Systems biology: a textbook
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Weinheim
Wiley-VCH
[2016]
|
| Ausgabe: | second, completely revised and enlarged edition |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xiii, 488 Seiten Illustrationen, Diagramme |
| ISBN: | 9783527336364 |
Internformat
MARC
| LEADER | 00000nam a2200000 c 4500 | ||
|---|---|---|---|
| 001 | BV042717866 | ||
| 003 | DE-604 | ||
| 005 | 20231009 | ||
| 007 | t| | ||
| 008 | 150727s2016 xx a||| |||| 00||| eng d | ||
| 016 | 7 | |a 1070857106 |2 DE-101 | |
| 020 | |a 9783527336364 |c softcover |9 978-3-527-33636-4 | ||
| 035 | |a (OCoLC)909797011 | ||
| 035 | |a (DE-599)DNB1070857106 | ||
| 040 | |a DE-604 |b ger |e rda | ||
| 041 | 0 | |a eng | |
| 049 | |a DE-20 |a DE-11 |a DE-355 |a DE-703 |a DE-29T |a DE-19 |a DE-858 |a DE-M49 |a DE-526 |a DE-188 |a DE-634 | ||
| 084 | |a WD 9200 |0 (DE-625)148253: |2 rvk | ||
| 084 | |a BIO 220f |2 stub | ||
| 245 | 1 | 0 | |a Systems biology |b a textbook |c Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald |
| 250 | |a second, completely revised and enlarged edition | ||
| 264 | 1 | |a Weinheim |b Wiley-VCH |c [2016] | |
| 264 | 4 | |c 2016 | |
| 300 | |a xiii, 488 Seiten |b Illustrationen, Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 0 | 7 | |a Systembiologie |0 (DE-588)4809615-5 |2 gnd |9 rswk-swf |
| 689 | 0 | 0 | |a Systembiologie |0 (DE-588)4809615-5 |D s |
| 689 | 0 | |5 DE-604 | |
| 700 | 1 | |a Klipp, Edda |d 1965- |e Sonstige |0 (DE-588)1018396683 |4 oth | |
| 700 | 1 | |a Liebermeister, Wolfram |d 1972- |e Sonstige |0 (DE-588)12920725X |4 oth | |
| 700 | 1 | |a Wierling, Christoph |d 1973- |e Sonstige |0 (DE-588)1100549315 |4 oth | |
| 700 | 1 | |a Kowald, Axel |d 1962- |e Sonstige |0 (DE-588)102567989X |4 oth | |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, EPUB |z 978-3-527-67567-8 |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, MOBI |z 978-3-527-67568-5 |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, PDF |z 978-3-527-67566-1 |
| 856 | 4 | 2 | |m DNB Datenaustausch |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028149113&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 943 | 1 | |a oai:aleph.bib-bvb.de:BVB01-028149113 | |
Datensatz im Suchindex
| _version_ | 1826219975412547584 |
|---|---|
| adam_text |
CONTENTS
PREFACE XYY
GUIDE TO D^ERENT TOPICS OF THE XIYYYY
ABOUT THE AUTHORS
XV
PART ONE INTRODUCTION TO SYSTEMS BIOLOGY YY
1 INTRODUCTION 3
1.1 BIOLOG IN TIME AND SPACE 3
1.2 MODELS AND MODELING YY4
1.2.1 WHAT IS A MODEL? 4
1.2.2 PURPOSE AND ADEQUATENESS OF MODELS 5
1.2.3 ADVANTAGES OF COMPUTATIONAL MODELING 5
1.3 BASIC NOTIONS FOR COMPUTATIONAL MODELS 6
1.3.1 MODEL SCOPE 6
1.3.2 MODEL STATEMENTS 6
1.3.3 SYSTEM STATE 6
1.3.4 VARIABLES PARAMETERS AND CONSTANTS 6
1.3.5 MODEL BEHAVIOR
YY
1.3.6 MODEL CLASSIFICATION 7
1.3.7 STEADY STATES 7
1.3.8 MODEL ASSIGNMENT IS NOT UNIQUE 7
1.4 NETWORKS 8
1.5 DATA INTEGRATION 8
1.6 STANDARDS 9
1.7 MODEL ORGANISMS 9
\.
