Adamatzky / Komosinski Artificial Life Models in Software

1. Auflage 2006
ISBN: 978-1-84628-214-0
Verlag: Springer-Verlag
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 350 Seiten

An informal introduction and guidance to modern software tools for modeling and simulation of life-like phenomena, this book offers detailed reviews of contemporary software for artificial life for both professionals and amateurs.

Autoren/Hrsg.

Adamatzky, Andrew

Komosinski, Maciej

Inhaltsverzeichnis

1;Preface;5
2;Contents;8
3;List of Contributors;10
4;Part I Virtual Living Worlds;12
4.1;1 Avida: Evolution Experiments with Self- Replicating Computer Programs;13
4.1.1;1.1 Introduction to Avida;13
4.1.1.1;1.1.1 History of Digital Life;14
4.1.1.2;1.1.2 The Scientific Motivation for Avida;16
4.1.2;1.2 The Avida Software;18
4.1.2.1;1.2.1 Avida Organisms;18
4.1.2.2;1.2.2 The Avida World;27
4.1.2.3;1.2.3 Test Environments;31
4.1.3;1.3 Using Avida;32
4.1.3.1;1.3.1 Performing Avida Experiments;32
4.1.3.2;1.3.2 Analyze Mode;35
4.1.4;1.4 A Summary of Avida Research;38
4.1.4.1;1.4.1 The Evolution of Complex Features;38
4.1.4.2;1.4.2 Survival of the Flattest;39
4.1.4.3;1.4.3 Evolution of Digital Ecosystems;40
4.1.5;1.5 Outlook;42
4.1.6;References;43
4.2;2 Framsticks: A Platform for Modeling, Simulating, and Evolving 3D Creatures;46
4.2.1;2.1 Available Software and Tools;47
4.2.2;2.2 Simulation;48
4.2.2.1;2.2.1 Body;49
4.2.2.2;2.2.2 Brain;50
4.2.2.3;2.2.3 Receptors and E.ectors;51
4.2.2.4;2.2.4 Environment;52
4.2.3;2.3 Framework and Evolution;52
4.2.3.1;2.3.1 Genetics;52
4.2.3.2;2.3.2 Scripting;56
4.2.3.3;2.3.3 Experiment De.nitions;57
4.2.3.4;2.3.4 Illustrative Example ("Standard Experiment” Definition);59
4.2.4;2.4 Advanced Tools for Research and Education;60
4.2.4.1;2.4.1 Brain Analysis;61
4.2.4.2;2.4.2 Clustering of Similar Individuals;62
4.2.4.3;2.4.3 History of Evolution;63
4.2.4.4;2.4.4 Understanding Evolved Behaviors: Fuzzy Control;63
4.2.5;2.5 Research Experiments;65
4.2.5.1;2.5.1 Comparison of Genotype Encodings;65
4.2.5.2;2.5.2 Automatic Optimization Versus Human Design;66
4.2.5.3;2.5.3 Clustering with Similarity Measure;67
4.2.5.4;2.5.4 Other Experiments;69
4.2.6;2.6 Education with Entertainment;71
4.2.7;2.7 Summary;73
4.2.8;Acknowledgment;74
4.2.9;References;74
4.3;3 Nerve Garden: Germinating Biological Metaphors in Net- based Virtual Worlds;76
4.3.1;3.1 History and Background of the Project;76
4.3.1.1;3.1.1 Artificial Life Meets the World Wide Web;76
4.3.1.2;3.1.2 Background: L-Systems;77
4.3.2;3.2 Nerve Garden I: Inspiration, Architecture, and Experience;78
4.3.2.1;3.2.1 Inspiration;78
4.3.2.2;3.2.2 Architectural Elements;78
4.3.2.3;3.2.3 Experience: What Was Learned;81
4.3.3;3.3 A Next Evolutionary Step: Nerve Garden II;83
4.3.4;3.4 The Role of ALife in Virtual Worlds on the Internet;85
4.3.4.1;3.4.1 Multi-User Online Worlds: A Rich Space for Biological Metaphors;85
4.3.4.2;3.4.2 Using ALife to Draw Attention Span;86
4.3.4.3;3.4.3 Artifical Life Techniques Powering Better Virtual World Architectures;86
