EMBnet News bulletin of 9 Nov 2007

[Laurent Falquet]

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* EMBnet News bulletin of 09-Nov-2007 *
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Dear Users,

Courses in 2008
---------------
We will organise several courses in 2008:

1) Lausanne January 28 - February 1: Bioinformatics of transcriptional  
regulation
2) Basel January 28 - February 1: Proteomics using Bioinformatics tools
3) Lausanne February 4-8: Statistical analysis applied to genome and  
proteome analyses
4) Lausanne September 1-5: Protein structure: prediction and analysis
5) Basel September 8-12: Unix/Perl for life sciences

1) Bioinformatics of transcriptional regulation (LS)
The course attempts to present the state of the art of bioinformatics  
methods and resources for studying transcriptional regulation. The  
practical part is largely based on databases and web-servers developed  
by our group and can be viewed as anintroduction to the usage of these  
tools:
	• The Eukaryotic Promoter Database EPD: Retrieval of useful and  
reliable information on promoters, and how to use this information for  
studying transcriptional regulatory mechanisms.
	• CleanEx: How to access, combine and effectively use public gene  
expression data.
	• HTP SELEX: A database of quantitative predictive models for  
transcription factor binding sites.
	• Signal Search Analysis (SSA): Motif discovery in functionally  
related DNA sequences and new tools to study the architecture of gene  
regulatory regions.
The theoretical part is aimed at providing an overview of public data  
and computationalmethods relevant to the understanding of gene  
regulation. Particular emphasis will be onthe analysis of so-called  
mass genome annotation (MGA) data such as CAGE for  
mappingtranscription start sites, or ChIP-seq for mapping in vivo  
transcription factor binding sites.

Registration opened until December 31st:
http://www.3eme-cycle.ch/biologie/pages/registrationEMBnet.php?code=21
For more information please contact Dr. Vassilios Ioannidis
vassilios.ioannidis at isb-sib.ch


2) Proteomics using Bioinformatics tools (BS)
The developments of techniques to separate and identify proteins like  
2D-
PAGE and Mass Spectrometry has been very successful over the last
years. The aim of this course is to introduce the theory and practice of
proteomics using bioinformatics tools, with the description and the
application of some of the most useful methods and computer programs
currently available.

Registration deadline January 1st:
The registration page will be announced soon on http://www.ch.embnet.org/pages/courses.html
or contact course organiser Dr. Lorenza.Bordoli at isb-sib.ch
This course is organized with the support of the Swiss Committee for
Molecular Biology (SKMB) (http://www.usgeb.ch/skmb.html).


3) Statistical analysis applied to genome and proteome analyses
The course is aimed at biomedical graduate students and research  
scientists.
The purpose of the course is to present and discuss selected methods  
that are
particularly useful in the analysis and interpretation of data  
produced with mod-
ern genomics and proteomics technologies. In the computer lab, methods  
will be
applied to case studies.
The course will cover unsupervised and supervised analysis methods for  
class dis-
covery and class discrimination and the modular analysis of data  
(mostly gene
expression); the analysis of SNP array data for gene-phenotype  
association studies
and motif identification in biological sequence data using improved  
background
models.

Registration opened until December 31st:
http://www.3eme-cycle.ch/biologie/pages/registration.php?code=4
For more information please contact Dr. Vassilios Ioannidis
vassilios.ioannidis at isb-sib.ch


4) Protein structure: prediction and analysis (LS)
The course covers the concepts of molecular modeling and simulation.
Major topics include force fields, statistical mechanics, molecular  
dynamics
and the analysis of simulation results. Attendees will work through  
short tutorial
on the topics discussed in the class. A basic knowledge of Unix is  
required for the
practical sessions of the course.

Registration opened until July 31st:
http://www.3eme-cycle.ch/biologie/pages/registration.php?code=12
For more information please contact Dr. Vassilios Ioannidis
vassilios.ioannidis at isb-sib.ch


5) Unix/Perl for life sciences (BS)
Using the web interface for Bioinformatics research is very convenient  
for
small amounts of data (e.g. less than 20 sequences). As soon as
researchers want to analyze more sequences (from 20 up to thousands
sequences or megabytes of data), the task becomes tedious.
The course aims at providing the very basic knowledge of Unix command-
line and PERL scripting abilities to analyze large amounts of data by
automating recurring tasks or by grouping several tasks into one
command.
This course is organized for biomedical researchers and no particular
programming knowledge is required.

Registration deadline August 15th:
The registration page will be announced soon on http://www.ch.embnet.org/pages/courses.html
or contact course organiser Dr. Lorenza.Bordoli at isb-sib.ch
This course is organized with the support of the Swiss Committee for
Molecular Biology (SKMB) (http://www.usgeb.ch/skmb.html).


How to contact us ?
-------------------

Don't forget our official help desk email address:

helpdesk at mail.ch.embnet.org

When sending an email to this address you will automatically receive
a ticket with a number. Your question will be answered by our team
or by an expert in the field from the Swiss Institute of Bioinformatics.

With our best regards,

Laurent Falquet, Swiss EMBnet node manager
and the Swiss EMBnet team members,
Lorenza Bordoli
Vassilios Ioannidis
Sébastien Moretti


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