Simulation algorithms for computational systems biology:
Gespeichert in:
| Hauptverfasser: | , , |
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| Format: | Elektronisch E-Book |
| Sprache: | English |
| Veröffentlicht: |
Cham
Springer
[2017]
|
| Schriftenreihe: | Texts in theoretical computer science
|
| Schlagworte: | |
| Online-Zugang: | DE-634 DE-Aug4 DE-573 DE-M347 DE-92 DE-898 DE-859 DE-860 DE-861 DE-863 DE-862 DE-523 DE-473 DE-19 DE-355 DE-703 DE-20 DE-706 DE-29 DE-739 Volltext Inhaltsverzeichnis |
| Beschreibung: | 1 Online-Ressource (XI, 238 Seiten, 52 illus., 23 illus. in color) |
| ISBN: | 9783319631134 |
| ISSN: | 1862-4499 |
| DOI: | 10.1007/978-3-319-63113-4 |
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Datensatz im Suchindex
| DE-BY-FWS_katkey | 658974 |
|---|---|
| _version_ | 1817386776269946880 |
| adam_text |
Contents
1 Introduction 1
1 1 Simulation Approaches for Biochemical Reactions 3
1 2 Further Reading 5
2 Stochastic Simulation of Biochemical Reaction Systems 7
2 1 Stochastic Chemical Kinetics 7
211 Biochemical Reactions 7
212 Reaction Propensity 11
213 Chemical Master Equation 13
2 2 Stochastic Simulation 16
2 3 Simulation Output Analysis 20
231 Confidence Interval Estimation 20
232 Probability Distribution Estimation 22
233 Illustrative Examples 22
2 4 Summary 27
2 5 Further Reading 27
3 Implementations of the Stochastic Simulation Algorithm 29
3 1 Direct Method 31
311 Enhanced Direct Method 34
3 2 Improvements for Direct Method 37
321 Direct Method with Sorted Reactions 38
322 Direct Method with Multi-level Search 43
323 Direct Method with Tree-Based Search 45
324 Direct Method with Composition-Rejection Search 55
3 3 Partial-Propensity Direct Method 58
331 PDM with Composition-Rejection Search 66
3 4 Benchmark of DM and Its Derived Algorithms 68
3 5 First Reaction Method 71
351 First Family Method 74
3 6 Next Reaction Method 75
IX
X
Contents
361 Modified Next Reaction Method 81
3 7 Benchmark of FRM and Its Derived Algorithms 85
3 8 Rejection-Based SSA 87
381 Simultaneous RSSA 95
3 9 Improvements for RSSA 96
391 RSSA with Tree-Based Search 96
392 RSSA with Composition-Rejection Search 99
393 RSSA with Table-Lookup Search 101
3 10 Benchmark of RSSA and Its Derived Algorithms 104
3 11 Summary 108
3 12 Further Reading Ill
4 Approximate Simulation of Biochemical Reaction Systems 113
4 1 Probability-Weighted Dynamic Monte Carlo Method 115
4 2 Bounded Acceptance Probability RSSA 118
4 3 r-Leaping Method 122
431 Leap Selection 125
432 Avoiding the Negative Population Problem 131
433 Switching to Exact Simulation 131
434 The r-Leaping Algorithm 132
4 4 Improvements for r-Leaping 133
441 Modified r-Leaping 133
442 Binomial r-Leaping 137
443 Implicit r-Leaping 138
4 5 ka-Leaping Method 140
451 Ä'-Leaping Method 142
4 6 Benchmark of Approximate Stochastic Algorithms 144
4 7 Chemical Langevin Method 147
4 8 Deterministic Simulation 148
481 From Biochemical Reactions to ODEs 150
482 Numerical Solution of ODEs 155
483 Improving the Accuracy of Numerical Methods 158
484 Multistep Methods 16
485 Adaptive Methods 16
486 Issues of Deterministic Simulation 17
4 9 Summary 17
4 10 Further Reading 17
5 Hybrid Simulation Algorithms 18
5 1 Motivation 18
5 2 Reaction-Based System Partitioning 18
5 3 Synchronization of Exact and Approximate Simulations 18
5 4 Hybrid Rejection-Based SSA (HRSSA) 19
541 Correctness of the Simulation of Slow Reactions 19
5 5 Hybrid Simulation with Stiffness 19
ts xi
551 Formulation of Reactions with Stiffness 198
• 552 Slow-Scale Stochastic Simulation Algorithm 202
*553 Nested Stochastic Simulation Algorithm 204
5 6 Summary 204
5 7 Further Reading 205
Benchmark Models 207
KAl Birth Process Model 207
A 2 Fast Isomerization Model 207
A 3 Oscillator Model 208
A 4 Schlögl Model 208
\A5 Oregonator Model 209
A 6 Gene Expression Model 210
*Al Folate Cycle Model 211
A 8 MAPK Cascade Model 212
A 9 FceRI Pathway Model 213