4.3.5;3.5 Other Examples of L-System-based Virtual World Construction and Considerations for the Future Use of L- Systems;87
4.3.6;References;88
4.3.7;Online Resources;89
4.4;4 GenePool: Exploring the Interaction Between Natural Selection and Sexual Selection;90
4.4.1;4.1 History;90
4.4.2;4.2 Background;91
4.4.2.1;4.2.1 Dawkins’ Call;91
4.4.2.2;4.2.2 Physics, in Various Forms;91
4.4.2.3;4.2.3 Sexual Selection;92
4.4.3;4.3 Description of the Software;92
4.4.3.1;4.3.1 Initialization;92
4.4.3.2;4.3.2 Food Bit Behavior;93
4.4.3.3;4.3.3 Swimbots;93
4.4.3.4;4.3.4 Locomotion Is Required for Mating;95
4.4.3.5;4.3.5 Special Body Parts;95
4.4.3.6;4.3.6 Swimbot Mental States;96
4.4.3.7;4.3.7 Energy Flow;96
4.4.3.8;4.3.8 Turning;97
4.4.3.9;4.3.9 Perceiving and Choosing Mates;98
4.4.3.10;4.3.10 Pseudo-FlatLand;98
4.4.3.11;4.3.11 Mating and Birth;99
4.4.4;4.4 Usage;99
4.4.4.1;4.4.1 Pool Menu;99
4.4.4.2;4.4.2 Love Menu;99
4.4.4.3;4.4.3 Stats Menu;99
4.4.4.4;4.4.4 Info Menu;99
4.4.4.5;4.4.5 A.ecting Views;100
4.4.4.6;4.4.6 Ways to Use GenePool;100
4.4.4.7;4.4.7 A Sample User Session;100
4.4.4.8;4.4.8 Mini-Dramas;101
4.4.4.9;4.4.9 Anthropomorphizing;101
4.4.5;4.5 Discoveries;101
4.4.5.1;4.5.1 Polymorphism?;101
4.4.5.2;4.5.2 Celebrating Diversity;103
4.4.6;4.6 Future Development;103
4.4.6.1;4.6.1 Recursive Embryology;103
4.4.6.2;4.6.2 Parental Investment and Gender;104
4.4.6.3;4.6.3 Environmental Variation;104
4.4.7;4.7 Similar Simulations;104
4.4.8;References;105
4.5;5 Sodarace: Adventures in Artificial Life;106
4.5.1;5.1 Introduction: The Sodarace Project;106
4.5.2;5.2 Scientific Background;108
4.5.2.1;5.2.1 Sodaconstructor: The Physics Engine of Sodarace;108
4.5.2.2;5.2.2 Sodarace Environmental Variables;110
4.5.2.3;5.2.3 Previous Work;110
4.5.3;5.3 Software for Artificial Life in Sodarace;111
4.5.3.1;5.3.1 Approaches to Optimization;111
4.5.3.2;5.3.2 Simulated Annealing and Daintywalker;112
4.5.3.3;5.3.3 Genetic Algorithms and the Amoeba;112
4.5.3.4;5.3.4 Genetic Algorithms from Scratch; the Wodka Way;112
4.5.4;5.4 Usage;112
4.5.4.1;5.4.1 Interactions in Sodarace: The Evolution of the Forums;112
4.5.4.2;5.4.2 Forum Involvement in Scientific Research Projects;113
4.5.4.3;5.4.3 Community Development of Peer-to-Peer Learning Web Sites;113
4.5.4.4;5.4.4 Programming Support Web Sites;114
4.5.4.5;5.4.5 Experimental Investigation into the Physics of Sodarace;114
4.5.4.6;5.4.6 The Pandora’s Box: An Example of the Spontaneous Development of Scientific Method;115
4.5.4.7;5.4.7 Interdisciplinary Interaction: Art & Music Meet Science and Engineering in Sodarace;116
4.5.4.8;5.4.8 Sodarace in Schools;116
4.5.5;5.5 Experiments with Sodarace;119
4.5.6;5.6 Summary: The Future of Sodarace;119
4.5.7;Acknowledgments;119
4.5.8;References;120
5;Part II Collective Artificial Life;121
5.1;6 Escaping the Accidents of History: An Overview of Artificial Life Modeling with Repast;122
5.1.1;6.1 Introduction;122
5.1.1.1;6.1.1 Artificial Life;123
5.1.1.2;6.1.2 Agent-based Modeling for Artificial Life;124
5.1.1.3;6.1.3 Chapter Organization;125
5.1.2;6.2 REPAST;125
5.1.2.1;6.2.1 The Repast Development Ecosystem;126