YY
YY
\ ESCHERICHIA COLL
YY
2 YY
YY
\ CEREVISIAE \\
1.7.3 CAENORHABDITIS ELEGANS 11
\.YYA DROSOPHILA MELANOGASTER \\
1.7.5 MUS MUSCULUS 12
REFERENCES 12
FURTHER READING 14
2 MODELING OF BIOCHEMICAL SYSTEMS 15
2.1 OVERSEW OF COMMON MODELING APPROACHES
FOR BIOCHEMICAL SYSTEMS 15
2.2 ODE SYSTEMS FOR BIOCHEMICAL NETWORKS 17
2.2.1 BASIC COMPONENTS OF ODE MODELS 18
2.2.2 ILLUSTRATIVE EXAMPLES OF ODE MODELS 18
REFERENCES 21
FURTHER READING 21
3 STRUCTURAL MODELING AND ANALYSIS OF
BIOCHEMICAL NETWORKS 23
3.1 STRUCTURAL ANALYSIS OF BIOCHEMICAL SYSTEMS 24
3.1.1 SYSTEM EQUATIONS 24
3.1.2 INFORMATION ENCODED IN THE STOICHIOMETRIC
MATRIXN 25
3.1.3 THE FLUX CONE 27
3.1.4 TLEMENTARY FLUX MODES AND EXTREME
PATHWAYS 27
3.1.5 CONSERVATION RELATIONS - NULL SPACE OF NT 29
3.2 CONSTRAINT-BASED FLUX OPTIMIZATION 30
3.2.1 FLUX BALANCE ANALYSIS 31
3.2.2 GEOMETRIC INTERPRETATION OF FLUX BALANCE
ANALYSIS 31
3.2.3 THERMODYNAMIC LONSTRAINTS 31
3.2.4 APPLICATIONS AND TESTS OF THE FLUX OPTIMIZATION
PARADIGM 32
3.2.5 EXTENSIONS OF FLUX BALANCE ANALYSIS 33
EXERCISES 35
REFERENCES 36
FURTHER READING 37
4 KINETIC MODELS OF BIOCHEMICAL NETWORKS:
INTRODUCTION 39
4.1 REACTION KINETICS AND THERMODYNAMICS 39
4.1.1 KINETIC MODELING OF ENZYMATIC REACTIONS 39
4.1.2 THE LAW OF MASS ACTION 40
4.1.3 REACTION THERMODYNAMICS 40
4.1.4 MICHAELIS-MENTEN KINETICS 42
4.1.5 REGULATION OF ENZYME ACTIVITY BY EFFECTORS 44
4.1.6 GENERALIZED MASS ACTION KINETICS 48
4.1.7 APPROXIMATE KINETIC FORMATS 48
4.1.8 CONVENIENCE KINETICS AND MODULAR RATE LAWS 49
4.2 METABOLIC CONTROL ANALYSIS 50
4.2.1 THE COEFFICIENTS OF CONTROL ANALYSIS 51
4.2.2 THE THEOREMS OF METABOLIC CONTROL THEORY 53
4.2.3 MATRIX EXPRESSIONS FOR CONTROL COEFFICIN^ 55
4.2.4 UPPER GLYCOLYSIS AS REALISTIC MODEL EXAMPLE 58
4.2.5 TIME-DEPENDENT RESPONSE COEFFICIENTS 59
EXERCISES 61
REFERENCES 61
FURTHER READING 62
5 DATA FORMATS, SIMULATION TECHNIQUES, AND
MODELING TOOLS 63
5.1 SIMULATION TECHNIQUES AND TOOLS 63
5.1.1 DIFFERENTIAL EQUATIONS 63
5.1.2 STOCHASTIC SIMULATIONS 64
5.1.3 SIMULATION TOOLS 65
5.2 STANDARDS AND FORMATS FOR SYSTEMS
BIOLOGY 72
5.2.1 SYSTEMS BIOLOGY MARKUP LANGUAGE 72
5.2.2 BIOPAX 74
5.2.3 SYSTEMS BIOLOGY GRAPHICAL NOTATION /4
5.3 DATA RESOURCES FOR MODELING OF CELLULAR
REACTION SYSTEMS 75
5.3.1 GENERAL-PURPOSE DATABASES 75
5.3.2 PATHWAY DATABASES 76
5.3.3 MODEL DATABASES 77
5.4 SUSTAINABLE MODELING AND MODEL
SEMANTICS 78
5.4.1 STANDARDS FOR SYSTEMS BIOLOGY MODELS 78
5.4.2 MODEL SEMANTICS AND MODEL COMPARISON 78
5.4.3 MODEL COMBINATION 80
5.4.4 MODEL VALIDITY 82
REFERENCES 83
FURTHER READING 85
6 MODEL FITTING, REDUCTION, AND COUPLING 87
6.1 PARAMETER ESTIMATION 88
6.1.1 REGRESSION, ESTIMATORS, AND MAXIMAL
LIKELIHOOD 88
6.1.2 PARAMETER IDENTIFIABILITY 90
6.1.3 BOOTSTRAPPING 91
6.1.4 BAYESIAN PARAMETER ESTIMATION 92
6.1.5 PROBABILITY DISTRIBUTIONS FOR RATE
CONSTANTS 94
6.1.6 OPTIMIZATION METHODS 97
6.2 MODEL SELECTION 99
6.2.1 WHAT IS A GOOD MODEL? 99
6.2.2 THE PROBLEM OF MODEL SELECTION 100
6.2.3 LIKELIHOOD RATIO TEST 102
6.2.4 SELECTION CRITERIA 102
6.2.5 BAYESIAN MODEL SELECTION 103
6.3 MODEL REDUCTION 104
6.3.1 MODEL SIMPLIFICATION 104
6.3.2 REDUCTION OF FAST PROCESSES 105
6.3.3 QUASI-EQUILIBRIUM AND QUASI-STEADY STATE 107
6.3.4 GLOBAL MODEL REDUCTION 108
6.4 COUPCD SYSTEMS AND EMERGENT
BEHAVIOR 110
6.4.1 MODELING OF COUPLED SYSTEMS 111
6.4.2 COMBINING RATE LAWS INTO MODELS 113
