Development of an Interactive Genome Browser - SSV | EPFL

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4 Οκτ 2013 (πριν από 3 χρόνια και 11 μήνες)

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SSV – 2010/2011


Titre du projet
DEVELOPMENT OF AN INTERACTIVE GENOME BROWSER,
TO VISUALISE, ANALYSE AND MINE LARGE SCALE
GENOMIC DATA
Laboratoire
Bioinformatics & Biostatistics Core Facility

Professeur


Responsable

Jacques Rougemont, Félix Naef

Marion Leleu (BBCF/UPDUB)
EPFL SV PTECH PTBB
AAB 0 26 (Bâtiment AAB)
Station 15
CH-1015 Lausanne

Contact
marion.leleu@epfl.ch

phone: 31832
_______________________________________________________________________________________


Background
Advancement in high-throughput technologies (e.g. tiling arrays, high-throughput sequencing) increases the
size and number of available datasets and annotations covering the whole genome. Manipulation and
interpretation of such data require interactive tools and appropriate statistical methods. None of the existing
solutions (browsers and software e.g. [1-3]) provide a complete and satisfying framework to perform those
tasks in an interactive and dynamic way.
Project
The Bioinformatics and Biostatistics Facility (BBCF) is currently working on the development of a web-
based interactive genome browser to visualise, analyse and mine whole genome datasets. The aims of the
project are
(i) Extend the functionalities of our version of the JBrowse genome browser [1] in order to make it
more interactive (javascript, rails)
(ii) Develop and integrate analysis scripts (perl, R and/or C++) to facilitate the manipulation and the
processing of genomics data (such as filtering, smoothing, selection and crossing of genomic
data)
(iii) Identify and implement appropriate statistical and data mining methods to accurately perform
multi-modal comparisons of genomic features (statistics, algorithmic and programming with
perl, R and/or C++)
(iv) Analyse major public whole-genome datasets [4-8] and characterize large-scale statistical
properties relevant for transcriptional regulation and chromatin structure
The selected student will actively participate in the development of one or several of these components
depending on his/her interests and skills, and on the needs of the project at the start of the internship.
References
[1] Skinner ME et al. Genome Res. (2009) 19(9):1630-8.
[2] Bock et al. Genome Biol (2009) 10(2) :R14.
[3] Giardine B et al. Genome Res. (2005) 15:1451–1455.
[4] Lieberman-Aiden et al. Science (2009) 326:289-93.
[5] Barski and Zhao. J Cell Biochem (2009) 107:11-8.
[6] Teytelman et al. PLoS ONE (2009) 4(8):e6700.
[7] Down et al. Nat Biotechnol (2008) 26(7):779-85.
[8] Nagalakshmi et al. Science (2008) 320 (5881):1344-9.