Fr Apr 1, 2011: SIB Bioinformatics Workshop: “UniProt protein sequence databases: use and pitfalls”

Dear All,

We are pleased to announce the SIB Bioinformatics Workshop entitled:

UniProt protein sequence databases: use and pitfalls

This workshop, to be held on Friday 1st April 2011, will give some basic theoretical and practical knowledge on protein sequence databases and, in particular, on the optimum use of the UniProt web site.

– Where do the protein sequences come from?

– What are the differences between UniProtKB/TrEMBL and UniProtKB/ Swiss-Prot?

– What are the manual and automated annotation pipelines ?

– How can protein sequence accuracy and annotation quality be estimated?

– How can large dataset (i.e. complete proteome) for a particular organism be retrieved?

– How can biological knowledge from a Blast result be extracted?

– What are the differences between UniProt and the NCBI protein sequence databases?

– How can accession numbers, GIs or other record identifiers corresponding to the proteins of interest be retrieved?

Important information as well as the registration page are available from:

http://edu.isb-sib.ch/course/view.php?id=94

Hope to see you there !

For the organizers,

Vassilios Ioannidis

**************************************************************

Vassilios Ioannidis, Ph.D., Vassilios.Ioannidis@isb-sib.ch

Swiss Institute of Bioinformatics

Vital-IT

Quartier Sorge, Bâtiment Génopode, 1015 Lausanne, Switzerland

Tel: +41 21 692 4076 / Fax: +41 21 692 4065

_______________________________________________

courses mailing list

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April 4-8, 2011: New SIB course: “Analysis of differential gene expression”

Dear all,

We are pleased to announce a new SIB course:

Analysis of differential gene expression

which will take place during the week of 4-8 April 2010.

This one-week course will discuss the statistical analysis of differential gene expression, based on techniques such as microarrays,
RNA-seq and qPCR. Lectures will be conducted in the morning, and students will analyse actual gene expression data in the afternoon.

Prior knowledge of basic statistics and of the R statistical language is highly recommended, as is the knowledge of Unix and a scripting language
(for some of the practicals); exact requirements will be indicated closer to the beginning of the course; check the web page for details.

Please note : the course is already full, with a long waiting-list. If you were interested but could not register, let us know by email, so that we can if/when we should organize the same course again.

The list of all SIB courses is available from the SIB website

For the organizers,

Frédéric Schütz

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StarOmics : Announcing StarOmics doctoral program for PhD students

Announcing StarOmics doctoral program for PhD students

The CUSO (Conférence Universitaire de Suisse Occidentale) is happy to announce the creation of StarOmics, a doctoral program dedicated to train biologists in the analysis of large scale biological data.

Next generation biologists will face challenges in their everyday tasks both in terms of integrating quantitative aspects and reasoning using the novel strategies of the modern biology.

The StarOmics (or *omics) doctoral program (http://biologie.cuso.ch/staromics/) intends to create a network of PhD students and professionals involved in any project related to Genomics, Transcriptomics, Proteomics, Metabolomics, Connectomics, and all other large scale data-generating technologies.

Students of this program will be offered training, workshops, and seminars in genome-wide and proteome-wide data analysis, biological modeling, quantitative image analysis, programming and statistics, in addition to their thorough education in experimental biology, through a didactic program that complements both their individual research topic and background. In addition several events will be organized (annual retreat, mini-symposia, soft skills courses), which besides their didactic value will also favor networking among the students and professors either within this program or jointly with the federation of doctoral programs of the CUSO (Ecology & Evolution, Plant Sciences, and Microbiology).

PhD students of this program will become conversant in both experimental and computational approaches, and will acquire the ability to integrate quantitative and experimental methods in their own research. Graduates from this program will have unprecedented scientific competence to permit them to become future leaders in biological research and beyond.

The students will not receive ECTS credits from the StarOmics doctoral program, but an attestation to get ECTS credits in their own university.

What are the benefits?
– a large offer of courses and workshops renewed every year
see current list here: http://biologie.cuso.ch/staromics/activities/ (select 2011)
– a network of colleagues
– a series of soft skills courses (how to present slides, how to write an article, how to write a grant…)
– no ECTS counting (but certificate to reclaim ECTS at you own University)
– substantial reimbursement of travel and accommodation expenses

What are the requirements?
To obtain a final certificate from the StarOmics program, the participants are asked to register for a certain number of activities over the 3-year period of the program. Several activities could be offered twice or more over the period in various locations, giving the students some flexibility.

