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

[Tom Liebmann]

I N V I T A T I O N

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

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

     onWednesday, August 31st, 2016, at 1:15 PM,
     in Room P-701 in the Paulinum, Augustusplatz.

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

There will be two talks. The first one is given by

     Nicole Hinzmann
     Department of Computer Science
     Leipzig University

and is entitled

     "Masakari - A graphical user interface for Chromatin Segmentation".

Abstract:

     Epigentics is the study of heritable changes of the phenotype which 
are not
     encoded in the genome. One research field of epigenetics is about 
the modifi-
     cations at histones. To analyze the co-occurrence and the evolution 
of these
     histone modifications, computer-assisted methods are mandatory due 
to the
     large amount of data involved. Masakari is a tool for chromatin 
segmentation.
     It is implemented in Java 8 and uses a client-server-architecture. 
The client
     provides an clearly structured interface representing interesting 
information
     about the data, and supporting different analysis. The server 
performs the
     necessary computations of the segmentation itself and statistics on 
the seg-
     mentation result. So it is possible to work with Masakari on 
clients with low
     computing power. Using Masakari the user can index one genome, create a
     data driven segmentation for a set of histone modifications and 
calculate the
     corresponding segmentation codes for histone modifications, compare 
them
     with additional histone modifications in the same or a different 
cell type, and
     search for motifs in the segments.

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

The second talk is given by

     Alrik Hausdorf
     Department of Computer Science
     Leipzig University

and is entitled

     "Masakari - Algorithms for Segmenting Chromatin"

Abstract:

     The analysis of differences in the chromatin state between 
different cell types or
     individuals is one of the central tasks in the field of 
epigenetics. A chromatin
     state consists of information of the genomic localization of 
several histone
     marks in one cell type or individual. Each mark is measured in one 
experiment.
     After analysis of all experiments, the user has one list of genomic 
locations
     of the measured histone mark for each experiment. To analyze the 
changes
     in the data set, a tool is needed for combine these lists. Masakari 
is a tool
     for computing segments, i.e. the longest sequential parts having 
the same
     combination of modifications. Additionally to the bare calculation 
of the
     segmented data, Masakari supports comparing different chromatin 
states based
     on the segments and computing motif coverage of each segment. In 
this thesis
     the Masakari program and its extensions are described. Different 
analyses for
     better understanding the computed data and extracting additional 
information
     from the segmentation were added to the exiting segmentation 
process. The
     motif coverage computation was accelerated by creating a threaded 
version. To
     use the computed data of Masakari within other programs, Masakari 
provides
     different export and import functionalities. Moreover Masakari 
helps the user
     to understand the input data and the segmentation result.

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

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

Yours sincerely,
Tom Liebmann

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