Computational steering of multi-scale biochemical networks:
Gespeichert in:
| 1. Verfasser: | |
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2013
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| Schlagworte: | |
| Online-Zugang: | kostenfrei Inhaltsverzeichnis |
| Beschreibung: | 159 S. graph. Darst. |
Internformat
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Datensatz im Suchindex
| _version_ | 1804150068892139520 |
|---|---|
| adam_text | IMAGE 1
CONTENTS
ABSTRACT V
Z U S A M M E N F A S S U N G VI
1 INTRODUCTION 1
1.1 OVERVIEW 1
1.2 MOTIVATIONS 3
1.3 OBJECTIVES 5
1.4 THESIS OUTLINE 6
2 COMPUTATIONAL STEERING: AN INTERACTIVE SIMULATION TECHNIQUE 9
2.1 INTRODUCTION 9
2.2 BATCH VERSUS INTERACTIVE SIMULATION 11
2.2.1 INTERACTIVE VISUALISATION 11
2.2.2 COMPUTATIONAL STEERING 12
2.3 APPROACHES 15
2.3.1 PROGRAM ANNOTATION 15
2.3.2 REDESIGNING THE SIMULATION APPLICATION 16
2.3.3 STEERING BY SCRIPTING 16
2..3.4 HIGH-LEVEL ABSTRACTIONS 17
2.3.5 SELECTING THE APPROPRIATE APPROACH 17
2.4 TASKS 19
2.4.1 MODEL EXPLORATION 19
2.4.2 ALGORITHM EXPERIMENTATION 19
2.4.3 PERFORMANCE OPTIMISATION 19
2.5 SOFTWARE 20
2.5.1 CUMULVS 21
2.5.2 CSE 21
2.5.3 DISCOVER 22
2.5.4 POSSE 23
2.5.5 REALITYGRID 23
2.5.6 SCIRUN 24
2.5.7 MAGELLAN 24
2.5.8 STEEL 25
VII
HTTP://D-NB.INFO/1032299347
IMAGE 2
CONTENTS
2.5.9 EPSN 25
2.5.10 OTHERS 26
2.6 CHALLENGES 26
2.6.1 PERFORMANCE OF COMPUTATIONAL STEERING SYSTEM 26
2.6.2 STEERING OF PARALLEL AND DISTRIBUTED APPLICATIONS 27
2.6.3 APPLICATION CONSISTENCY 28
2.7 CLOSING REMARKS 28
3 SIMULATION APPROACHES O F BIOCHEMICAL NETWORKS 2 9
3.1 INTRODUCTION 29
3.2 PRELIMINARIES 30
3.3 DETERMINISTIC APPROACH 31
3.3.1 TYPES OF ODE SOLVERS 32
3.3.2 PROBLEM OF THE DETERMINISTIC APPROACH 34
3.4 STOCHASTIC APPROACH 34
3.4.1 CHEMICAL MASTER EQUATION 35
3.4.2 DIRECT METHOD 36
3.4.3 FIRST R.EACTION METHOD 37
3.4.4 NEXT REACTION METHOD 37
3.4.5 TAU-LEAPING METHOD 39
3.4.6 OTHERS 41
3.5 HYBRID APPROACH 42
3.5.1 REACTION PARTITIONING 42
3.5.2 SIMULATOR SYNCHRONISATION 44
3.6 PETRI NETS 46
3.6.1 STOCHASTIC PETRI NETS 49
3.6.2 CONTINUOUS PETRI NETS 51
3.6.3 HYBRID PETRI NETS 53
3.6.4 HIGH-LEVEL PETRI NETS 55
3.7 CLOSING REMARKS 56
4 GENERALISED HYBRID PETRI N E T S 5 7
4.1 INTRODUCTION 57
4.2 GENERALISED HYBRID PETRI NETS 58
4.2.1 MODELLING 58
4.2.2 FORMAL DEFINITION 63
4.2.3 SEMANTICS 65
4.2.4 GENERATION OF THE CORRESPONDING ODES 67
4.2.5 MARKING-DEPENDENT ARC WEIGHTS 68
4.2.6 CONFLICT RESOLUTION 71
4.3 SIMULATION OF GHPN 74
IMAGE 3
CONTENTS
4.3.1 SIMULATION OF STATICALLY PARTITIONED GHPN[ 0 74
4.3.2 TRANSITION PARTITIONING 77
4.4 IMPLEMENTATION ASPECTS 79
4.4.1 STOCHASTIC SIMULATION ALGORITHM 80
4.4.2 SELECTING AN APPROPRIATE ODE SOLVER 80
4.4.3 DETECTING DISCRETE EVENTS 81
4.5 SPN. CPN AND GHPN: THE BIG PICTURE 81
4.6 COMPARISON WITH OTHER HYBRID PETRI NET TOOLS 83
4.7 EXAMPLES 83
4.7.1 BREAK-REPAIR MODEL 85
4.7.2 GOUTSIAS MODEL 85
4.8 CONCLUSIONS 89
5 A COMPUTATIONAL STEERING FRAMEWORK 9 1
5.1 INTRODUCTION 91
5.2 REQUIREMENTS AND CHARACTERISTICS 92
5.3 FRAMEWORK 93
5.3.1 OVERVIEW 93
5.3.2 STEERING SERVER 95
5.3.3 GRAPHICAL USER INTERFACE 97
5.3.4 APPLICATION PROGRAMMING INTERFACE 98
5.3.5 SIMULATORS 101
5.4 BACKTRACKING 103
5.5 STEERING ALGORITHMS FOR SIMULATION OF BIOCHEMICAL NETWORKS 103
5.5.1 W H A T COULD BE STEERED 105
5.5.2 DETERMINISTIC SIMULATION 106
5.5.3 STOCHASTIC SIMULATION 107
5.5.4 HYBRID SIMULATION 108
5.6 IMPLEMENTATION ISSUES 109
5.6.1 MODEL SYNCHRONISATION 109
