Matlab® in Bioscience and Biotechnology

Leonid Burstein

• Publisher: Woodhead Publishing
• Year: 2011
• Print ISBN: 9781907568046
• eBook ISBN: 9781908818034
• Topic: Biological Sciences
• Subtopic: Applied Mathematics
• Index: Biological Sciences

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.- This is the first book intended as a manual introducing biologists and other biotechnology engineers to work with Matlab- It is suitable for beginners and inexperienced users; however, applications of Matlab to advanced problems such as the Monte Carlo method, curve fitting, and reliable machine diagnostics make the book relevant to university teachers as well- The book is different in that it assumes a modest mathematical background for the reader and introduces the mathematical or technical concepts with a somewhat traditional approach; Matlab is then used as a tool for subsequent computer solution

1

Introduction

Everything that can be counted – should be.

Anonymous

Biological engineering is defined as application of engineering principles to the widest spectrum of living systems – from molecular biology, biochemistry and microbiology, to bio-medicine, genetics and bioinformatics. And as in general engineering, computers and the ability to use them are vitally important. This is true also for other professionals of any bio-industry. Thus, bio-specialists and scientists working in these areas need to have the computational resources to be able to solve various problems. A widespread and powerful tool for such purposes is MATLAB® – the software for technical computing. It is designed to solve both general and specific problems; of these, the latter are treated with so-called toolboxes, which currently include means specialized for bio-problems. An obstacle to the effective understanding and implementation of MATLAB® in practice is the inadequate level of math reached by students and specialists in areas of bioscience, combined with a lack of textbooks tailored to such audiences. This book is intended as a remedy. It is organized as follows.

I begin by covering primary MATLAB® programming and then move to more complicated problems by means of this language; the material is illustrated throughout by examples from different areas of bioengineering and biological science. The topics were chosen on the basis of several years of teaching MATLAB® for biotechnologists and they are presented so that inexperienced users can progress gradually, with the previously presented material being the only prerequisite for each new chapter.

Chapter 2 introduces the MATLAB® environment, language design, help options, variables, matrix and array manipulations, elementary and special functions, flow chart control, conditional statements and other basic MATLAB® features.

In Chapter 3 the plotting tool is described by using examples of graphic presentation in various calculations. Mastering the material in Chapter 2 and Chapter 3 will allow readers to create their own MATLAB® programs.

Chapter 4 presents the MATLAB® script- and m-files; the commands for numerical integration, differentiation, inter-/extrapolation and curve fitting, together with their various applications, are given.

In Chapter 5, particular solutions for ordinary and partial differential equations are briefly presented together with examples from bio-systems involving a single differential equation or a set. This chapter assumes a somewhat greater familiarity with mathematics.

In the final chapter the bioinformatics tool is introduced through applications employed in sequence analysis and statistics. Emphasis is placed on DNA and protein sequence database access and further pairwise or multiple alignments.

The Appendix details the studied MATLAB® commands and functions.

Application problems included at the end (and sometimes in the middle) of each chapter are solved with commands accessible to the reader; the solutions are not necessarily the shortest or most original, but should be easy to understand and follow up. Readers are invited to write their own solutions and check the results against those given herein. At the end of each chapter are questions and problems, and readers are encouraged to attempt them for better assimilation of the material. The contexts and values used in the problems are not factual and are intended for learning purposes only.

The MATLAB® used in the book is R2010a, version 7.10.0. Each subsequent version should incorporate all previous ones; hence, the fundamental commands given here should be valid in future versions. It is assumed that the user has a computer with MATLAB® installed on it and is able to perform basic computer operations.

Each command is explained here in its simplest form; additional information is available in the MATLAB®-help or original MATLAB® documentation.

Let us begin.

2

MATLAB® basics

MATLAB® came into being in the 1970s as a tool for mathematicians and educators, but was soon adopted by engineers as an effective means for technical computing. Its name is a composite of the words ‘Matrix’ and ‘Laboratory’, emphasizing that its main element is the matrix. Such an approach permitted unification of the processes of various calculations, graphics, modeling, simulation and algorithm development. This chapter introduces the main windows and starting procedure, describes the main commands for simple arithmetic, algebraic and matrix operations, and presents the basic loops and relational and logical operators.

2.1 Starting with MATLAB®

MATLAB® can be installed on computers running different operation systems, but I will assume here that the reader uses a personal computer running a Windows operating system. To start one has simply to click on the MATLAB® icon (Figure 2.1) provided with a MATLAB® subscription; the icon is placed on the Quick Lunch bar or on the Windows Desktop. Another way to start the program is to select MATLAB® 20010a in the MATLAB®- directory in the ‘All Programs’ option of the Windows ‘Start’ menu.

Figure 2.1 MATLAB® icon (enlarged). The image can be produced with the logo command; the background color has been changed.

2.1.1 MATLAB® Desktop and its windows

The window that first opens is the MATLAB® Desktop (Figure 2.2), which comprises four windows: Command, Current Folder, Workspace and Command History.

Figure 2.2 MATLAB® desktop.

These are the most intensively used windows and are briefly described further. There are also Help, Editor and Figure windows that do not appear with the MATLAB® Desktop and are described in the chapters where they are used.

The Desktop also contains: the Menu, which can be changed depending on the tool being used; the MATLAB® Tools bar, which contains the more common functions; the Shortcuts bar, where one can place icons for quick running ...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• Dedication
• Preface
• List of figures and tables
• About the author
• Chapter 1: Introduction
• Chapter 2: MATLAB® basics
• Chapter 3: MATLAB® graphics
• Chapter 4: Script, function files and some useful MATLAB® functions
• Chapter 5: Ordinary and partial differential equation solvers
• Chapter 6: Bioinformatics tool for sequence analysis
• Appendix: MATLAB® characters, operators and commands
• Index