A 10 B Cell Antigen Receptor Signaling Model 214
A 11 Linear Chain Model 214
B Random Number Generation 217
B l Uniform Random Number Generator 217
B 2 Non-uniform Random Number Generator 218
B21 General Techniques 218
B22 Exponential Distribution 220
B23 Erlang Distribution 220
B24 Normal Distribution 221
B25 Discrete Distribution with Given Probability Vector 222
B26 Poisson Distribution 222
B27 Binomial Distribution 223
B28 Multinomial Distribution 224
References |
| any_adam_object | 1 |
| author | Marchetti, Luca Priami, Corrado 1964- Thanh, Vo Hong |
| author_GND | (DE-588)1113211474 |
| author_facet | Marchetti, Luca Priami, Corrado 1964- Thanh, Vo Hong |
| author_role | aut aut aut |
| author_sort | Marchetti, Luca |
| author_variant | l m lm c p cp v h t vh vht |
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| dewey-ones | 005 - Computer programming, programs, data, security |
| dewey-raw | 005.1 |
| dewey-search | 005.1 |
| dewey-sort | 15.1 |
| dewey-tens | 000 - Computer science, information, general works |
| discipline | Informatik |
| doi_str_mv | 10.1007/978-3-319-63113-4 |
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| id | DE-604.BV044529982 |
| illustrated | Not Illustrated |
| indexdate | 2024-12-03T04:04:51Z |
| institution | BVB |
| isbn | 9783319631134 |
| issn | 1862-4499 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-029929283 |
| oclc_num | 1009086557 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-860 DE-Aug4 DE-898 DE-BY-UBR DE-861 DE-523 DE-859 DE-473 DE-BY-UBG DE-29 DE-863 DE-BY-FWS DE-20 DE-862 DE-BY-FWS DE-92 DE-573 DE-M347 DE-703 DE-706 DE-739 DE-634 DE-188 DE-19 DE-BY-UBM |
| owner_facet | DE-355 DE-BY-UBR DE-860 DE-Aug4 DE-898 DE-BY-UBR DE-861 DE-523 DE-859 DE-473 DE-BY-UBG DE-29 DE-863 DE-BY-FWS DE-20 DE-862 DE-BY-FWS DE-92 DE-573 DE-M347 DE-703 DE-706 DE-739 DE-634 DE-188 DE-19 DE-BY-UBM |
| physical | 1 Online-Ressource (XI, 238 Seiten, 52 illus., 23 illus. in color) |
| psigel | ZDB-2-SCS ZDB-2-SCS_2017 |
| publishDate | 2017 |
| publishDateSearch | 2017 |
| publishDateSort | 2017 |
| publisher | Springer |
| record_format | marc |
| series2 | Texts in theoretical computer science |
| spellingShingle | Marchetti, Luca Priami, Corrado 1964- Thanh, Vo Hong Simulation algorithms for computational systems biology Computer science Algorithms Bioinformatics Systems biology Computer Science Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics Systems Biology Informatik |
| title | Simulation algorithms for computational systems biology |
| title_auth | Simulation algorithms for computational systems biology |
| title_exact_search | Simulation algorithms for computational systems biology |
| title_full | Simulation algorithms for computational systems biology Luca Marchetti, Corrado Priami, Vo Hong Thanh |
| title_fullStr | Simulation algorithms for computational systems biology Luca Marchetti, Corrado Priami, Vo Hong Thanh |
| title_full_unstemmed | Simulation algorithms for computational systems biology Luca Marchetti, Corrado Priami, Vo Hong Thanh |
| title_short | Simulation algorithms for computational systems biology |
| title_sort | simulation algorithms for computational systems biology |
| topic | Computer science Algorithms Bioinformatics Systems biology Computer Science Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics Systems Biology Informatik |
| topic_facet | Computer science Algorithms Bioinformatics Systems biology Computer Science Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics Systems Biology Informatik |
| url | https://doi.org/10.1007/978-3-319-63113-4 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029929283&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT marchettiluca simulationalgorithmsforcomputationalsystemsbiology AT priamicorrado simulationalgorithmsforcomputationalsystemsbiology AT thanhvohong simulationalgorithmsforcomputationalsystemsbiology |