[BBC] ALLBIO training workshop - Analysing thousands of bacterial genomes

[Jacques van Helden]

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                   ALLBIO training workshop
          Analysing thousands of bacterial genomes:
           gene annotation, metabolism, regulation
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ALLBIO training workshop – Marseille, June 23-25, 2014

Practical info
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Registration, schedule, details:
   http://www.allbioinformatics.eu/doku.php?id=public:valid-ulb

Organizer: Jacques van Helden <Jacques.van-Helden at univ-amu.fr>

Dates: June 23-25, 2014
Location: Site de Luminy, 
    Aix-Marseille Université (AMU), 
    Marseille, France
Expected participants: 20
Cost: 0€
Registration: before June 11, 2014


Motivation
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Sequencing technologies allow microbiologists to sequence, for a
moderate cost, not only the genome of their favourite species, but a
few dozens of related species, a collection of strains, and even to
characterize inter-individual variations. The Ensembl Genomes resource
contains over 10,000 completely sequenced genomes. The availability of
such data requires new bioinformatics resources suited for annotating,
querying and analysing multitudes of sequenced bacterial genomes in
parallel. 

This training workshop will show how to combine several specialized
bioinformatics resources to extract information about bacterial genes
and their annotations (Ensembl Genomes), metabolism (MICROSCOPE), and
regulation (RSAT). The course will be oriented towards comparative
genomics, and give a perspective about advances that can be expected
from the massive reduction of sequencing costs resulting from Next
Generation Sequencing.

The course will mainly be based on user-friendly Web interfaces. It
will also include a basic introduction about the programmatic access
to bioinformatics resources, showing by simple and well-documented
examples how to automatize the collection of data, and extract
information from multiple data sets.

Target audience
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This course is addressed to microbiologists confronted to the need to
use bioinformatics resources to analyse multiple genomes.

Prerequisites
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The course does not require any computing skills. A basic knowledge of
the Linux environment is welcome, but not required.

Computer environment
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The training room is equipped with Linux computers, but participants
are welcome to bring their own laptop if they wish to work in their
familiar environment.

Contents
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This training course will include

- Short talks illustrating the functionalities offered by bioinformatics resources suited for the analysis of multiple bacterial genomes. 

- Practicals based on concrete study cases;
    * collecting multiple genomes from bacteria;
    * comparing annotations between different species;
    * extracting metabolic information for selected genomes;
    * metabolic projection: coverage of reference pathways by enzymes
      found in a genome;
    * phylogenetic profiling: detecting genes co-occurrences across
      genomes;
    * phylogenetic footprints: detection of conserved cis-regulatory
      elements.

- Practicals on programmatic use of the tools:
    * extracting data for multiple genomes;
    * combining data from diverse sources.


Teachers
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Dan Staines
    European Bioinformatics Institute (EBI), UK
    Ensembl Genomes
    http://ensemblgenomes.org/

François LeFevre, Eugeni Belda, Claudine Médigue
    Genoscope (CEA), France
    MICROSCOPE
    http://www.genoscope.cns.fr/agc/microscope/

Jacques van Helden, Denis Puthier
    Aix-Marseille Université (AMU), France
    Regulatory Sequence Analysis Tools (RSAT)
    http://www.rsat.eu/


Funding
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This training workshop is funded by the ALLBIO project
(http://www.allbioinformatics.eu/), whose goal is to establish the
link between bioinformatics and biologist communities who express
uncovered needs for other fields than human genomics (microbial,
plant, livestock).

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