6.43 MODULAR RESPONSE ANALYSIS 113
6.4.4 EMERGENT BEHAVIOR IN COUPLED SYSTEMS 114
6.4.5 CAUSAL INTERACTIONS AND GLOBAL BEHAVIOR 115
EXERCISES 116
REFERENCES 117
FURTHER READING 119
7 DISCRETE, STOCHASTIC, AND SPATIAL MODELS 121
7.1 DISCRETE MODELS 122
7.1.1 BOLEAN NETWORKS 122
7.1.2 PETRI NETS 124
7.2 STOCHASTIC MODELING OF BIOCHEMICAL
REACTIONS 127
7.2.1 CHANCE IN BIOCHEMICAL REACTION SYSTEMS 127
7.2.2 THE CHEMICAL MASTER EQUATION 129
7.2.3 STOCHASTIC SIMULATION 129
/.2.4 CHEMICAL LANGEVIN EQUATION AND
NOISE 130
7.2.5 DYNAMIC FLUCTUATIONS 132
7.2.6 FROM STOCHASTIC TO DETERMINISTIC
MODELING 133
7.3 SPATIAL MODELS 133
7.3.1 TYPES OF SPATIAL MODELS 134
7.3.2 COMPARTMENT MODELS 135
7.3.3 REACTION-DIFFUSION SYSTEMS 136
7.3.4 ROBUST PATTERN FORMATION IN EMBRYONIC
DEVELOPMENT 138
7.3.5 SPONTANEOUS PATTERN FORMATION 139
7.3.6 LINEAR STABILITY ANALYSIS OF THE ACTIVATOR-
INHIBITOR MODEL 140
EXERCISES 142
REFERENCES 143
FURTHER READING 144
8 NETWORK STRUCTURE, DYNAMICS, AND
FUNCTION 145
8.1 STRUCTURE OF BIOCHEMICAL NETWORKS 146
8.1.1 RANDOM GRAPHS 147
8.1.2 SCALE-FREE NETWORKS 148
8.1.3 CONNECTIVITY AND NODE DISTANCES 149
8.1.4 NETWORK MOTIFS AND SIGNIFICANCE TESTS 150
8.1.5 EXPLANATIONS FOR NETWORK STRUCU 151
8.2 REGULATION NETWORKS AND NETWORK
MOTIFS 152
8.2.1 STRUCTURE OF TRANSCRIPTION NEBVORKS 153
8.2.2 REGULATION EDGES AND THEIR STEADY-STATE
RESPONSE 156
8.2.3 NEGATIVE FEEDBACK 156
8.2.4 ADAPTATION MOTIF 157
8.2.5 FEED-FORWARD LOOPS 158
8.3 MODULARITY AND GENE FUNCTIONS 160
8.3.1 CELL FUNCTIONS ARE REFLECTED IN STRUCTURE,
DYNAMICS, REGULATION
YY
AND GENETICS 160
8.3.2 METABOLICS PATHWAYS AND ELEMENTARY
MODES 162
8.3.3 EPISTASIS CAN INDICATE FUNCTIONAL MODULES 163
8.3.4 EVOLUTION OF FUNCTION AND MODULES 163
8.3.5 INDEPENDENT SYSTEMS AS A TACIT MODEL
ASSUMPTION 165
8.3.6 MODULARITY AND BIOLOGICAL FUNCTION ARE
CONCEPTUAL ABSTRACTIONS 165
EXERCISES 16B
REFERENCES 167
FURTHER READING 169
9 GENE EXPRESSION MODELS 171
9.1 MECHANISMS OF GENE EXPRESSION
REGULATION 171
9.1.1 TRANSCRIPTION FACTOR-INITIATED GENE
REGULATION 171
9.1.2 GENERAL PROMOTER STRUCTURE 173
9.1.3 PREDICTION AND ANALYSIS OF PROMOTER
ELEMENTS 174
9.1.4 POSTTRANSCRIPTIONAL REGULATION THROUGH
MICRORNAS 176
9.2 DYNAMIC MODELS OF GENE REGULATION 180
9.2.1 A BASIC MODEL OF GENE EXPRESSION AND
REGULATION 180
9.2.2 NATURAL AND SYNTHETIC GENE REGULATOR
NE^ORKS 183
9.2.3 GENE EXPRESSION MODELING WITH STOCHASTIC
EQUATIONS 186
9.3 GENE REGULATION FUNCTIONS 187
9.3.1 THE LAC OPERON IN
E. COLI 187
9.3.2 GENE REGULATION FUNCTIONS DERIVED FROM
EQUILIBRIUM BINDING 188
9.3.3 THERMODYNAMIC MODELS OF PROMOTER
OCCUPANCY 189
9.3.4 GENE REGULATION FUNCTION OF THE LAC
PROMOTER 191
9.3.5 INFERRING TRANSCRIPTION FACTOR ACTIVITIES FROM
TRANSCRIPTION DATA 192
9.3.6 N
E^ORK COMPONENT ANALYSIS 194
9.3.7 CORRESPONDENCES BETWEEN MRNA AND PROTEIN
LEVELS 196
9.4 FLUCTUATIONS IN GENE EXPRESSION 196
9.4.1 STOCHASTIC MODEL OF TRANSCRIPTION AND
TRANSLATION 197
9.4.2 INTRINSIC AND EXTRINSIC VARIABILITY 200
9.4.3 TEMPORAL FLUCTUATIONS IN GENE
CASCADES 202
EXERCISES 203
REFERENCES 205
FURTHER READING 207
YYYY VARIABILITY, ROBUSTNESS, AND INFORMATION 209
10.1 VARIABILITY AND BIOCHEMICAL M
ODEL 210
10.1.1 VARIABILITY AND UNCERTAINTY ANALYSS 210
10.1.2 FLUX SAMPLING 212
10.1.3 ELASTICITY SAMPLING 213
10.1.4 PROPAGATION OF PARAMETER VARIABILITY IN KINETIC
