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CATEGORIES:CoSBi Computational and Systems Biology Series
SUMMARY:Stochastic simulation algorithms and analysis of b
iological systems - Sean Sedwards\, CoSBi
DTSTART;TZID=Europe/London:20090519T140000
DTEND;TZID=Europe/London:20090519T150000
UID:TALK14748AThttp://talks.cam.ac.uk
URL:http://talks.cam.ac.uk/talk/index/14748
DESCRIPTION:*Abstract*: The so-called 'exact' Gillespie stocha
stic simulation algorithms have spawned a number o
f successors which aim to speed up the computation
ally intense process of stochastic simulation of c
hemically reacting systems. While some of these s
uccessors achieve a speed-up by compromising exact
ness\, usually via judicious approximation\, other
s are both faster and remain exact. In this latte
r vein\, the Gibson-Bruck algorithm has apparent m
arket-leading asymptotic performance and is the be
nchmark by which contenders are measured. In fact
\, it has been found that it's theoretical perform
ance may not be realised in practical systems whic
h do not approach asymptotic dimensions and that i
ts overhead may allow it to be beaten by simpler a
lgorithms. More surprisingly\, in the stochastic
simulation of some complex hierarchical systems wh
ose interactions are combinatorial in nature\, the
Gibson-Bruck algorithm also loses its theoretical
edge due to one of its assumptions about chemical
systems not holding.\n \nWe thus present an algor
ithm which gives an improvement of performance ove
r the Gibson-Bruck algorithm equivalent to O(n) vs
. O(n log n) when used to simulate the complex int
eractions of populations of cells containing chemi
stry. We further show that the idea behind the al
gorithm can be usefully exploited for the simulati
on of practical\, non-hierarchical chemical system
s. Finally\, we present a promising new technique
for the analysis of stochastic simulations which
allows the creation of a space of phenotype\, thus
allowing the comparison of models and algorithms.
\n\n*Biography*: Sean Sedwards studied electronics
at University College London and later set up a c
ompany to design and manufacture hi-fi amplifiers.
Recently\, seeking a change of career\, he return
ed to academia. At Oxford Brookes University he at
tained first class honours in computer science and
won the John Birch award for the most outstanding
graduate. Beyond his current research in systems
biology he has a broad range of scientific interes
ts and recently worked on chaotic artificial neuro
ns.
LOCATION:Small public lecture room\, Microsoft Research Ltd
\, 7 J J Thomson Avenue (Off Madingley Road)\, Cam
bridge
CONTACT:Dr Fabien Petitcolas
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