Bioinformatics Computing / Edition 1

Bioinformatics Computing / Edition 1

by Bryan Bergeron
     
 

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ISBN-10: 0131008250

ISBN-13: 2900131008259

Pub. Date: 11/30/2002

Publisher: Prentice Hall

In Bioinformatics Computing, Harvard Medical School and MIT faculty member Bryan Bergeron presents a comprehensive and practical guide to bioinformatics for life scientists at every level of training and practice. After an up-to-the-minute overview of the entire field, he illuminates every key bioinformatics technology, offering practical insight into the full range

Overview

In Bioinformatics Computing, Harvard Medical School and MIT faculty member Bryan Bergeron presents a comprehensive and practical guide to bioinformatics for life scientists at every level of training and practice. After an up-to-the-minute overview of the entire field, he illuminates every key bioinformatics technology, offering practical insight into the full range of bioinformatics applications -- both new and emerging.

Product Details

ISBN-13:
2900131008259
Publisher:
Prentice Hall
Publication date:
11/30/2002
Edition description:
New Edition
Pages:
439

Table of Contents

Prefacexiii
Acknowledgmentsxxii
Chapter 1The Central Dogma2
The Killer Application4
Parallel Universes8
Watson's Definition15
Top-Down Versus Bottom-Up19
Information Flow23
From Data to Knowledge25
Convergence28
Control30
Archiving34
Numerical Processing35
Communications39
Endnote40
Chapter 2Databases42
Definitions48
Data Management51
Pharmacogenomics and Aggression54
Complexity64
Data Life Cycle66
Data Creation and Acquisition66
Use68
Data Modification68
Archiving70
Repurposing74
Disposal75
Managing the Life Cycle75
Database Technology75
Database Architecture80
Database Management Systems84
Interfaces93
Implementation96
Infrastructure100
Endnote102
Chapter 3Networks104
Geographical Scope112
Communications Models113
Transmissions Technology114
Protocols116
Bandwidth119
Topology120
Hardware123
Media123
Network Electronics126
Contents133
Security134
Antiviral Utilities134
Authentication135
Firewalls136
Encryption136
Process138
Ownership139
Implementation139
Management141
On the Horizon141
Endnote142
Chapter 4Search Engines144
The Search Process148
The Search152
Results155
Search Engine Technology155
Intelligent Agents156
Portals158
User Interface Tools159
Utilities162
Searching and Information Theory163
Computational Methods166
Search Algorithms166
Approximate Searches168
Search Engines and Knowledge Management171
On the Horizon174
Endnote175
Chapter 5Data Visualization176
Sequence Visualization182
Sequence Maps182
Structure Visualization186
Visualization Tools187
Rendering Tools187
User Interface198
User Interface Components199
Alternative Metaphors203
Display Architecture205
Animation Versus Simulation209
General-Purpose Technologies209
On the Horizon212
Endnote214
Chapter 6Statistics216
Statistical Concepts218
Progress220
Microarrays222
Imperfect Data231
Basics237
Randomness237
Variability Is Cumulative238
Approximation238
Interface Noise239
Assumptions239
Sampling and Distributions241
Hypothesis Testing243
Quantifying Randomness243
Data Analysis245
Tool Selection250
Statistics of Alignment253
Clustering and Classification254
On the Horizon258
Endnote258
Chapter 7Data Mining260
Methods264
Selection and Sampling266
Preprocessing and Cleaning266
Transformation and Reduction270
Data-Mining Methods270
Evaluation272
Visualization272
Designing New Queries272
Technology Overview272
Infrastructure273
Pattern Recognition and Discovery274
Machine Learning278
Inductive Logic Programming280
Genetic Algorithms280
Neural Networks283
Statistical Methods284
Decision Trees287
Hidden Markov Models289
Text Mining290
Natural Language Processing290
Text Summarization295
Tools296
On the Horizon298
Endnote300
Chapter 8Pattern Matching302
Fundamentals305
Pairwise Sequence Alignment306
Local Versus Global Alignment308
Multiple Sequence Alignment308
Computational Methods310
Dot Matrix Analysis311
Substitution Matrices313
Dynamic Programming317
Word Methods324
Bayesian Methods326
Multiple Sequence Alignment327
Dynamic Programming327
Progressive Strategies327
Iterative Strategies328
Other Strategies329
Tools329
Nucleotide Pattern Matching330
Polypeptide Pattern Matching332
Utilities338
Sequence Databases338
On the Horizon339
Endnote339
Chapter 9Modeling and Simulation342
Drug Discovery348
Fundamentals350
Components350
Process351
Perspectives355
Numeric Considerations358
Algorithms361
Hardware364
Issues365
Protein Structure366
Ab Initio Methods368
Heuristic Methods377
Systems Biology383
Tools383
On the Horizon385
Endnote385
Chapter 10Collaboration388
Collaboration and Communications390
Asynchronous Communications393
Synchronous Communications393
Asynchronous Collaboration394
Synchronous Collaboration394
Standards399
Niche Solutions400
Tool and Data Accessibility400
Data Uniformity402
Interoperability403
Open Source408
Issues409
Platform Dependence409
Security410
Intellectual Property410
Economics411
On the Horizon413
Endnote414
Bibliography419
Index428

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