MODELS 214
10.1.5 MODELS WITH PARAMETER FLUCTUATIONS 216
10.2 ROBUSTNESS MECHANISMS AND SCALING
LAWS 217
10.2.1 ROBUSTNESS IN BIOCHEMICAL SYSTEMS 218
10.2.2 ROBUSTNESS BY BACKUP E
LEM
N 219
10.2.3 FEEDBACK CONTROL 219
10.2.4 PERFECT ROBUSTNESS BY STRUCTURE 222
10.2.5 SCALING LAWS 224
10.2.6 TIME SCALING, SUMMATION LAWS, AND
ROBUSTNESS 227
10.2.7 THE ROLE OF ROBUSTNESS IN EVOLUTION AND
MODELING 228
10.3 ADAPTATION AND EXPLORATION STRATEGIES 229
10.3.1 INFORMATION TRANSMISSION IN SIGNALING
PATHWAYS 230
10.3.2 ADAPTATION AND FOLD-CHANGE DETECTION 230
10.3.3 TWO ADAPTATION MECHANISMS: S
EN
SG
RANDOM SWITCHING 231
10.3.4 SHANNON INFORMATION AND THE VALUE OF
INFORMATION 232
10.3.5 METABOLIC SHIFTS AND ANTICIPATION 233
10.3.6 EXPLORATION STRATEGIES 234
EXERCISES 236
REFERENCES 237
FURTHER READING 239
11 OPTIMALITY AND EVOLUTION 241
11.1 OPTIMALITY IN SYSTEMS B
IOLOG MODELS 243
11.1.1 MATHEMATICAL CONCEPTS FOR OPTIMALITY AND
COMPROMISE 245
11.1.2 METABOLISM IS SHAPED BY OPTIMALITY 248
11.1.3 OPTIMALITY APPROACHES IN METABOLIC
MODELING 250
11.1.4 METABOLIC STRATEGIES 252
11.1.5 OPTIMAL METABOLIC ADAPTATION 253
11.2 OPTIMAL ENZYME CONCENTRATIONS 255
11.2.1 OPTIMIZATION OF CATALYTIC PROPERTIES OF SINGLE
ENZYMES 255
11.2.2 OPTIMAL DISTRIBUTION OF ENZYME CONCENTRATIONS
IN A METABOLIC PATHWAY 257
11.2.3 TEMPORAL TRANSCRIPTION PROGRAMS 259
11.3 EVOLUTION AND SELF-ORGANIZATION 261
11.3.1 INTRODUCTION 261
11.3.2 SELECTION EQUATIONS FOR BIOLOGICAL
MACROMOLECULES 263
11.3.3 THE QUASISPECIES MODEL: SELF-REPLICATION WITH
MUTATIONS 265
11.3.4 THE HYPERCYCLE 267
11.3.5 OTHER MATHEMATICAL MODELS OF EVOLUTION: SPIN
GLAS MODEL 269
11.3.6 THE NEUTRAL THEORY OFMOLECULAR
EVOLUTION 270
11.4 EVOLUTIONARY GAME THEORY 271
11.4.1 SOCIAL INTERACTIONS 272
11.4.2 GAME THEORY 273
11.4.3 EVOLUTIONAL GAME THEOTY 274
11.4.4 REPLICATOR EQUATION FOR POP^^ 274
11.4.5 EVOLUTIONARILY STABLE STRATEGIES 275
11.4.6 DYNAMICAL BEHAVIOR IN THE ROCK-SCISSORS-PAPER
GAME 276
11.4.7 EVOLUTION OF COOPERATIVE BEHAVIOR 276
11.4.8 COMPROMISES BETWEEN METABOLIC YIELD AND
EFFICIENCY 278
EXERCISES 279
REFERENCES 280
FURTHER READING 283
12 MODELS OF BIOCHEMICAL SYSTEMS 285
12.1 METABOLIC SYSTEMS 285
12.1.1 BASIC ELEMENTS OF METABOLIC MODELS 286
12.1.2 TOY MODEL OF UPPER GLYCOLYSIS 286
12.1.3 THREONINE SYNTHESIS PATHWAY MODEL 289
12.2 SIGNALING PATHWAYS 291
12.2.1 FUNCTION AND STRUCTURE OF INTRA- AND INTERCELLULAR
COMMUNICATION 292
12.2.2 RECEPTOR-LIGAND INTERACTIONS 293
12.2.3 STRUCTURAL COMPONENTS OF SIGNALS
PATHWAYS 295
12.2.4 ANALYSIS OF DYNAMIC AND REGULATORY FEATURES
OF SIGNALING PATHWAYS 304
12.3 THE CELL CYCLE 307
12.3.1 STEPS IN THE CYCLE 309
12.3.2 MINIMAL CASCADE MODEL OF A MITOTIC
OSCILLATOR 310
12.3.3 MODELS OF BUDDING YEAST CELL CYCLE 311
12.4 THE AGING PROCESS 314
12.4.1 EVOLUTION OF THE AGING PROCESS 316
12.4.2 USING STOCHASTIC SIMULATIONS TO STUDY
MITOCHONDRIAL DAMAGE 318
12.4.3 USING DELAY DIFFERENTIAL EQUATIONS TO STUDY
MITOCHONDRIAL DAMAGE 323
EXERCISES 327
REFERENCES 327
PART TWO REFERENCE SECTION 331
13 CELL BIOLOGY 333
13.1 THE ORIGIN OF LIFE 334
13.2 MOLECULAR B
IOLOG OF THE CELL 336
13.2.1 CHEMICAL BONDS AND FORCES IMPORTANT IN
BIOLOGICAL MOLECULES 336
13.2.2 FUNCTIONAL GROUPS IN BIOLOGY 338
13.2.3 MAJOR CLASSES OF BIOLOGICAL MOECULES 338
13.3 STRUCTURAL CELL BIOLOGY 345
13.3.1 STRUCTURE AND FUNCTION OF BO
MEMBRANES 347
13.3.2 NUCLEUS 349
