MATLAB in bioscience and biotechnology

MATLAB® in bioscience and biotechnology presents an introductory Matlab course oriented towards various collaborative areas of biotechnology and bioscience. It concentrates on Matlab fundamentals and gives examples of its application to a wide range of current bioengineering problems in computational biology, molecular biology, bio-kinetics, biomedicine, bioinformatics, and biotechnology. In the last decade Matlab has been presented to students as the first computer program they learn. Consequently, many non-programmer students, engineers and scientists have come to regard it as user-friendly and highly convenient in solving their specific problems. Numerous books are available on programming in Matlab for engineers in general, irrespective of their specialization, or for those specializing in some specific area, but none have been designed especially for such a wide, interdisciplinary, and topical area as bioengineering. Thus, in this book, Matlab is presented with examples and applications to various school-level and advanced bioengineering problems - from growing populations of microorganisms and population dynamics, reaction kinetics and reagent concentrations, predator-prey models, mass-transfer and flow problems, to sequence analysis and sequence statistics.

Author Notes

Dr. Leonid Burstein is Senior Lecturer at large at Technion - Israel Institute of Technology, at the ORT Braude College, in the Biotechnology and Software Engineering Departments, and at a number of other universities in Western and Lower Galilee.

Preface	p. xi
List of figures and tables	p. xiii
About the author	p. xvii
1 Introduction	p. 1
2 Matlab® basics	p. 3
2.1 Starting with Matlab®	p. 3
2.2 Vectors, matrices and arrays	p. 15
2.3 Flow control	p. 33
2.4 Questions for self-checking and exercises	p. 44
2.5 Answers to selected exercises	p. 48
3 Matlab® graphics	p. 49
3.1 Generation of XY plots	p. 49
3.2 Generation of XYZ plots	p. 62
3.3 Specialized 2D and 3D plots	p. 73
3.4 Application examples	p. 79
3.5 Questions for self-checking and exercises	p. 88
3.6 Answers to selected exercises	p. 93
4 Script, function files and some useful Matlab® functions	p. 95
4.1 Script file	p. 95
4.2 Functions and function files	p. 100
4.3 Some useful Matlab® functions	p. 104
4.4 Application examples	p. 116
4.5 Questions for self-checking and exercises	p. 127
4.6 Answers to selected exercises	p. 129
5 Ordinary and partial differential equation solvers	p. 133
5.1 Solving ordinary differential equations with ODE solvers	p. 133
5.2 Solving partial differential equations with the PDE solver	p. 151
5.3 Questions for self-checking and exercises	p. 162
5.4 Answers to selected exercises	p. 167
6 Bioinformatics tool for sequence analysis	p. 171
6.1 About toolboxes	p. 171
6.2 The functions of the Bioinformatics toolbox™	p. 172
6.3 Public databases, data formats and commands for their management	p. 173
6.4 Sequence analysis	p. 182
6.5 Sequence analysis examples	p. 197
6.6 Questions for self-checking and exercises	p. 209
6.7 Answers to selected exercises	p. 211
Appendix: Matlab® characters, operators and commands	p. 217
Index	p. 223

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Author Notes

Table of Contents