5.6.2 SOCKETS AND THREADS 110
5.6.3 COMMUNICATING MODEL SPECIFICATION I L L
5.6.4 COMMUNICATING OUTPUT MATRIX I L L
5.7 COMPARISON 113
5.8 CONCLUSIONS 114
6 CASE S T U D I E S 1 1 5
6.1 THE T7 PHAGE MODEL 116
6.1.1 SLOW AND FAST REACTIONS 118
6.1.2 SIMULATION RESULTS 118
6.2 THE EUKARYOTIC CELL CYCLE 119
IMAGE 4
CONTENTS
6.2.1 RELATED WORK 122
6.2.2 THE MODEL 123
6.2.3 DECISION TO PERFORM DIVISION 126
6.2.4 CELL DIVISION AND MARKING-DEPENDENT, ARC WEIGHTS 126
6.2.5 TRANSITION PARTITIONING 126
6.2.6 SIMULATION RESULTS 128
6.3 CIRCADIAN OSCILLATION 129
6.3.1 MODEL OVERVIEW 132
6.3.2 SIMULATION RESULTS 133
6.3.3 ONLINE STEERING OF THE MODEL PARAMETERS 135
6.3.4 COLOURED MODEL 136
6.4 DISCUSSION 138
6.5 CONCLUSIONS 140
7 CONCLUSIONS AND FUTURE WORK 1 4 1
7.1 CONCLUSIONS 141
7.1.1 GENERALISED HYBRID PETRI NETS 141
7.1.2 COMPUTATIONAL STEERING FRAMEWORK 142
7.1.3 CASE STUDIES 142
7.2 OUTLOOK 143
7.2.1 EXTENDING GENERALISED HYBRID PETRI NETS 143
7.2.2 EXTENDING THE COMPUTATIONAL STEERING FRAMEWORK 145
BIBLIOGRAPHY 1 4 7
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| spelling | Herajy, Mostafa 1980- Verfasser (DE-588)1031274065 aut Computational steering of multi-scale biochemical networks vorgelegt von Mostafa Herayj 2013 159 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Cottbus, Techn. Univ., Diss., 2013 Biochemie (DE-588)4006777-4 gnd rswk-swf Systemmodell (DE-588)4304916-3 gnd rswk-swf Hybrides System (DE-588)4510314-8 gnd rswk-swf Petri-Netz (DE-588)4045388-1 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Biochemie (DE-588)4006777-4 s Systemmodell (DE-588)4304916-3 s Hybrides System (DE-588)4510314-8 s Petri-Netz (DE-588)4045388-1 s DE-604 Erscheint auch als Online-Ausgabe urn:nbn:de:kobv:co1-opus-27255 http://opus.kobv.de/btu/volltexte/2013/2725/ kostenfrei Volltext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025726257&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Herajy, Mostafa 1980- Computational steering of multi-scale biochemical networks Biochemie (DE-588)4006777-4 gnd Systemmodell (DE-588)4304916-3 gnd Hybrides System (DE-588)4510314-8 gnd Petri-Netz (DE-588)4045388-1 gnd |
| subject_GND | (DE-588)4006777-4 (DE-588)4304916-3 (DE-588)4510314-8 (DE-588)4045388-1 (DE-588)4113937-9 |
| title | Computational steering of multi-scale biochemical networks |
| title_auth | Computational steering of multi-scale biochemical networks |
| title_exact_search | Computational steering of multi-scale biochemical networks |
| title_full | Computational steering of multi-scale biochemical networks vorgelegt von Mostafa Herayj |
| title_fullStr | Computational steering of multi-scale biochemical networks vorgelegt von Mostafa Herayj |
| title_full_unstemmed | Computational steering of multi-scale biochemical networks vorgelegt von Mostafa Herayj |
| title_short | Computational steering of multi-scale biochemical networks |
| title_sort | computational steering of multi scale biochemical networks |
| topic | Biochemie (DE-588)4006777-4 gnd Systemmodell (DE-588)4304916-3 gnd Hybrides System (DE-588)4510314-8 gnd Petri-Netz (DE-588)4045388-1 gnd |
| topic_facet | Biochemie Systemmodell Hybrides System Petri-Netz Hochschulschrift |
| url | http://opus.kobv.de/btu/volltexte/2013/2725/ http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025726257&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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