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A T T E N T I O N:<br>
Please note the room, day, and starting time being different
this time.<br>
<br>
<br>
<br>
I N V I T A T I O N<br>
<font face="sans-serif"> </font><br>
<font face="sans-serif">===============================================<br>
<br>
to the Research Seminar 'Computer Graphics, Image Processing, and
Visualization'<br>
<br>
</font><font face="sans-serif"> on<font face="sans-serif">
Tuesday, October 11th, 2016, at 10:15 AM,<br>
in Room P-702 in the Paulinum, Augustusplatz.</font><br>
</font><br>
<font face="sans-serif">===============================================</font><br>
<br>
A talk is given by<br>
<br>
Daniel Gerighausen<br>
Department of Computer Science<br>
Leipzig University.<br>
<br>
Abstract:<br>
<br>
<font face="sans-serif"> The DNA forms with special proteins,
so-called histones, the framework of<br>
the chromatin, which forms the chromosomes in eukaryotic
cells. Chromatin<br>
state changes play an essential role in the regulation of
transcription of<br>
many genes, thus controlling cell differentiation. A large
part of these<br>
changes is due to histone modifications that alter the
accessibility of the<br>
DNA. An important approach of analyzing these histone
modifications is the<br>
peak calling. Using ChIP-seq, a DNA sequencing method, it is
possible to<br>
target with special antibodies only these modified histones
and sequence<br>
the DNA, which is wrapped around them. This DNA fragments are
then<br>
sequenced and mapped to the reference genome. To overcome the
sequencing<br>
bias of this kind of sequencing, the cell type is also
sequenced with an<br>
unspecific antibody to create a background. With this
experiment and<br>
background data the peak calling is is performed. Peak Caller
like MACS can<br>
call peaks in single experiments, but cannot combine multiple
replicates to<br>
circumvent errors in the data. Usually, the replicates were
merged into one<br>
data set to calculate the peak calling, but this leads to
errors in<br>
statistical model of MACS.<br>
<br>
Sierra Platinum overcomes this issue and combines multiple
ChIP-seq<br>
experiments in a single peak calling process. Additionally, it
provides<br>
several visualizations to guide the user to evaluate the
experiments and<br>
enables the user to down weight or exclude single experiments
from the peak<br>
calling based on this guidance. Furthermore, the user can
directly compare<br>
the results of the different parameterizations within the GUI
of Sierra<br>
Platinum.<br>
<br>
Due to the size of the input files and the algorithms that
combine the<br>
experiments the memory consumption and computation time is
intensive.<br>
Therefore, it is necessary to run Sierra Platinum on special
hardware for<br>
large scale experiments. To enable to more user to use Sierra
Platinum, we<br>
hereby present the Sierra Platinum Service. It is hosted at<br>
sierra.sca-ds.de. Furthermore, the service can be easily
deployed on<br>
additional servers using a docker image.<font
face="sans-serif"><br>
<br>
</font><font face="sans-serif"><font face="sans-serif">===============================================<br>
</font></font><br>
On behalf of Professor Scheuermann all those interested are
cordially invited to attend.<br>
<br>
Yours sincerely,</font><br>
Tom Liebmann
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