Chapter 6: Parameter estimation #
Linking data to models: data regression
Jaqaman and Danuser (2006) Nature Reviews Molecular Cell BiologyAn excellent reference on parameter estimation / regression that makes many critical points.
Good practices for building dynamical models in systems biology
Azeloglu and Iyengar (2015) Science SignalingA critical analysis of possible pitfalls in dynamical modelling, with a detailed flowchart for rigorous model development.
Reverse engineering and identification in systems biology: strategies, perspectives and challenges
Villaverde and Banga (2014) Journal of the Royal Society InterfaceA nice survey of some important topics related to reverse engineering and system identification in systems biology.
Recent developments in parameter estimation and structure identification of biochemical and genomic systems
Chun-Chou and Voit (2009) Mathematical BiosciencesA useful overview of parameter estimation in biological systems.
Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods
Moles et al. (2003) Genome ResearchA critical comparison of methods for parameter estimation.
Programming biological models in Python using PySB
Lopez et al. (2013) Molecular Systems BiologyDescribes PySB, a new approach to create models as programs.
Dynamical modeling and multi-experiment fitting with PottersWheel
Maiwald and Timmer (2008) BioinformaticsPottersWheel is a MATLAB toolbox for numerically fast mechanistic mathematical modeling, and can be applied to any ODE system.
Evolutionary Computation
Foster (2001) Nature Reviews GeneticsAn excellent overview of evolutionary computation.
Sensitivity analysis approaches applied to systems biology models
Zi (2011) IET Systems BiologyA very nice overview of sensitivity analysis for systems biology.
An Introduction to Genetic Algorithms, by Melanie Mitchell (1995)
A lucid introduction to genetic algorithms.
GAs for Travelling Salesperson Problem
Discusses GAs to solve TSP, including a tutorial with interactive Java Applets.