Other Stochastic Methods and Prism
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This chapter introduces the reader to the concept of stochastic systems. It motivates the importance of noise and stochastic fluctuations in biological modeling and introduces some of the basic concepts of stochastic systems, including Markov chains and partition functions. The main objective of this theoretical part is to provide the reader with sufficient theoretical background to be able to understand original research papers in the field. Strong emphasis is placed on conveying a conceptual understanding of the topics, while avoiding burdening the reader with unnecessary mathematical detail. The second part of this chapter describes PRISM, which is a powerful computational tool for formulating, analyzing and simulating Markov-chain models. Throughout the chapter, concepts are illustrated using biologically-motivated case studies.
KeywordsMarkov Chain Partition Function Model Check Transition Matrix Master Equation
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