[Forschungsseminar-BSV] Research Seminar 'Computer Graphics, Image Processing, and Visualization'

[Tom Liebmann]

A T T E N T I O N:
     Please note the room, day, and starting time being different this time.



I N V I T A T I O N

===============================================

to the Research Seminar 'Computer Graphics, Image Processing, and 
Visualization'

     onTuesday, October 11th, 2016, at 10:15 AM,
     in Room P-702 in the Paulinum, Augustusplatz.

===============================================

A talk is given by

     Daniel Gerighausen
     Department of Computer Science
     Leipzig University.

Abstract:

     The DNA forms with special proteins, so-called histones, the 
framework of
     the chromatin, which forms the chromosomes in eukaryotic cells. 
Chromatin
     state changes play an essential role in the regulation of 
transcription of
     many genes, thus controlling cell differentiation. A large part of 
these
     changes is due to histone modifications that alter the 
accessibility of the
     DNA. An important approach of analyzing these histone modifications 
is the
     peak calling. Using ChIP-seq, a DNA sequencing method, it is 
possible to
     target with special antibodies only these modified histones and 
sequence
     the DNA, which is wrapped around them. This DNA fragments are then
     sequenced and mapped to the reference genome. To overcome the 
sequencing
     bias of this kind of sequencing, the cell type is also sequenced 
with an
     unspecific antibody to create a background. With this experiment and
     background data the peak calling is is performed. Peak Caller like 
MACS can
     call peaks in single experiments, but cannot combine multiple 
replicates to
     circumvent errors in the data. Usually, the replicates were merged 
into one
     data set to calculate the peak calling, but this leads to errors in
     statistical model of MACS.

     Sierra Platinum overcomes this issue and combines multiple ChIP-seq
     experiments in a single peak calling process. Additionally, it provides
     several visualizations to guide the user to evaluate the 
experiments and
     enables the user to down weight or exclude single experiments from 
the peak
     calling based on this guidance. Furthermore, the user can directly 
compare
     the results of the different parameterizations within the GUI of Sierra
     Platinum.

     Due to the size of the input files and the algorithms that combine the
     experiments the memory consumption and computation time is intensive.
     Therefore, it is necessary to run Sierra Platinum on special 
hardware for
     large scale experiments. To enable to more user to use Sierra 
Platinum, we
     hereby present the Sierra Platinum Service. It is hosted at
     sierra.sca-ds.de. Furthermore, the service can be easily deployed on
     additional servers using a docker image.

===============================================

On behalf of Professor Scheuermann all those interested are cordially 
invited to attend.

Yours sincerely,
Tom Liebmann
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