2 annual retreats
3 practical courses
6 workshops
1 joint seminar presentation
2 minisymposiums
2 soft skills training

Who can register?
Any PhD student in Western Switzerland Universities (Bern, Fribourg, Geneva, Lausanne, Neuchâtel) with a project using technologies of high throughput or large scale data generation. They must be in the first year of their thesis.

How to register?
a) Please fill in this form: http://biologie.cuso.ch/staromics/registration/
Don’t forget to mention any other doctoral program you are already part of or intend to join.
b) Send us your CV at staromics@cuso.ch

For any question please contact the coordinator of the program:
Corinne Dentan
Coordinator of StarOmics
Center for Integrative Genomics
Génopode Building
University of Lausanne
CH-1015 Lausanne
Phone: +41 (0)21 692 39 30
Email: corinne.dentan@unil.ch
http://biologie.cuso.ch/staromics

We wish you a nice Holiday Season and hope to meet you in the StarOmics activities in 2011.

Prof. Nouria Hernandez, Chair of the committee
Prof. Beat Suter, Representative of the University of Bern
Prof. Simon Sprecher, Representative of the University of Fribourg
Prof. Karl-Heinz Krause, Representative of the University of Geneva
Prof. Ioannis Xenarios, representative of the University of Lausanne
Prof. Pilar Junier, Representative of the University of Neuchâtel

7-11 February 2011: SIB/StarOmics course “Introduction to statistics for biologists”

Dear all,

We are pleased to announce a new SIB course:

Introduction to statistics for biologists

which will take place in Geneva during the week of 7-11 February 2011.

This course is designed to provide graduate students in the biomedical sciences with experience in the application of basic statistical analysis techniques to a variety of biological problems.

Attendees will work through short tutorials on the topics discussed in the class. During the practical exercises students will learn how to work with the widely used “R” language and environment for statistical computing and graphics.

Registration is now open; see the web site for more details.

The list of all SIB courses is available from the SIB website at:
http://www.isb-sib.ch/education/

Frédéric Schütz

April 11-14, 2011; Conf. “Enabling Systems Biology”, London UK

April 11-14th, 2011, University College, London, UK

The conference “Enabling Systems Biology” is a one-off conference focusing on the interface between computational approaches in systems biology with experimental techniques. A world-leading set of invited speakers will be talking, and there will be a number of talks drawn from the set of submitted abstracts. Registration deadline is March 1st 2011.

More information

Confirmed Speakers are:

Ewan Birney          (EBI, Cambridge, UK)
Christine Orengo     (UCL, London)
James Adjaye         (MPI, Berlin)
Giulio Superti-Furga (CMM, Vienna)
Geoff Barton         (U. Dundee, Dundee)
Michael Boutros      (DKFZ, Heidelberg)
Martha Bulyk         (Harvard Medical School, Cambridge, US)
Gianni Cesareni      (U. Tor Vergata, Rome)
Bertie Goettgens     (CIMR, Cambridge, UK)
John Hancock         (MRC Harwell, UK)
Jean-Karim Heriche   (EMBL, Heidelberg)
Jaap Heringa         (VU, Netherlands)
Henning Hermjakob    (EBI, Cambridge, UK)
Edda Klipp           (Humboldt University, Berlin)
Xuedong Liu          (U Colorado, Boulder)
Tomi Makela          (U Helsinki, Finland)
Aristidis Moustakas  (Ludwig Institute, Uppsala)
Stuart Newfeld       (Tempe, Arizon)
Erich Nigg           (BioZentrum, Zurich)
Christos Ouzounis    (Institute of Agrobiotechnology, Thessaloniki)
Bernhard Palsson     (UCSD, San Diego)
Dietmar Schomburg    (Technical University Braunschweig)
Eran Segal           (Weizmann Institute, Jerusalem)
Peter Sorger         (Harvard, Cambridge, US)
Alfonso Valencia     (CNIO, Madrid)
Jaak Vilo            (Quretec, Tartu)
Hans Westerhoff      (University of Manchester, Manchester)
Ioannis Xenarios     (SIB, Geneva)

PLoS Biol.; Group Reymond

Phenotypic Consequences of Copy Number Variation: Insights from Smith-Magenis and Potocki-Lupski Syndrome Mouse Models

Guénola Ricard, Jessica Molina, Jacqueline Chrast, Wenli Gu, Nele Gheldof, Sylvain Pradervand, Frédéric Schütz, Juan I. Young, James R. Lupski, Alexandre Reymond, and Katherina Walz
PLoS Biol. 2010 November; 8(11): e1000543. Published online 2010 November 23. doi: 10.1371/journal.pbio.1000543.
PMCID: PMC2990707