Computational Methods in Systems Biology: International Conference CMSB 2007, Edinburgh, Scotland, September 20-21, 2007, Proceedings (Lecture Notes in Computer Science, 4695)

This book constitutes the refereed proceedings of the International Conference on Computational Methods in Systems Biology, CMSB 2007, held in Edinburgh, Scotland, September 20-21, 2007. The 16 revised full papers presented were carefully reviewed and selected. The papers present a variety of techniques from computer science, such as language design, concurrency theory, software engineering, and formal methods, for biologists, physicists, and mathematicians interested in the systems-level understanding of cellular processes. Cover......Page 1 Lecture Notes in Bioinformatics 4695......Page 2 Computational Methods in Systems Biology......Page 4 ISBN-13 9783540751397......Page 5 Preface......Page 6 Organization......Page 8 Table of Contents......Page 10 Background......Page 13 Illustrative Example: Unimolecular Decay......Page 14 Chemical Langevin Equation......Page 16 Gene Regulation Model......Page 17 Moments for Chemical Master Equation......Page 18 Moments for Chemical Langevin Equation......Page 20 Numerical Experiment for a Bimolecular Case......Page 21 References......Page 25 Introduction......Page 27 Stochastic Chemical Kinetics......Page 29 Relation to Continuous-Time Markov Chains......Page 30 Direct Stochastic Simulation of Single Models......Page 31 Simultaneous Stochastic Simulation of Multiple Models......Page 33 Mathematical Foundations of Importance Sampling......Page 34 Importance Sampling for Biological Networks......Page 35 Reversing Roles in Importance Sampling......Page 38 Runtime Comparison......Page 39 Conclusion......Page 41 References......Page 42 Introduction......Page 44 Related Work......Page 45 Stochastic Logical Networks......Page 46 Fast SLN Reconstruction Algorithm......Page 47 Inferring the Type of Regulation......Page 48 Measuring Quality of Reconstruction......Page 49 Experiments......Page 50 Discrete Boolean Network Model of Mammalian Cell Cycle......Page 51 Continuous Kinetic Model of Mammalian Cell Cycle......Page 52 Reconstruction of Mammalian Cell Cycle Network from Microarray Data......Page 53 Discussion......Page 54 References......Page 56 Introduction......Page 59 Biological Model......Page 60 The Dizzy model......Page 61 Dizzy......Page 62 Usual transcription and CoTC......Page 63 Labelling......Page 64 Description of the model......Page 65 Validation of the model......Page 68 Some analysis results......Page 71 Conclusions......Page 72 References......Page 73 Introduction......Page 75 Constraint-LTL over the Reals......Page 76 The Existential Fragment $\exists$ -Constraint-LTL......Page 77 Formula Instantiation Algorithm......Page 78 Cell Cycle Data......Page 81 MAPK Signal Transduction Data......Page 85 Experimental Data......Page 86 Conclusion......Page 88 References......Page 89 Introduction......Page 91 Context Sensitive Thomas Formalism......Page 92 Timed Automata......Page 95 Modeling the Components......Page 97 Capturing the Network Dynamics......Page 100 Context Sensitivity of Time Delays......Page 102 Perspectives......Page 105 References......Page 106 Introduction......Page 107 Multi-Compartment Gillespie Stochastic Model......Page 109 The Stochastic $\pi$@ Language......Page 110 Syntax and Semantics......Page 111 Chemical Reactions......Page 115 Biological Modellings......Page 116 Related Work......Page 119 Conclusion......Page 120 References......Page 121 Introduction......Page 123 Experimental Results......Page 124 Overview......Page 126 Details of the Simulation......Page 127 Summary......Page 131 References......Page 132 Introduction......Page 133 The Beta Workbench......Page 134 A Compositional Model For Signalling Pathways......Page 137 Evolutionary Framework......Page 139 Mutations......Page 140 An Example: MAPK Cascade......Page 143 References......Page 146 Introduction and Motivations......Page 148 The Narrative Language......Page 149 Case Study: A Narrative Model of the Gp130 Signalling Pathway......Page 153 Beta-binders......Page 156 The Translation Algorithm......Page 157 Case Study: The Translation of the Gp130 Signalling Pathway Model......Page 160 References......Page 162 Motivations......Page 164 A Process Calculi Based Stochastic Model......Page 168 Neuro-processes......Page 170 Paired Pulse Facilitation......Page 172 Short-Term Synaptic Depression......Page 174 Extending the Stochastic Model and Further Considerations......Page 176 References......Page 177 Introduction......Page 180 The nanoκ Calculus: Syntax and Semantics......Page 182 Markov Chains and the nanoκ Calculus......Page 187 nanoκ Calculus at Work: The Rotaxane Case Study......Page 189 Modeling the Rotaxane RaH in nanoκ Calculus......Page 190 Simulation Results......Page 192 References......Page 194 Introduction......Page 196 Biological Example......Page 197 Simulation Algorithm......Page 200 Correctness......Page 204 Implementation......Page 208 Conclusions......Page 209 References......Page 211 Motivation......Page 212 Biochemical Context......Page 213 Overview of the Framework......Page 214 Qualitative Modelling......Page 216 Qualitative Analysis......Page 217 Stochastic Modelling......Page 219 Stochastic Analysis......Page 221 Continuous Analysis......Page 224 Summary and Outlook......Page 226 References......Page 227 Introduction......Page 229 Modeling Biochemical Reactions as Chemical Graph Transformations......Page 230 Reconstructing Metabolic Pathways by Bidirectional Chemical Search......Page 232 Results and Discussion......Page 239 References......Page 243 Introduction......Page 245 Regulatory Graphs......Page 246 Regulatory Graphs and Multi-valued Decision Diagrams......Page 247 Analysis of Regulatory Circuits......Page 248 Functionality Context and Sign of an Interaction......Page 250 Functionality Context and Sign of a Regulatory Circuit......Page 251 Application to Regulatory Networks Controlling T Cell Activation and Differentiation......Page 254 T Cell Differentiation......Page 255 T Cell Activation......Page 257 Conclusion......Page 258 References......Page 259 Author Index......Page 261 Systems biology is an exciting new?eld bringing together life scientists, mat- maticians, computer scientists and engineersto explorea new and deeper und- standing of biological systems. Computational models and methods of analysis are essential components of the systems biology programme, not only re?ecting, but also driving wet lab experimentation and the formation of new hypotheses about system behaviour. This volumecontains theproceedingsofthe?fth meeting oftheinternational conference on Computational Methods in Systems Biology. The?rst conference was in Trento, Italy in 2003. The second meeting was in Paris in 2004, and in 2005 the conference came to Edinburgh for the?rst time. Last year's meeting was again in Trento and this year the conference was again in Edinburgh. This year the conference attracted over 60 paper submissions. Sixteen of these were selected for presentation at the conference. In choosing the 16 best papers, the conference Chairs received wonderful support from the Programme Committee, who deliveredthoroughandinsightful reviewsofallpapersina very short time scale. We thank all of the members of the Programme Committee and their sub-referees for their industriousness. We also thank the authors for responding swiftly to the comments of the referees and revising their papers to address these comments earnestly. The electronic submission of papers, refereeing and Programme Committee workweremadepossiblebytheexcellentEasyChairfreeconferencemanagement system. EasyChairmanagedalloftheaspectsofthereviewprocessfromsubm- sion to review and discussion, through to sending decisionsby e-mailto authors. EasyChair compiled the list of referees which appears in this front matter. We give hearty thanks to Andrei Voronkov for providing this wonderful service to the scienti?c community