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

[Vanessa Kretzschmar]

Attention:
  - different weekday
  - different room (new link)
  - more than one talk (increased duration possible)


I N V I T A T I O N

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

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

     on Monday, March the 29th, 2021, at 01:15 PM,
     via web conferencing. 
(https://conf.fmi.uni-leipzig.de/b/van-bwb-jil-vk2)

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

A talk will be given by

     Tomas Daetz

and is entitled:

     'New Interactions for RNApuzzler using VARNA'

Abstract:

     From multi-cellular organisms to eukaryotic cells to viruses, RNA is a
     key component to understand how this organism works. To determine the
     function of such molecules, it is necessary to analyze their structure,
     as this is vital to determine their function. One way to analyze those
     structure is through the drawings of the so-called secondary structure.
     There are many algorithms to draw such structures, being RNApuzzler one
     of the few guaranteeing fast planar drawings. RNApuzzler is only 
available
     in the ViennaRNA package, which just offers static drawings in the old
     PostScript format and has no GUI. Thus, RNApuzzler is not very flexible
     and user-friendly. In this work, we added a SVG file support for the
     ViennaRNA and integrated RNApuzzler in VARNA, another visualization 
tool
     for secondary structures to overcome these shortcomings. VARNA also
     provides dynamic interactions via a GUI to customize the drawings, 
which
     have also been adapted and extended for RNApuzzler.

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

Another talk will be given by

     Jacob Pollack

and is entitled:

     'Alignment-based visual quality control of nanopore sequencing data'

Abstract:

     Recent developments in nanopore sequencing allow rapid generation of
     long reads of DNA fragments using low-cost and compact devices. The
     differences to conventional sequencing methods result in a need for a
     dedicated analysis tool that takes into account the special properties
     and challenges of nanopore sequencing data, such as the long reads and
     the relatively high error rate. For appropriate visual quality control,
     an alignment-based approach is particularly useful, using BAM files in
     addition to the FAST5 files generated during sequencing, as this allows
     reads to be viewed in the context of the genomic region they belong to.
     Previous alignment-based tools for ana- lyzing nanopore sequencing data
     give basic quality control statistics but do not provide options for
     viewing the sequences of individual read alignments. An interactive
     visual analysis, of the read alignments can help identify patterns in
     the sequences that may indicate sequencing errors. A web application
     implemented in python was developed to support the import of FAST5 and
     BAM files. The contained read alignments can be examined with 
interactive
     plots, allowing in particular the detection and selection of patterns
     in the sequences. It is also possible to search for further occurrences
     of such patterns and to export the corresponding reads as new FAST5 and
     BAM files. The resulting python project, as well as an example dataset,
     is provided at https://git.informatik.uni-leipzig.de/jp31zusu/blappy.

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

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

Yours sincerely
Vanessa Kretzschmar
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