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