5.1.3;6.3 RepastJ in the Eclipse Development Environment;131
5.1.3.1;6.3.1 Repast Concepts;133
5.1.3.2;6.3.2 Using Repast;136
5.1.4;6.4 Repast Artificial Life Models;137
5.1.4.1;6.4.1 Artificial Evolution and Ecosystems;137
5.1.4.2;6.4.2 Artificial Societies;139
5.1.4.3;6.4.3 Artificial Biological Systems;141
5.1.5;6.5 Conclusions;145
5.1.6;References;146
5.2;7 EINSTein: A Multiagent-based Model of Combat;149
5.2.1;7.1 Background;149
5.2.2;7.2 Land Combat as a Complex Adaptive System;151
5.2.3;7.3 Agent-based Modeling and Simulation;151
5.2.4;7.4 EINSTein;153
5.2.4.1;7.4.1 Features;154
5.2.4.2;7.4.2 Source Code;154
5.2.4.3;7.4.3 Design Philosophy;156
5.2.4.4;7.4.4 Program Flow;157
5.2.5;7.5 Combat Engine;157
5.2.5.1;7.5.1 Agents;157
5.2.5.2;7.5.2 Battlefield;158
5.2.5.3;7.5.3 Agent Personalities;158
5.2.5.4;7.5.4 Penalty Function;159
5.2.5.5;7.5.5 Meta-Rules;160
5.2.5.6;7.5.6 Combat;161
5.2.5.7;7.5.7 Run Modes;162
5.2.6;7.6 Sample Patterns and Behavior;162
5.2.6.1;7.6.1 Qualitative Classes of Behavior;164
5.2.6.2;7.6.2 Lanchesterian Combat;165
5.2.6.3;7.6.3 A Step Away from Lanchester;167
5.2.6.4;7.6.4 Swarming Forces;169
5.2.6.5;7.6.5 Non-Monotonicity;170
5.2.7;7.7 Genetic Algorithm Breeding;174
5.2.7.1;7.7.1 Search Space;174
5.2.7.2;7.7.2 Mission Fitness;175
5.2.7.3;7.7.3 EINSTein’s GA Recipe;176
5.2.7.4;7.7.4 Sample GA Breeding Experiment #1;177
5.2.7.5;7.7.5 Sample GA Breeding Experiment #2;180
5.2.8;7.8 Discussion;183
5.2.8.1;7.8.1 Other Features and Future Enhancements;185
5.2.8.2;7.8.2 Why Are Agent-based Models of Combat Useful?;186
5.2.9;Acknowledgments;189
5.2.10;References;189
5.3;8 StarLogo: A Programmable Complex Systems Modeling Environment for Students and Teachers;192
5.3.1;8.1 Background;192
5.3.2;8.2 Approaches to Modeling;194
5.3.3;8.3 Additional Design Criteria;195
5.3.4;8.4 The StarLogo Platform;196
5.3.4.1;8.4.1 Termites Example;197
5.3.5;8.5 StarLogo Design Through the Ages;200
5.3.5.1;8.5.1 The StarLogo Virtual Machine;200
5.3.5.2;8.5.2 The Anatomy of a Virtual Machine;201
5.3.5.3;8.5.3 The Process Scheduler and Its Processes;202
5.3.5.4;8.5.4 The StarLogo Interface;204
5.3.6;8.6 Learning to Model Through;206
5.3.7;8.7 Lessons Learned;207
5.3.7.1;8.7.1 Fire;207
5.3.7.2;8.7.2 But This One Goes to 1000;209
5.3.7.3;8.7.3 The Evolution of Rabbits and Grass;210
5.3.7.4;8.7.4 The Tides Are Turning;212
5.3.8;8.8 Conclusion;212
5.3.9;Acknowledgments;213
5.3.10;References;213
5.4;9 On the Evolution of Sonic Ecosystems;215
5.4.1;9.1 Introduction;215
5.4.1.1;9.1.1 Artificial Life Art;216
5.4.1.2;9.1.2 Related Work;217
5.4.2;9.2 Eden: An Artificial Life Artwork;217
5.4.3;9.3 Agents and Environments;219
5.4.3.1;9.3.1 The Eden World;219
5.4.3.2;9.3.2 Agent Implementation;220
5.4.3.3;9.3.3 Image;225
5.4.3.4;9.3.4 Sound;226
5.4.4;9.4 Interaction;228
5.4.4.1;9.4.1 The Problem of Aesthetic Evolution;229
5.4.4.2;9.4.2 Eden as a Reactive System;230
5.4.5;9.5 Results;231
5.4.6;9.6 Conclusion;232
5.4.7;References;233
6;Part III Magic of Discrete Worlds;235
6.1;10 Exploring Cellular Automata with MCell;236
