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SUMMARY:A parallel perspective of the dynamics of biological reactive syst
 ems - Tommaso Mazza\, CoSBi
DTSTART:20090401T100000Z
DTEND:20090401T110000Z
UID:TALK14751@talks.cam.ac.uk
CONTACT:Dr Fabien Petitcolas
DESCRIPTION:*Abstract*: The adoption of a particular fate by cellular mech
 anisms is usually thought of as being deterministic. However\, several fin
 dings have highlighted the relevance of noise and hence of stochasticity. 
 Many simulator tools have been developed to capture\, reproduce and capita
 lize on this property. They use formal models to produce individual markov
 ian trajectories\, usually calculated by the SSA or one of its variants. S
 tatistical inference on the simulation output may require a fairly large n
 umber of trajectories in order to generate accurate results. On the other 
 side\, with the aim to tackle complexity of nature and to faithfully repro
 duce its (intrinsically parallel) behaviours\, some algorithms have been d
 esigned to deal with chemical motion through cellular compartments and wit
 h asynchronous firing of independent chemical reactions. Any of such attem
 pt led scientists to simulate in parallel\, but under heavy assumptions.\n
 \nHaving in mind that biological systems consist of networks of interactin
 g biological components\, we define an optimised stochastic simulation alg
 orithm that takes advantage of the partitioning of models. The resulting a
 lgorithm enjoys the following properties: it is free from any restrictive 
 assumptions (apart from those directly dealing with SSA)\; it is proactive
  to self-adjusting in run-time when the system changes\; it is scalable an
 d correct. Then\, we show how to deal with a basic matter of parallel stoc
 hastic simulation\, namely the maintenance of correct simulation time amon
 gst the simulated parts. Finally\, we give some insights on message-passin
 g policy of communications among computing-cores and parallel random seed 
 generations: both of which are fundamentals aspects in such a framework.\n
 \n*Biography*: Tommaso Mazza was born in Catanzaro\, Italy\, on 8 June 197
 9. He studied Computer Science Engineering at the University of Calabria a
 nd received a PhD in Computer Science and Biomedical Engineering in Novemb
 er 2007 from the ‘Magna Graecia’ University of Catanzaro. In 2004\, he
  worked on the Cofin 2003 Project titled “Tumori ereditari della mammell
 a: studi genetici ed analisi del proteoma” (“Hereditary tumours: genet
 ic studies and proteomic analysis”). In 2005\, he worked on the design o
 f a common interface to translate mass spectrometry raw data (MALDI-TOF an
 d LC) into mzData. In March 2006\, he visited CoSBi\, where he dynamically
  collaborated in the design and implementation of Cyto-Sim\, a stochastic 
 simulator of biochemical processes. Moreover\, he worked on the definition
  of a common interface for unmarshalling SBML models into the Cyto-Sim syn
 tax and vice-versa. In summer 2006\, Tommaso visited Microsoft Research Ca
 mbridge where he investigated the possibility of parallelizing and distrib
 uting simulation algorithms. In 2007\, he joined the Bioinformatics Italia
 n Society (B.IT.S.). Tommaso joined CoSBi in January 2008.
LOCATION:Small public lecture room\, Microsoft Research Ltd\, 7 J J Thomso
 n Avenue (Off Madingley Road)\, Cambridge
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