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SUMMARY:Stochastic simulation algorithms and analysis of biological system
 s - Sean Sedwards\, CoSBi
DTSTART:20090519T130000Z
DTEND:20090519T140000Z
UID:TALK14748@talks.cam.ac.uk
CONTACT:Dr Fabien Petitcolas
DESCRIPTION:*Abstract*: The so-called 'exact' Gillespie stochastic simulat
 ion algorithms have spawned a number of successors which aim to speed up t
 he computationally intense process of stochastic simulation of chemically 
 reacting systems.  While some of these successors achieve a speed-up by co
 mpromising exactness\, usually via judicious approximation\, others are bo
 th faster and remain exact.  In this latter vein\, the Gibson-Bruck algori
 thm has apparent market-leading asymptotic performance and is the benchmar
 k by which contenders are measured.  In fact\, it has been found that it's
  theoretical performance may not be realised in practical systems which do
  not approach asymptotic dimensions and that its overhead may allow it to 
 be beaten by simpler algorithms.  More surprisingly\, in the stochastic si
 mulation of some complex hierarchical systems whose interactions are combi
 natorial 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 algorithm which gives an improvement of performance o
 ver the Gibson-Bruck algorithm equivalent to O(n) vs. O(n log n) when used
  to simulate the complex interactions of populations of cells containing c
 hemistry.  We further show that the idea behind the algorithm can be usefu
 lly exploited for the simulation of practical\, non-hierarchical chemical 
 systems.  Finally\, we present a promising new technique for the analysis 
 of stochastic simulations which allows the creation of a space of phenotyp
 e\, thus allowing the comparison of models and algorithms.\n\n*Biography*:
  Sean Sedwards studied electronics at University College London and later 
 set up a company to design and manufacture hi-fi amplifiers. Recently\, se
 eking a change of career\, he returned to academia. At Oxford Brookes Univ
 ersity he attained first class honours in computer science and won the Joh
 n Birch award for the most outstanding graduate. Beyond his current resear
 ch in systems biology he has a broad range of scientific interests and rec
 ently worked on chaotic artificial neurons.
LOCATION:Small public lecture room\, Microsoft Research Ltd\, 7 J J Thomso
 n Avenue (Off Madingley Road)\, Cambridge
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