, 10:00-11:00, room RB18B (course #37)
Human replication timing program: determination by deep sequencing & role in genome evolution (instructor = Chunlong Chen)



2013

Friday Jan 18, 10:00-11:00, room RB18B (course #38)
Assembling BAC sequences based on Illumina sequencing data (instructor = Annabel Wilbley, MNHN)

Friday Mar 1, 10:00-11:00, room RB18B (course #39)
Impact of replication on human genome evolution (instructor = Chunlong Chen)

Friday Mar 15, 10:00-11:00, room RB18B (course #40)
Ant genomics (instructor = Yannick Wurm, Queen Mary University, London)

Friday Mar 22, 10:00-11:00, room RB18B (course #41)
Regular expressions (part 1) (instructor = Patrick Fuchs)

Friday Apr 12, 10:00-11:00, room RB18B (course #41-bis)
Regular expressions, sed (part 2) (instructor = Patrick Fuchs)

Friday Apr 19, 10:00-11:00, room RB18B (course #42)
Bioconductor (instructor = Claire Vandiedonck)

Friday Apr 26, 10:00-11:00, room RB18B (course #43)
Unix streams (part 3) (instructor = Patrick Fuchs)

Friday May 17, 10:00-11:00, room RB18B (course #44)
awk (part 4) (instructor = Patrick Fuchs)

Friday May 24, 10:00-11:00, room RB18B (course #45)
awk (part 5) (instructor = Patrick Fuchs)

Friday July 5, 10:00-11:00, room RB18B (course #46)
commands and processes (part 6) (instructor = Patrick Fuchs)


2011-2012 requirements
Please bring your laptop. It can be Linux, Mac or Windows. Currently there is no internet connection in the room, so, BEFORE THE FIRST COURSE, you should make sure that your computer has the following:

(1) download the example files from http://practicalcomputing.org/files/pcfb_examples.zip

(2) download a powerful texteditor (the default ones will not be useful for the class):
    - for Linux: jEdit (in Ubuntu: use the Synaptic Package Manager to install jedit. Once the installation is complete, jEdit can be launched by selecting the Programming submenu from the Applications menu)
    - for Mac OS X: TextWrangler (you may need to drop files onto the program's icon or use the Open Dialog box within textWrangler to open files).
    - for Windows: jEdit (click on the download link on the jEdit web site and select the Windows Installer for the stable version. Follow the instructions when you launch the installer. You will need to have Java Runtime Environment (JRE) 1.4 or greater installed. Once you've installed jEdit, select Find... from the Search menu and make sure that Regular Expressions is checked).

(3) for Windows only: dowwnload Cygwin from cygwin.com. When you install Cygwin, be sure to install the following useful packages (they will not be installed by default): nano, python, curl (click on the circular arrow next to "Skip" for each package).

(4) install MYSQL (for courses 19 and 21 only):
For Mac and Windows:
Go to the website:www.mysql.com/downloads
Download MySQL community server (the RDBMS itself) and MySQL Workbench (a graphical interface) :
Choose your operating system and its version (for the mac's OS version : clic on the Apple and then This Mac)
For Mac : Dowload the DMG archieve package ; all Apple computers built since 2007 are 64 bit .
Run the 2 package installers :
Mysql-xxx.pkg
MySQLStartupItem.pkg
Drug the MySQL.prefPane to your /Library/PreferencePanes
Edit your .bash_profile to add /usr/local/mysql/bin by taping in your terminal : export PATH="$PATH=:/usr/local/mysql/bin"
Restart your computer
Install your MySQL Workbench by drugging it to the application folder
For more details read the ReadMe.txt !

For Linux:
In Synaptic : Install mysqlcommon and mysqlserver
When it asks for a password, enter one that can be used for all the users of your computer, or click enter for no password.
Using MySQL under NIS/YP requires a mysql user account to be added on the local system with:
adduser --system --group --home /var/lib/mysql mysql
You should also check the permissions and ownership of the /var/lib/mysql directory:
As root:
#cd /var/lib/mysql
#ls -la
Should give:
drwxr-xr-x   mysql    mysql
If not : #chmod a+rx mysql
Edit your .bashrc to add /usr/local/mysql/bin by taping in your terminal : export PATH="$PATH=:/usr/local/mysql/bin"
reboot
Download MySQL Workbench from  www.mysql.com/downloads
Select the correct file for download (for 32- or 64- bits, write 'uname -a' in a terminal to see whether you are on a 32 or 64-bit machine)
Click right on the downloaded .deb file and select install