This book constitutes the refereed proceedings of the 7th International Conference on Computational Methods in Systems Biology, CMSB 2009, held in Bologna, Italy, August 31 - September 1, 2009. The 18 revised full papers presented together with the summaries of 3 invited papers were carefully reviewed and selected from more than 45 submissions. The papers cover theoretical or applied contributions that are motivated by a biological question focusing on modeling approaches, including process algebra, simulation approaches, analysis methods, in particular model checking and flux analysis, and case studies.
Author(s): Pierpaolo Degano, Roberto Gorrieri
Series: Lecture Notes in Bioinformatics 5688
Edition: 1
Publisher: Springer
Year: 2009
Language: English
Pages: 341
Cover......Page 1
Lecture Notes in Bioinformatics 5688......Page 2
Computational Methods
in Systems Biology......Page 3
ISBN-13 9783642038440......Page 4
Preface......Page 6
Organization......Page 8
Table of Contents......Page 10
Introduction......Page 13
General Features of Interacting Protein Complexes......Page 14
Structure and Evolutionary Based Methods......Page 16
Details on Data Bases......Page 21
Our Approach: ISPRED......Page 23
Scoring the Performance......Page 24
Results......Page 25
Conclusions......Page 27
References......Page 28
Introduction and Motivations......Page 30
Algorthimic Systems Biology......Page 31
Biological Narratives......Page 32
Components......Page 33
Complexing Rules......Page 34
Compartments and Space......Page 35
References......Page 36
Introduction......Page 38
BlenX......Page 40
BlenX4Bio......Page 41
BlenX4Bio Modeling......Page 43
Spatial Architecture of Cell Compartments......Page 44
Components......Page 47
Complexes......Page 51
Binding Affinities......Page 52
Translocation Affinities......Page 57
Dynamics......Page 60
Conclusions and Future Work......Page 61
References......Page 62
Introduction......Page 64
The Circadian Clock of Neurospora Crassa......Page 66
Bio-PEPA......Page 67
The Bio-PEPA Model of the Circadian Clock......Page 68
Validation of the Model......Page 70
Effect of the Scaling Factor Ω on Stochasticity......Page 71
Investigating the Role of Positive Feedback......Page 72
Sensitivity Analysis for the 12:12 LD System......Page 73
Conclusions......Page 76
References......Page 77
Introduction......Page 80
Preliminaries......Page 82
Quantitative Pathway Logic......Page 83
Simulation and Analysis of QPL Models......Page 85
Discrete Functional Petri Nets......Page 87
Model Equivalence......Page 89
Implementation......Page 91
Related Work and Conclusions......Page 92
References......Page 93
Introduction......Page 95
Inference of the Transduction Network......Page 97
Data Source and Definition of the Weights......Page 98
Results......Page 99
Discussion......Page 105
References......Page 106
Introduction......Page 108
Isabelle......Page 110
Formal Analysis of Genetic Networks......Page 111
A Case Study: The Genetic Toggle......Page 114
Modelling the Genetic Toggle......Page 115
Verifying the Genetic Toggle......Page 116
Conclusions......Page 121
References......Page 122
Introduction......Page 123
The Heat Shock Response in Eukaryotes......Page 125
A Functional Decomposition of the Heat Shock Response Model......Page 128
Disentangling the Functional Roles of the Control Feedbacks......Page 129
Discussion......Page 135
References......Page 136
Introduction......Page 138
Reachability: Linear and Nonlinear Systems......Page 141
Dynamic Hybridization......Page 145
Experimental Results......Page 148
Discussion......Page 149
References......Page 151
Introduction......Page 154
Mammalian Cell Division Cycle......Page 156
Irinotecan......Page 157
Syntax and Differential Semantics of BIOCHAM Reaction Models......Page 159
Querying BIOCHAM Models in Temporal Logic......Page 160
Three Different Modules......Page 161
A Diagrammatic Coupled Model......Page 162
Specifying and Validating the Links through Model-Checking......Page 163
Conclusion and Perspectives......Page 166
References......Page 167
Introduction......Page 170
Preliminaries......Page 174
Decidability Results......Page 177
Undecidability Results......Page 179
Related Work......Page 180
Conclusions......Page 182
References......Page 183
Introduction......Page 185
Stochastic Model......Page 187
Transition Class Models......Page 188
Chemical Master Equation......Page 189
Trajectory Generation......Page 190
Output Analysis......Page 191
Numerical Reachability Analysis......Page 192
Experimental Results......Page 195
References......Page 198
Introduction......Page 201
Bio-PEPA......Page 203
Semantic Equivalences......Page 206
Compression Bisimulation......Page 207
Equivalence and Congruence Results......Page 208
Example......Page 213
Conclusions and Further Research......Page 214
References......Page 215
Introduction......Page 217
The Original Algorithm......Page 219
The Improved Algorithm......Page 221
Numerical Evaluation on Benchmark Problems......Page 222
Problems from the Literature......Page 223
Problems of Increasing Size......Page 225
Discussion......Page 227
References......Page 228
Introduction......Page 230
Specifying Properties in Temporal Logic......Page 232
Existing Statistical Probabilistic Model Checking Algorithms......Page 233
Bayesian Statistical Model Checking......Page 234
Bayesian Statistics......Page 235
Algorithm......Page 236
Benchmarks......Page 238
PRISM Benchmarks......Page 239
SBML Experiments......Page 241
Conclusions and Future Work......Page 243
References......Page 244
Introduction......Page 247
Imperativeπ-Calculus......Page 249
A Model of Osmosis: Variable Volumes and Surfaces......Page 255
Programming BioAmbients......Page 257
References......Page 261
Introduction......Page 263
The Bayesian Dynamics Model......Page 265
The Markov Chain {\it MC$_{ideal}$}......Page 266
The BDM Representation......Page 268
The EGF-NGF Signaling Pathway and Its BDM......Page 270
Probabilistic Inference......Page 271
Parameter Estimation......Page 273
Global Sensitivity Analysis......Page 275
References......Page 276
Introduction......Page 278
Logical Modelling of Regulatory Networks......Page 279
Regulatory Graphs......Page 280
Logical Regulatory Graph Reduction......Page 281
Dynamics of the Reduced Model......Page 284
Application: Segment Polarity......Page 288
Conclusions and Prospects......Page 290
References......Page 291
Introduction......Page 293
Modeling Formalism and Solution Techniques......Page 294
Analysis Techniques Based on Structural Properties......Page 295
A Stochastic Petri Nets Based Approach Applied to Signal Transduction Pathways for the Angiogenesis Process......Page 296
Model Construction......Page 297
Model Simplification......Page 299
Model Analysis for Accuracy Assessment......Page 303
Discussion......Page 306
References......Page 307
Motivation......Page 308
Preliminaries......Page 309
Basic Algorithm......Page 312
Optimization Techniques......Page 315
Benchmarks......Page 317
Conclusions......Page 322
References......Page 323
Introduction......Page 325
Abstraction of a Time Series in Terms of Qualitative Transition Systems......Page 327
Abstraction of a Time Series in Terms of Timed Words......Page 328
Abstraction of a Timed Word in Terms of Qualitative Transition System......Page 329
Abstraction of the Transient Behavior of Deterministic Parametrized Models......Page 330
Accounting for Noise by Comparing Critical Points......Page 332
Searching a Trajectory with a Given Periodic Orbit......Page 334
Estimating the Period of Orbits......Page 336
Searching for Given Transient Behavior in a Parameter Subspace......Page 337
Discussion and Conclusions......Page 338
References......Page 339
Author Index......Page 341