6.1.1;10.1 What Is MCell?;236
6.1.1.1;10.1.1 Program Interface;237
6.1.1.2;10.1.2 Some History;238
6.1.1.3;10.1.3 Other Popular CA Simulators;238
6.1.2;10.2 Description of the Software;239
6.1.2.1;10.2.1 Areas of Application;239
6.1.2.2;10.2.2 Supported Cellular Automata Rules;240
6.1.2.3;10.2.3 Cellular Automata Patterns;250
6.1.2.4;10.2.4 Interesting Rules and Experiments;252
6.1.3;10.3 Program Usage;255
6.1.3.1;10.3.1 Browsing Cellular Automata Patterns;255
6.1.3.2;10.3.2 Designing Cellular Automata Patterns;256
6.1.3.3;10.3.3 Exploring Cellular Automata Rules;256
6.1.3.4;10.3.4 Program Configuration;258
6.1.3.5;10.3.5 Analyses;258
6.1.4;10.4 Extending MCell;261
6.1.4.1;10.4.1 Programming User Rules;261
6.1.4.2;10.4.2 Extending the MCell Interface;261
6.1.4.3;10.4.3 Going Java;262
6.1.5;10.5 Summary;263
6.1.6;References;263
6.2;11 Discrete Dynamics Lab: Tools for Investigating Cellular Automata and Discrete Dynamical Networks;265
6.2.1;11.1 Basins of Attraction;267
6.2.2;11.2 Discrete Dynamical Networks;267
6.2.3;11.3 Space-Time Patterns and Basins of Attraction;270
6.2.4;11.4 DDLab User Interface;272
6.2.5;11.5 Initial Choices;273
6.2.6;11.6 Setting the Network Size;274
6.2.7;11.7 The Neighborhood k or k-mix;275
6.2.8;11.8 Wiring;279
6.2.9;11.9 Rules;279
6.2.10;11.10 The Initial Network State, the Seed;282
6.2.11;11.11 Networks of Subnetworks;283
6.2.12;11.12 Presentation Options for Space-Time Patterns;284
6.2.13;11.13 Presentation Options for Attractor Basins;285
6.2.14;11.14 Filing;286
6.2.15;11.15 Mutations;287
6.2.16;11.16 Network Architecture;289
6.2.17;11.17 The Network Graph;289
6.2.18;11.18 Static Parameters Measures;290
6.2.19;11.19 Measures on Space-Time Patterns;290
6.2.20;11.20 Measures on Attractor Basins;294
6.2.21;11.21 Reverse Algorithms;295
6.2.22;11.22 Chain Rules and Encryption;296
6.2.23;11.23 Sequential Updating;296
6.2.24;11.24 Sculpting Attractor Basins;297
6.2.25;11.25 Acknowledgments;298
6.2.26;References;299
7;Part IV Artificial Life Arts;300
7.1;12 Simulated Breeding - A Framework of Breeding Artifacts on the Computer;301
7.1.1;12.1 Introduction;301
7.1.2;12.2 Basic Framework of IEC;303
7.1.3;12.3 SBART and SBEAT;304
7.1.3.1;12.3.1 SBART;304
7.1.3.2;12.3.2 SBEAT;306
7.1.4;12.4 Breeding in a Field Window;308
7.1.5;12.5 Multifield User Interface;308
7.1.5.1;12.5.1 Migration Among Fields;310
7.1.5.2;12.5.2 Protection of Individual;310
7.1.5.3;12.5.3 Effects of Multi.led Interface;311
7.1.6;12.6 Partial Breeding;312
7.1.7;12.7 Direct Genome Operation;314
7.1.8;12.8 Production Samples;316
7.1.9;12.9 Future Works;318
7.1.10;12.10 Conclusion;320
7.1.11;Acknowledgments;320
7.1.12;References;321
7.2;13 Enriching Aesthetics with Artificial Life;323
7.2.1;13.1 Introduction;323
7.2.2;13.2 Wonder and the Sublime in Art and Nature;324
7.2.3;13.3 Sublime Software;327
7.2.4;13.4 The Betrayal of Points and Lines;328
7.2.5;13.5 Moving Beyond Two Dimensions;329
7.2.6;13.6 Spaces That Build Themselves;331
7.2.7;13.7 Conclusion;333
7.2.8;References;334
8;A Appendix: Artificial Life Software;336
9;Index;341