Deterministic Versus Stochastic Modelling in Biochemistry and Systems Biology

By Paola Lecca, Ian Laurenzi and Ferenc Jordan

Stochastic kinetic methods are currently considered to be the most realistic and elegant means of representing and simulating the dynamics of biochemical and biological networks. Deterministic versus stochastic modelling in biochemistry and systems biology introduces and critically reviews the deterministic and stochastic foundations of biochemical kinetics, covering applied stochastic process theory for application in the field of modelling and simulation of biological processes at the molecular scale. Following an overview of deterministic chemical kinetics and the stochastic approach to biochemical kinetics, the book goes onto discuss the specifics of stochastic simulation algorithms, modelling in systems biology and the structure of biochemical models. Later chapters cover reaction-diffusion systems, and provide an analysis of the Kinfer and BlenX software systems. The final chapter looks at simulation of ecodynamics and food web dynamics.

• Introduces mathematical concepts and formalisms of deterministic and stochastic modelling through clear and simple examples
• Presents recently developed discrete stochastic formalisms for modelling biological systems and processes
• Describes and applies stochastic simulation algorithms to implement a stochastic formulation of biochemical and biological kinetics

• Language: English
• Publisher: Elsevier Science
• Release date: Apr 9, 2013
• ISBN: 9781908818218

Paola Lecca

Paola Lecca received a M.S. in Theoretical Physics from the University of Trento (Italy) in 1997 and a PhD in Computer Science in 2006 from the International Doctorate School in Information and Communication Technologies at the University of Trento (Italy). Since 1998 she held Researcher and Principal Investigator positions in research centers and in academia. From 1998 to 2000 she was Research Assistant at the Fondazione Bruno Kessler - Center for Information Technologies of Trento by the research unit of Predictive Models for Biomedicine & Environment. From 2001 to 2002 Dr. Lecca worked at the Department of Physics of University of Trento in the area of data manipulation and predictive modelling in research programs of the National Institute of Nuclear Physics. In 2006 she joined to The Microsoft-Research University of Trento Centre for Computational and Systems Biology (COSBI), Italy. At COSBI Dr. Lecca led the group of Data Manipulation and Knowledge Inference. From 2012 to 2015 Dr. Lecca continued her researches at the Laboratory of Computational Oncology of the Centre for Integrative Biology (CIBIO) of University of Trento, Italy. She is currently collaborating with the Department of Mathematics of University of Trento, where she develops optimized techniques of simulation of hybrid (stochastic and deterministic) dynamical biochemical systems.She is a Professional Member of Association for Computing Machinery and author of seventy publications including books and journal and conference papers on international journals in computational biology, bioinformatics, and biophysics. She carries on an intense editorial activity as editor and reviewer for high impact factor journals in these subjects, and leads the organization of school and symposia of bioinformatics.