[BBC] [Gtpb] Fwd: URGENT: Expressions of interest - Training on 3C-based analysis and modelling...

[Pedro Fernandes]

Dear friends and colleagues,

Apologies for this mass posting.

Some of you have previously expressed interest in our courses for  
hands-on training on TADbit and TADkit (http://www.3DGenomes.org  
http://www.3dgenomes.org ). We are about to open a new course in the  
GTPB programme from the 6th to 9th of June. Additional info on the  
course can be found at the end of the e-mail.

3DAROC16
3C-based data analysis and 3D reconstruction of chromatin folding


May we ask you to *quickly* inform us if you would be interested in  
attending, or recommending that your collaborators would attend?
We will run the course on those dates but we need to find-out whether  
or not we should offer it in  a later date, November 2016 for example.

Best,
Pedro

-- 
Pedro Fernandes
Instituto Gulbenkian de Ciência
Apartado 14
2781-901 OEIRAS
PORTUGAL
Tel +351 21 4407912
http://gtpb.igc.gulbenkian.pt


>>>>>>>>>>>>

Course description
3C-based methods, such as Hi-C, produce a huge amount of raw data as  
pairs of DNA reads that are in close spatial proximity in the cell  
nucleus. Overall, those interaction matrices have been used to study  
how the genome folds within the nucleus, which is one of the most  
fascinating problems in modern biology. The rigorous analysis of those  
paired-reads using computational tools has been essential to fully  
exploit the experimental technique, and to study how the genome is  
folded in the space. Currently, there is a clear expansion on the  
wealth of data on genome structure with the availability of many  
datasets of Hi-C experiments down to 1Kb resolution (see for example:  
http://hic.umassmed.edu/welcome/welcome.php ;  
http://promoter.bx.psu.edu/hi-c/view.php or  
http://www.aidenlab.org/data.html ). In this course, participants will  
learn to use TADbit, a software designed and developed to manage all  
dimensionalities of the Hi-C data:
? 1D - Map paired-end sequences to generate Hi-C interaction matrices
? 2D - Normalize matrices and identify constitutive domains (TADs,  
compartments)
? 3D - Generate populations of structures which satisfy the Hi-C  
interaction matrices
? 4D - Analyze and compare different samples.
Participants can bring- specific biological questions and/or their own  
3C-based data to analyze during the course. At the end of the course,  
participants will be familiar with the TADbit software and will be  
able to fully analyze Hi-C data. Note: Although the TADbit software is  
central in this course, alternative software will be discussed for  
each part of the analysis.

Target Audience
The course design is oriented towards experimental researchers and  
bioinformaticians at the graduate and post-graduate levels. The last  
edition of this course was attended by people with different  
backgrounds and interested in the genome organization. Moreover, Hi-C  
data have recently been used in metagenomics studies to accurately  
cluster metagenome assembly contigs into groups that contain nearly  
complete genomes of each species.
It is likely that the participants to this course aim at getting  
involved in generating Hi-C data for chromosome structure  
determination or that they just want to be able to correctly interpret  
and analyse publicly available data.

Course Pre-requisites
Recommended Linux and basic Python programming skills, graduate level  
in Life Sciences.

Course fee Eur 360.00, lunches and coffee-breaks included.

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