Analysing thousands of bacterial genomes:
gene annotation, metabolism and regulation

ALLBIO training workshop
Marseille, June 22-25, 2014

Computer setting

The training will take place in a seminar room of the Novotel. The hotel has a wi-fi connection, but we will also install a direct connection by ethernet cable, in order to improve the bandwidth.

Most participants are equipped with a laptop computer, and will use it for the training. We rented some additional laptops for the remaining participants.

Software requirement

Web browser

The two first days will essentially rely on Web resources, that can be consulted with any modern Web browser (Chrome/Firefox/Safari). With Internet Explorer, version 8 is the minimum but browsing will be improved with later versions (e.g. IE 10).

Visualization tools

During the course, we will generate data in tabular form (e.g. phylogenetic profiles), and networks (e.g. co-occurrence of gene pairs across bacterial genomes). To visualize, explore and further improve the interpretaion of the result, we will use two user-friendly tools classically used for microarray analysis and network analysis.

To avoir spending too much time on installation tasks during the training, we ask participants to pre-install the following programs on their personal computers.

CytoScape http://www.cytoscape.org/
TMEV http://www.tm4.org/mev.html/
GENE-E https://www.broadinstitute.org/cancer/software/GENE-E/download.html
Java Treeview http://sourceforge.net/projects/jtreeview/files/

Command-line access

The training includes introductory sessions about the command-line utilisation of bioinformatics tools,in a Unix shell. The course will be adapted for participants with no prior experience in Unix.

Participants equipped with a Windows operating system should install putty and WinSCP (or Filezilla).

Participants equipped with a Mac OSX or Linux operating system should install Filezilla.

putty Windows http://www.putty.org/ Run a Unix shell on a remote computer
WinSCP Windows http://winscp.net/ Transfer data from the remote computer to local PC.
Filezilla Mac OSX
Windows
Linux
https://filezilla-project.org/ Transfer data from the remote computer to local PC.


Jacques van Helden (Jacques.van-Helden@univ-amu.fr)