13.3.3 C^OSOL 349
13.3.4 MITOCHONDRIA 350
13.3.5 ENDOPLASMIC RETICULUM AND GOLGI
COMPLEX 350
13.3.6 OTHER ORGANELLES 351
13.4 EXPRESSION OF GENES 351
13.4.1 TRANSCRIPTION 351
13.4.2 PROCESSING OF THE MRNA 353
13.4.3 TRANSLATION 353
13.4.4 PROTEIN SORTING AND POSTTRANSLATIONAL
MODIFICATIONS 355
13.4.5 REGULATION OF GENE EXPRESSION 355
EXERCISES 350
REFERENCES 356
FURTHER READING 356
14 EXPERIMENTAL TECHNIQUES 357
14.1 RESTRICTION ENZYMES AND GEL
ELECTROPHORESIS 358
14.2 CLONING VECTORS AND DNA LIBRARIES 359
14.3 ID AND 2D PROTEIN GELS 361
14.4 HYBRIDIZATION AND BLOTTING TECHNIQUES 362
14.4.1 SOUTHERN BLOTTING 363
14.4.2 NORTHERN BLOTTING 363
14.4.3 WESTERN BLOTTING 363
14.4.4 IN SITU HYBRIDIZATION 364
14.5 FURTHER PROTEIN SEPARATION TECHNIQUES 364
14.5.1 CENTRIFUGATION 364
14.5.2 COLUMN CHROMATOGRAPHY 364
14.6 POLYMERASE CHAIN REACTION 365
14.7 NEXT-GENERATION SEQUENCING 366
14.8 DNA AND PROTEIN CHIPS 367
14.8.1 DNA CHIPS 367
14.8.2 PROTEIN CHIPS 367
14.9 RNA-SEQ 368
14.10 YEAST T
YY
VO-HYBRID SYSTEM 368
14.11 MASS SPECTROMETRY 369
14.12 TRANSGENIC ANIMALS 370
14.12.1 MICROINJECTION N
D ES CELLS 370
14.12.2 GENOME EDITING USING ZFN, TALEYY, AND
CRISPR 370
14.13 RNA INTERFERENCE 371
14.14 CHIP.ON.CHIP AND CHIP-PET 372
14.15 GREEN FLUORESCENT PROTEIN 374
14.16 SINGLE-CELL EXPERIMENTS 375
14.17 SURFACE PLASMON RESONANCE 376
EXERCISES 377
REFERENCES 377
15 MATHEMATICAL AND PHYSICAL CONCEPTS 381
15.1 LINEAR ALGEBRA 381
15.1.1 LINEAR EQUATIONS 381
15.1.2 MATRICES 384
15.2 DYNAMIC SYSTEMS 386
15.2.1 DESCRIBING DYNAMICS WITH ORDINARY DIFFERENTIAL
EQUATIONS 386
15.2.2 LINEARIZATION OF AUTONOMOUS SYSTEM 388
15.2.3 SOLUTION OFLINEAR ODE SYSTEMS 388
15.2.4 STABILITY OF STEADY STATES 388
15.2.5 GLOBAL STABILITY OF STEADY STATES 390
15.2.6 LIMITCYCLES 390
15.3 STATISTICS 391
15.3.1 BASIC CONCEPTS OF PROBABILITY THEORY 391
15.3.2 DESCRIPTIVE STATISTICS 396
15.3.3 TESTING STATISTICAL HYPOTHESES 399
15.3.4 LINEAR MODELS 401
15.3.5 PRINCIPAL COMPONENT ANALYSIS 404
15.4 STOCHASTIC PROCESSES 405
15.4.1 CHANCE IN PHYSICAL THEORIES 405
15.4.2 MATHEMATICAL RANDOM PROCESSES 406
15.4.3 BROWNIAN MOTION AS A RANDOM PROCESS 407
1^ 4 4 MARKOV PROCESSES 409
15.4.5 MARKOV CHAINS 410
15.4.6 JUMP PROCESSES IN CONTINUOUS TIME 410
15.4.7 CONTINUOUS RANDOM PROCESSES 411
15.4.8 MOMENT-GENERATING FUNCTIONS 412
15.5 CONTROL OF LINEAR DYNAMICAL SYSTEMS 412
15.5.1 LINEAR DYNAMICAL SYSTEMS 413
15.5.2 SYSTEM RESPONSE AND LINEAR FILTERS 414
15.5.3 RANDOM FLUCTUATIONS AND SPECTRAL DENSITY 415
15.5.4 THE GRAMIAN MATRICES 415
15.5.5 MODEL REDUCTION 416
15.5.6 OPTIMAL CONTROL 416
15.6 BIOLOGICAL THERMODYNAMICS 417
15.6.1 MICROSTATE AND STATISTICAL ENSEMBLE 417
15.6.2 BOLTZMANN DISTRIBUTION AND FREE ENERGY 418
15.6.3 ENTROPY 419
15.6.4 EQUILIBRIUM CONSTANT AND ENERGIES 421
15.6.5 CHEMICAL REACTION SYSTEMS 422
15.6.6 NONEQUILIBRIUM REACTIONS 424
15.6.7 THE ROLE OF THERMODYNAMICS IN SYSTEMS
BIOLOGY 425
15.7 MULTIVARIATE STATISTICS 426
15.7.1 PLANNING AND DESIGNING EXPERIMENTS FOR
CASE-CONTROL STUDIES 426
15.7.2 TESTS FOR DIFFERENTIAL EXPRESSION 427
15.7.3 MULTIPLE TESTING 428
15.7.4 ROC CURVE ANALYSIS 429
15.7.5 CLUSTERING ALGORITHMS 430
15.7.6 CLUSTER VALIDATION 435
15.7.7 OVERREPRESENTATION AND ENRICHMENT
ANALYSES 436
15.7.8 CLASSIFICATION METHODS 438
EXERCISES 441
REFERENCES 443
16 DATABASES 445
16.1 GENERAL-PURPOSE DATA RESOURCES 445
