UNIVERSITY OF HERTFORDSHIRE
             COMPUTER SCIENCE RESEARCH COLLOQUIUM

                            presents

                         "Breaking Bad.
               Or: When do you think it stops?"

                    Dr. RenĂ te Boekhorst
     (School of Computer Science, University of Hertfordshire)

                     25 February 2015 (Wednesday)
                          1 pm -2 pm

                  Hatfield, College Lane Campus
                       Seminar Room D102

                  Everyone is Welcome to Attend

                  Refreshments will be available

Abstract:


The inspiration for this talk comes from a problem that forms part of
the PhD project of Nathan Beka.  His project is about factors that affect
the reliability of "Next Generation Sequencing" (NGS) of DNA.

An important step in NGS is the shearing of the DNA-to-be-sequenced
in a large number of fragments (which preferably should neither be too
small nor to be too large). This is done by an intriguing technique the
result of which is a certain distribution - preferably a Gaussian one - of
fragment sizes.  Companies delivering the shearing devices claim that the
fragmentation occurs "at random" and as such its results are habitually
addressed in bioinformatic publications. But as is so often the case,
what exactly is meant by "at random" is not explained and neither is it
clarified how the feat is brought about.  This ambiguity is the results of
not considering valid statistical modelling of the fragmentation process.

In this talk I will present an overview of a classical approach from
physics and statistical models of the stochastic interruption of
sequences. The statistical models are generic and go beyond DNA or
the fragmentation of any material in particular; their fundament is
the distribution of termination events and failures. Therefore, the
applications range from the distribution of "waiting times", the "random"
terminations of bouts of behaviour, inter-event intervals of any kind
(such as computer failures), the pulverisation of rocks and meteorites,
size distributions of bubbles, brain parts, genes and, last not least,
of fragments of DNA.

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Hertfordshire Computer Science Research Colloquium
http://cs-colloq.stca.herts.ac.uk