Komosinski / Adamatzky Artificial Life Models in Software

2. Auflage 2009
ISBN: 978-1-84882-285-6
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 441 Seiten

The advent of powerful processing technologies and the advances in software development tools have drastically changed the approach and implementation of computational research in fundamental properties of living systems through simulating and synthesizing biological entities and processes in artificial media. Nowadays realistic physical and physiological simulation of natural and would-be creatures, worlds and societies becomes a low-cost task for ordinary home computers. The progress in technology has dramatically reshaped the structure of the software, the execution of a code, and visualization fundamentals. This has led to the emergence of novel breeds of artificial life software models, including three-dimensional programmable simulation environment, distributed discrete events platforms and multi-agent systems. This second edition reflects the technological and research advancements, and presents the best examples of artificial life software models developed in the World and available for users.

Autoren/Hrsg.

Komosinski, Maciej

Adamatzky, Andrew

Inhaltsverzeichnis

1;Preface;5
2;Contents;8
3;List of Contributors;17
4;Part I Virtual Environments;20
4.1;Chapter 1 Avida: A Software Platform for Research in Computational Evolutionary Biology;21
4.1.1;1.1 Introduction to Avida;21
4.1.2;1.2 The Scientific Motivation for Avida;25
4.1.3;1.3 The Avida Software;26
4.1.4;1.4 A Summary of Avida Research;45
4.1.5;1.5 Outlook;49
4.1.6;References;50
4.2;Chapter 2 Foundations of and Recent Advances in Artificial Life Modeling with Repast 3 and Repast Simphony;54
4.2.1;2.1 Introduction;54
4.2.2;2.2 REPAST;57
4.2.3;2.3 Repast Artificial Life Models;70
4.2.4;2.4 Conclusions;74
4.2.5;References;75
4.3;Chapter 3 Sodarace: Continuing Adventures in Artificial Life;78
4.3.1;3.1 The Sodarace Project;78
4.3.2;3.2 Introduction;79
4.3.3;3.3 Sodarace, the Scientific Background;81
4.3.4;3.4 Software for Artificial Life in Sodarace;84
4.3.5;3.5 Lessons Learned on Approaches for Artificial Life in Sodarace;84
4.3.6;3.6 Interactions in Sodarace: The Evolution of the Forums;88
4.3.7;3.7 Experiments with Sodarace;91
4.3.8;3.8 Summary: The Future of Sodarace;93
4.3.9;References;94
4.4;Chapter 4 3D Multi-Agent Simulations in the breve Simulation Environment;95
4.4.1;4.1 Overview;95
4.4.2;4.2 Motivations;100
4.4.3;4.3 Writing Simulations in breve;102
4.4.4;4.4 Breve Features and Technical Details;107
4.4.5;4.5 Development History and Future Developmen;111
4.4.6;4.6 ALife/AI Research with breve;112
4.4.7;4.7 Educational Applications of breve;116
4.4.8;4.8 Conclusion;120
4.4.9;References;120
4.5;Chapter 5 Framsticks: Creating and Understanding Complexity of Life;123
4.5.1;5.1 Available Software and Tools;124
4.5.2;5.2 Simulation;127
4.5.3;5.3 Genetics and Evolution;136
4.5.4;5.4 Scripting;139
4.5.5;5.5 Advanced Features for Research and Education;145
4.5.6;5.6 Research and Experiments;150
4.5.7;5.7 Education with Entertainment;160
4.5.8;5.8 Summary;162
4.5.9;References;163
5;Part II Lattice Worlds;165
5.1;Chapter 6 StarLogo TNG: Making Agent-Based Modeling Accessible and Appealing to Novices;166
5.1.1;6.1 Computational Modeling;166
5.1.2;6.2 Original Design Criteria;170
