Chapter 1: Introduction – Matlab® in Bioscience and Biotechnology

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Introduction

Everything that can be countedshould 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.