16.1.1 PATHGUIDE 445
16.1.2 BIONUMBERS 446
16.2 NUCLEOTIDE SEQUENCE DATABASES 446
16.2.1 DATA REPOSITORIES OF THE NATIONAL
CENTER FOR BIOTECHNOLOGY
INFORMATION 446
16.2.2 GENBANK/REFSEQ/UNIGENE 446
16.2.3 ENTEZ
447
16.2.4 EMBL NUCLEOTIDE SEQUENCE DATABASE 447
16.2.5 EUROPEAN NUCLEOTIDE ARCHIVE 447
16.2.6 ENSEMBL 447
16.3 PROTEIN DATABASES 448
16.3.1 UNIPROT/SWISSYYPROT/TREMBL 448
16.3.2 PROTEIN DATA BANK 448
16.3.3 PANTHER 448
16.3.4 INTERPRO 448
16.3.5 IHOP 449
16.4 ONTOLO^ DATABASES 449
16.4.1 GENE ONTOLOGY 449
16.5 PATHWAY DATABASES 449
16.5.1 KEGG 450
16.5.2 REACTOME 450
16.5.3 CONSENSUSPATHDB 451
16.5.4 WIKIPATHWAYS 451
16.6 ENZYME REACTION KINETICS
DATABASES 451
16.6.1 BRENDA 451
16.6.2 SABIO.RK 452
16.7 MODEL EJECTIO
N
S 452
16.7.1 BIOMODELS 452
16.7.2 JWS ONLINE 452
16.8 COMPOUND AND DRUG DATABASES 452
16.8.1 CHEBI 453
16.8.2 GUIDE TO PHARMACOLOGY 453
16.9 TRANSCRIPTION FACTOR DATABASES 453
16.9.1 JASPAR 453
16.9.2 TRED 453
16.9.3 TRANSCRIPTION FACTOR ENCYCLOPE^^ 454
16.10 MICROARRAY AND SEQUENCING
DATABASES 454
16.10.1 GENE EXPRESION OMNIBUS 454
16.10.2 ARRAYEXPRESS 454
REFERENCES 455
17 SOFTWARE TOOLS FOR MODELING 457
17.1 13C-FLUX2 458
17.2 ANTIMONY 458
17.3 BERKELEY MADONNA 459
17.4 BIOCHAM 459
17.5 BIONETGEN 459
17.6 BIOPYTHON 459
17.7 BIOTAPESTRY 460
17.8 BIOUML 460
17.9 CELLDESIGNER 460
17.10 CELLNETANALYZER 460
17.11 COPASI 461
17.12 CPNTOOLS 461
17.13 C^OSCAPE 461
17.14 E-CELL 461
17.15 YYYYYY2 461
17.16 FENICS PROJECT 462
17.17 GENETIC NETWORK ANALYZER (GNA) 462
17.18 JARNAC 462
17.19 JDESIGNER 463
17.20 JSIM 463
17.21 KNIME 463
17.22 LIBSBML 464
17.23 MASON 464
17.24 MATHEMATICA 4^4.
17.25 MATHSBML 465
17.26 MATLAB 465
17.27 MESORD 465
17.28 OCTAVE 465
17.29 OMIX VISUALIZATION 466
17.30 OPENCOR 466
17.31 OSCYYYY18 466
17.32 PHYSIODESIGNER 466
17.33 POTTERSWHEEL 467
1734 PYBIOS 467
17.35 PYSCES 467
17.36 R 468
17.37 SAAM II 468
17.38 SBMLEDITOR 468
17.39 SEMANTICSBML 468
17.40 SBML-YYYYYY.YYYYYY 469
17.41 SBMLSIMULATOR 469
17.42 SBMLSQUEEZER 469
17.43 SBMLTOOLBOX 470
17.44 SBTOOLBOX2 470
17.45 SBML VALIDATOR 470
17.46 SENSA 470
17.47 SMARTCELL 471
17.48 STELLA 471
17.49 STEPS 471
17.50 STOCHKIT2 471
17.51 SYSTEMMODELER 472
17.52 SYSTEMS B
IOLOG WORKBENCH 472
17.53 TAVERNA 472
17.54 VANTED 473
17.55 VIRTUAL CELL (VCELL) 473
17.56 XCELLERATOR 473
17.57 XPPAUT 473
EXERCISES
474
YY
REFERENCES 474
INDEX 475 |
| any_adam_object | 1 |
| author_GND | (DE-588)1018396683 (DE-588)12920725X (DE-588)1100549315 (DE-588)102567989X |
| building | Verbundindex |
| bvnumber | BV042717866 |
| classification_rvk | WD 9200 |
| classification_tum | BIO 220f |
| ctrlnum | (OCoLC)909797011 (DE-599)DNB1070857106 |
| discipline | Biologie |
| edition | second, completely revised and enlarged edition |
| format | Book |
| fullrecord | <?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>00000nam a2200000 c 4500</leader><controlfield tag="001">BV042717866</controlfield><controlfield tag="003">DE-604</controlfield><controlfield tag="005">20231009</controlfield><controlfield tag="007">t|</controlfield><controlfield tag="008">150727s2016 xx a||| |||| 00||| eng d</controlfield><datafield tag="016" ind1="7" ind2=" "><subfield code="a">1070857106</subfield><subfield code="2">DE-101</subfield></datafield><datafield tag="020" ind1=" " ind2=" "><subfield code="a">9783527336364</subfield><subfield