5.1.3;6.3 StarLogo;171
5.1.4;6.4 StarLogo: The Next Generation;172
5.1.5;6.5 The StarLogo TNG Virtual Machine;179
5.1.6;6.6 StarLogo TNG Example Model;183
5.1.7;6.7 Field Testing;190
5.1.8;6.8 Conclusion;195
5.1.9;References;196
5.2;Chapter 7 From Artificial Life to In Silico Medicine: NetLogo as a Means of Translational Knowledge Representation in Biomedical Research;198
5.2.1;7.1 Introduction;198
5.2.2;7.2 Facilitating Dynamic Knowledge Representation: The NetLogo Toolkit;205
5.2.3;7.3 NetLogo Models of Acute Inflammation;209
5.2.4;7.4 Conclusion;223
5.2.5;References;224
5.3;Chapter 8 Discrete Dynamics Lab: Tools for Investigating Cellular Automata and Discrete Dynamical Networks;230
5.3.1;8.1 Introduction;230
5.3.2;8.2 DDLab’s Interface and Initial Choices;241
5.3.3;8.3 Network Parameters;245
5.3.4;8.4 Network Architecture;254
5.3.5;8.5 Running Space-Time Patterns and Attractor Basins;256
5.3.6;8.6 Measures and Data;263
5.3.7;8.7 Reverse Algorithms;269
5.3.8;8.8 Chain-Rules and Dynamical Encryption;270
5.3.9;8.9 DDLab Website, Manual, and Reviews;272
5.3.10;References;272
5.4;Chapter 9 EINSTein: A Multiagent-Based Model of Combat;274
5.4.1;9.1 Background;274
5.4.2;9.2 Land Combat as a Complex Adaptive System;276
5.4.3;9.3 Agent-Based Modeling and Simulation;277
5.4.4;9.4 EINSTein;278
5.4.5;9.5 Combat Engine;283
5.4.6;9.6 Sample Patterns and Behavior;288
5.4.7;9.7 Genetic Algorithm Breeding;304
5.4.8;9.8 Discussion;313
5.4.9;9.9 Overview of Features in Newer Versions;320
5.4.10;9.10 Next Step;326
5.4.11;References;327
6;Part III Artificial Chemistries;331
6.1;Chapter 10 From Artificial Chemistries to Systems Biology: Software for Chemical Organization Theory;332
6.1.1;10.1 Introduction;332
6.1.2;10.2 Using Tools from Systems Biology: SBML and SBW;335
6.1.3;10.3 Chemical Organization Theory;337
6.1.4;10.4 Software for the Computation of Chemical Organizations;346
6.1.5;10.5 Conclusion;353
6.1.6;References;354
6.2;Chapter 11 Spatially Resolved Artificial Chemistry;356
6.2.1;11.1 Introduction;356
6.2.2;11.2 Concepts;358
6.2.3;11.3 Available Software and Tools;371
6.2.4;11.4 Conclusion;377
6.2.5;References;378
7;Part IV Artificial Life Arts;381
7.1;Chapter 12 Simulated Breeding: A Framework of Breeding Artifacts on the Computer;382
7.1.1;12.1 Introduction;382
7.1.2;12.2 Basic Framework of IEC;384
7.1.3;12.3 SBART and SBEAT;385
7.1.4;12.4 Breeding in a Field Window;389
7.1.5;12.5 Multifield User Interface;390
7.1.6;12.6 Partial Breeding;393
7.1.7;12.7 Direct Genome Operation;396
7.1.8;12.8 Production Samples;397
7.1.9;12.9 Future Works;401
7.1.10;12.10 Conclusion;402
7.1.11;References;402
7.2;Chapter 13 The Evolution of Sonic Ecosystems;404
7.2.1;13.1 Introduction;404
7.2.2;13.2 Eden: An Artificial Life Artwork;406
7.2.3;13.3 Agents and Environments;409
7.2.4;13.4 Interaction;418
7.2.5;13.5 Results;421
7.2.6;13.6 Conclusion;423
7.2.7;References;423
7.3;Chapter 14 Enriching Aesthetics with Artificial Life;426
7.3.1;14.1 Introduction;426
7.3.2;14.2 Wonder and the Sublime in Art and Nature;427
7.3.3;14.3 Sublime Software;430
7.3.4;14.4 The Betrayal of Points and Lines;432
7.3.5;14.5 Moving Beyond Two Dimensions;433
7.3.6;14.6 Spaces That Build Themselves;435
7.3.7;14.7 An Ecosystemic Approach to Writing Artistic Software;437
7.3.8;14.8 Conclusion;440
7.3.9;References;441
7.4;Appendix: Artificial Life Software;443
8;Index;448