Guide to Simulation and Modeling for Biosciences

1. Front Matter

   Pages i-xii

   PDF

2. Foundations of Modeling

   • David J. Barnes, Dominique Chu

   Pages 1-14

3. Agent-Based Modeling

   • David J. Barnes, Dominique Chu

   Pages 15-78

4. ABMs Using Repast Simphony

   • David J. Barnes, Dominique Chu

   Pages 79-119

5. Differential Equations

   • David J. Barnes, Dominique Chu

   Pages 121-174

6. Mathematical Tools

   • David J. Barnes, Dominique Chu

   Pages 175-206

7. Other Stochastic Methods and Prism

   • David J. Barnes, Dominique Chu

   Pages 207-264

8. Simulating Biochemical Systems

   • David J. Barnes, Dominique Chu

   Pages 265-299

9. Biochemical Models Beyond the Perfect Mixing Assumption

   • David J. Barnes, Dominique Chu

   Pages 301-324

10. Back Matter

    Pages 325-339

    PDF

This accessible text presents a detailed introduction to the use of a wide range of software tools and modeling environments for use in the biosciences, as well as the fundamental mathematical background. The practical constraints presented by each modeling technique are described in detail, enabling the researcher to determine which software package would be most useful for a particular problem. Features: introduces a basic array of techniques to formulate models of biological systems, and to solve them; discusses agent-based models, stochastic modeling techniques, differential equations, spatial simulations, and Gillespie’s stochastic simulation algorithm; provides exercises; describes such useful tools as the Maxima algebra system, the PRISM model checker, and the modeling environments Repast Simphony and Smoldyn; contains appendices on rules of differentiation and integration, Maxima and PRISM notation, and some additional mathematical concepts; offers supplementary material at an associated website.

• Agent-Based Modeling
• Algorithms
• Bio-Modeling
• Computational Biology
• Computer Algebra
• Differential Equation Models
• Linear Optimization
• Markov Chains
• Model

• University of Kent, Canterbury, United Kingdom

  David J. Barnes

• School of Computing, University of Kent, Canterbury, United Kingdom

  Dominique Chu

David J. Barnes is a senior lecturer in computer science at the University of Kent, UK, with a strong background in the teaching of programming and the implementation of computational models of biological systems.

Dominique Chu is a senior lecturer in computer science at the University of Kent, UK. He is an expert in mathematical and computational modeling of biological systems, with years of experience in these fields.

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