code="c">softcover</subfield><subfield code="9">978-3-527-33636-4</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(OCoLC)909797011</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)DNB1070857106</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-604</subfield><subfield code="b">ger</subfield><subfield code="e">rda</subfield></datafield><datafield tag="041" ind1="0" ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-20</subfield><subfield code="a">DE-11</subfield><subfield code="a">DE-355</subfield><subfield code="a">DE-703</subfield><subfield code="a">DE-29T</subfield><subfield code="a">DE-19</subfield><subfield code="a">DE-858</subfield><subfield code="a">DE-M49</subfield><subfield code="a">DE-526</subfield><subfield code="a">DE-188</subfield><subfield code="a">DE-634</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">WD 9200</subfield><subfield code="0">(DE-625)148253:</subfield><subfield code="2">rvk</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">BIO 220f</subfield><subfield code="2">stub</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Systems biology</subfield><subfield code="b">a textbook</subfield><subfield code="c">Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald</subfield></datafield><datafield tag="250" ind1=" " ind2=" "><subfield code="a">second, completely revised and enlarged edition</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="a">Weinheim</subfield><subfield code="b">Wiley-VCH</subfield><subfield code="c">[2016]</subfield></datafield><datafield tag="264" ind1=" " ind2="4"><subfield code="c">2016</subfield></datafield><datafield tag="300" ind1=" " ind2=" "><subfield code="a">xiii, 488 Seiten</subfield><subfield code="b">Illustrationen, Diagramme</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="b">n</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="b">nc</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Systembiologie</subfield><subfield code="0">(DE-588)4809615-5</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="689" ind1="0" ind2="0"><subfield code="a">Systembiologie</subfield><subfield code="0">(DE-588)4809615-5</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2=" "><subfield code="5">DE-604</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Klipp, Edda</subfield><subfield code="d">1965-</subfield><subfield code="e">Sonstige</subfield><subfield code="0">(DE-588)1018396683</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Liebermeister, Wolfram</subfield><subfield code="d">1972-</subfield><subfield code="e">Sonstige</subfield><subfield code="0">(DE-588)12920725X</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Wierling, Christoph</subfield><subfield code="d">1973-</subfield><subfield code="e">Sonstige</subfield><subfield code="0">(DE-588)1100549315</subfield><subfield code="4">oth</subfield></datafield><datafield tag="700" ind1="1" ind2=" "><subfield code="a">Kowald, Axel</subfield><subfield code="d">1962-</subfield><subfield code="e">Sonstige</subfield><subfield code="0">(DE-588)102567989X</subfield><subfield code="4">oth</subfield></datafield><datafield tag="776" ind1="0" ind2="8"><subfield code="i">Erscheint auch als</subfield><subfield code="n">Online-Ausgabe, EPUB</subfield><subfield code="z">978-3-527-67567-8</subfield></datafield><datafield tag="776" ind1="0" ind2="8"><subfield