Bloomfield Computer Simulation and Data Analysis in Molecular Biology and Biophysics

An Introduction Using R
1. Auflage 2009
ISBN: 978-1-4419-0083-8
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 321 Seiten

Reihe: Biological and Medical Physics, Biomedical Engineering

This book provides an introduction to two important aspects of modern bioch- istry, molecular biology, and biophysics: computer simulation and data analysis. My aim is to introduce the tools that will enable students to learn and use some f- damental methods to construct quantitative models of biological mechanisms, both deterministicandwithsomeelementsofrandomness;tolearnhowconceptsofpr- ability can help to understand important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data. The availability of very capable but inexpensive personal computers and software makes it possible to do such work at a much higher level, but in a much easier way, than ever before. TheExecutiveSummaryofthein?uential2003reportfromtheNationalAcademy of Sciences, 'BIO 2010: Transforming Undergraduate Education for Future - search Biologists' [12], begins The interplay of the recombinant DNA, instrumentation, and digital revolutions has p- foundly transformed biological research. The con?uence of these three innovations has led to important discoveries, such as the mapping of the human genome. How biologists design, perform, and analyze experiments is changing swiftly. Biological concepts and models are becoming more quantitative, and biological research has become critically dependent on concepts and methods drawn from other scienti?c disciplines. The connections between the biological sciences and the physical sciences, mathematics, and computer science are rapidly becoming deeper and more extensive.

Autoren/Hrsg.

Bloomfield, Victor

Inhaltsverzeichnis

1;Preface;6
2;Contents;10
3;Part I The Basics of R;18
3.1;Chapter 1 Calculating with R;19
3.1.1;1.1 Installing R;19
3.1.2;1.2 Finding help with R;20
3.1.3;1.4 Arithmetic;21
3.1.4;1.5 Complex numbers;21
3.1.5;1.6 Assigning variables;22
3.1.6;1.7 Standard mathematical functions;23
3.1.7;1.8 Vectors;24
3.1.8;1.9 Generating sequences;27
3.1.9;1.10 Logical vectors;29
3.1.10;1.12 Other data structures;35
3.2;Chapter 2 Plotting with R;39
3.2.1;2.1 Some common plots;39
3.2.2;2.2 Customizing plots;44
3.2.3;2.3 Superimposing data series in a plot;55
3.2.4;2.4 Placing two or more plots in a .gure;58
3.2.5;2.5 Error bars;60
3.2.6;2.6 Locating and identifying points on a plot;61
3.2.7;2.7 Problems;62
3.3;Chapter 3 Functions and Programming;64
3.3.1;3.1 Built-in functions in R;64
3.3.2;3.2 User-de.ned functions;67
3.3.3;3.3 Programming;70
3.3.4;3.4 Numerical analysis with R;73
3.3.5;3.5 Problems;80
3.4;Chapter 4 Data and Packages;83
3.4.1;4.1 Writing and reading data to .les;83
3.4.2;4.2 Packages;86
3.4.3;4.3 Data frames;87
3.4.4;4.4 Factors;89
3.4.5;4.5 The contributed package seqinr;90
3.4.6;4.6 Problems;95
4;Part II Simulation of Biological Processes;97
4.1;Chapter 5 Equilibrium and Steady State Calculations;98
4.1.1;5.1 Calculation of the concentration of species in a reacting mixture at equilibrium;98
4.1.2;5.2 Single strand–double helix equilibrium in oligonucleotides;111
4.1.3;5.3 Steady-state enzyme kinetics;116
4.1.4;5.4 Non-linear least-squares .tting;122
4.1.5;5.5 Problems;123
4.2;Chapter 6 Differential Equations and Reaction Kinetics;126
4.2.1;6.1 Analytically solvable models;126
4.2.2;6.2 Numerical integration of ODEs;132
4.2.3;6.3 Stochastic differential equations;146
4.2.4;6.4 Problems;148
4.3;Chapter 7 Population Dynamics: Competition, Predation, and Infection;153
4.3.1;7.1 Models of homogeneous populations of organisms;153
4.3.2;7.2 Models of microbial growth;158
4.3.3;7.3 Models of Epidemics;161
4.3.4;7.4 Problems;167
4.4;Chapter 8 Diffusion and Transport;170
4.4.1;8.1 Transport by simple diffusion;170
4.4.2;8.2 Diffusion in a driving .eld: electrophoresis;177
4.4.3;8.3 Countercurrent diffusion;177
4.4.4;8.4 Diffusion as a random process: Brownian motion;178
4.4.5;8.5 Compartmental models in physiology and pharmacokinetics;180
4.4.6;8.6 Problems;183
4.5;Chapter 9 Regulation and Control of Metabolism;185
4.5.1;9.1 Successive enzyme reactions;185
4.5.2;9.2 Metabolic control analysis;191
4.5.3;9.3 Biochemical systems theory;194
4.5.4;9.4 Problems;198
4.6;Chapter 10 Models of Regulation;200
4.6.1;10.1 Regulation of transcription: Feed-forward loops;200
4.6.2;10.2 Regulation of signaling: Bacterial chemotaxis;202
4.6.3;10.3 Regulation of development: Morphogenesis;206
4.6.4;10.4 Problems;211
5;Part III Analyzing DNA and Protein Sequences;213
5.1;Chapter 11 Probability and Population Genetics;214
5.1.1;11.1 Some fundamentals of probability;214
5.1.2;11.2 Stochastic population models;217
5.1.3;11.4 Probability distribution functions;223
5.1.4;11.5 Population Genetics;235
5.1.5;11.6 Problems;238
5.2;Chapter 12 DNA Sequence Analysis;240
5.2.1;12.1 Getting a sequence from theWeb;240
5.2.2;12.2 Single base sequences and frequencies;244
5.2.3;12.3 Dinucleotide sequences and frequencies;246
5.2.4;12.4 Simulation of restriction sites;251
5.2.5;12.5 Detecting periodicity in a sequence;253
5.2.6;12.6 Problems;255
6;Part IV Statistical Analysis in Molecular and Cellular Biology;256
6.1;Chapter 13 Statistical Analysis of Data;257
6.1.1;13.1 Summary statistics for a single group of data;257
6.1.2;13.2 Statistical comparison of two samples;264
6.1.3;13.3 Analysis of spectral data;273
6.1.4;13.4 Problems;282
6.2;Chapter 14 Microarrays;284
6.2.1;14.1 Introduction;284
6.2.2;14.2 Preprocessing overview;285
6.2.3;14.3 The affy package;286
6.2.4;14.4 Importing data not in standard form;289
6.2.5;14.5 The need for preprocessing;289
6.2.6;14.6 Preprocessing steps;291
6.2.7;14.7 Using the results of preprocessing;296
6.2.8;14.8 Statistical analysis of differential gene expression;298
6.2.9;14.9 Detecting groups of genes;302
6.2.10;14.10 Power analysis;308
6.2.11;14.11 Problems;312
7;Appendix A Basic String Manipulations in R;314
7.1;Elementary string manipulations;314
7.2;Genetic code translation;316
7.3;References;318
8;Index;321