code="i">Erscheint auch als</subfield><subfield code="n">Online-Ausgabe, MOBI</subfield><subfield code="z">978-3-527-67568-5</subfield></datafield><datafield tag="776" ind1="0" ind2="8"><subfield code="i">Erscheint auch als</subfield><subfield code="n">Online-Ausgabe, PDF</subfield><subfield code="z">978-3-527-67566-1</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="m">DNB Datenaustausch</subfield><subfield code="q">application/pdf</subfield><subfield code="u">http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028149113&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA</subfield><subfield code="3">Inhaltsverzeichnis</subfield></datafield><datafield tag="943" ind1="1" ind2=" "><subfield code="a">oai:aleph.bib-bvb.de:BVB01-028149113</subfield></datafield></record></collection> |
| id | DE-604.BV042717866 |
| illustrated | Illustrated |
| indexdate | 2025-03-10T15:04:46Z |
| institution | BVB |
| isbn | 9783527336364 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-028149113 |
| oclc_num | 909797011 |
| open_access_boolean | |
| owner | DE-20 DE-11 DE-355 DE-BY-UBR DE-703 DE-29T DE-19 DE-BY-UBM DE-858 DE-M49 DE-BY-TUM DE-526 DE-188 DE-634 |
| owner_facet | DE-20 DE-11 DE-355 DE-BY-UBR DE-703 DE-29T DE-19 DE-BY-UBM DE-858 DE-M49 DE-BY-TUM DE-526 DE-188 DE-634 |
| physical | xiii, 488 Seiten Illustrationen, Diagramme |
| publishDate | 2016 |
| publishDateSearch | 2016 |
| publishDateSort | 2016 |
| publisher | Wiley-VCH |
| record_format | marc |
| spelling | Systems biology a textbook Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald second, completely revised and enlarged edition Weinheim Wiley-VCH [2016] 2016 xiii, 488 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Systembiologie (DE-588)4809615-5 gnd rswk-swf Systembiologie (DE-588)4809615-5 s DE-604 Klipp, Edda 1965- Sonstige (DE-588)1018396683 oth Liebermeister, Wolfram 1972- Sonstige (DE-588)12920725X oth Wierling, Christoph 1973- Sonstige (DE-588)1100549315 oth Kowald, Axel 1962- Sonstige (DE-588)102567989X oth Erscheint auch als Online-Ausgabe, EPUB 978-3-527-67567-8 Erscheint auch als Online-Ausgabe, MOBI 978-3-527-67568-5 Erscheint auch als Online-Ausgabe, PDF 978-3-527-67566-1 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028149113&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Systems biology a textbook Systembiologie (DE-588)4809615-5 gnd |
| subject_GND | (DE-588)4809615-5 |
| title | Systems biology a textbook |
| title_auth | Systems biology a textbook |
| title_exact_search | Systems biology a textbook |
| title_full | Systems biology a textbook Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald |
| title_fullStr | Systems biology a textbook Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald |
| title_full_unstemmed | Systems biology a textbook Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald |
| title_short | Systems biology |
| title_sort | systems biology a textbook |
| title_sub | a textbook |
| topic | Systembiologie (DE-588)4809615-5 gnd |
| topic_facet | Systembiologie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028149113&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT klippedda systemsbiologyatextbook AT liebermeisterwolfram systemsbiologyatextbook AT wierlingchristoph systemsbiologyatextbook AT kowaldaxel systemsbiologyatextbook |