Concept Index

• abstract domain: Domains
• acceptor interface: Domains
• active marker: The Swarm Design Pattern
• affinity: The Swarm Design Pattern
• allostery: Domains
• architecture: Contributing to Monod
• behaved program: Some Definitions
• behavior essence function: Protein Construction and Properties
• behavior function: Protein Construction and Properties
• behavior function --- causal: Protein Construction and Properties
• behavior function --- finite: Protein Construction and Properties
• behavior function --- predictable: Protein Construction and Properties
• behavior function --- spacing independent: Protein Construction and Properties
• binding: The Swarm Design Pattern
• biology: Biological Inspiration
• BMD: Domains
• boolean multiplexor domain (BMD): Domains
• boundary domain: Domains
• Brownian search: The Swarm Design Pattern
• calculator based on Incubator: The Incubator Calculator Example
• calculator based on Incubator: incubcalc
• causal behavior function: Protein Construction and Properties
• Clarke, Arthur C.: To Study the Future of Computation
• click method: The Hive Design Pattern
• command-line arguments: Command-line Arguments
• command-line arguments --- alltests: Test Suite
• compartment: Compartments
• compartment: Biological Inspiration
• compilation: Compilation
• concrete domain: Domains
• conformation change --- domain: Domains
• conformation engine --- domain: Domains
• CPU thrashing: Biological Inspiration
• cut in an operation history: Protein Construction and Properties
• Cytoplasm: The Design Stack
• design patterns: Three Design Patterns
• design stack: The Design Stack
• determinism: Some Definitions
• deterministic program: Some Definitions
• direction --- interface: Domains
• documentation: Contributing to Monod
• documentation: Documentation
• documentation: Orientation
• domain: Domains
• domain assembly: Protein Construction and Properties
• domain assembly --- stabilizing: Protein Construction and Properties
• domain assembly --- well-defined: Protein Construction and Properties
• domain assembly state: Protein Construction and Properties
• domain conformation change: Domains
• domain conformation engine: Domains
• domain functional logic: Domains
• domain interface: Domains
• domain projection sites: Domains
• domains: Biological Inspiration
• energy: Biological Inspiration
• energy: Energy
• error handling: The Incubator Calculator Example
• essentially equivalent behavior functions: Protein Construction and Properties
• evolutionary operators: Genetic Programming
• execution threads: The Hive Design Pattern
• exposure: The Swarm Design Pattern
• expressor interface: Domains
• extent of an operation history: Protein Construction and Properties
• finite behavior function: Protein Construction and Properties
• FIXME: So what is Monod
• flavors of domains: Domains
• fragment of ligand: The Incubator Design Pattern
• fun: So what is Monod
• functional logic --- domain: Domains
• geometrical structure: Biological Inspiration
• goals: Goals
• grounded Incubator: Some Definitions
• h-behaved program: Some Definitions
• h-deterministic program: Some Definitions
• hallucinatory flash: Goals
• hardware: Hardware
• harness: The Incubator Design Pattern
• harness: The Swarm Design Pattern
• harness: The Hive Design Pattern
• Heisenbug: Logging
• history: History
• Hive: The Design Stack
• Hive: The Hive Design Pattern
• homologous crossover: Genetic Programming
• Incubator: The Incubator Design Pattern
• Incubator: incubcalc
• Incubator: The Design Stack
• Incubator --- at rest: Some Definitions
• Incubator --- grounded: Some Definitions
• Incubator --- primed: Some Definitions
• Incubator --- program: Some Definitions
• Incubator input: Some Definitions
• Incubator output: Some Definitions
• input history: Protein Construction and Properties
• interface --- domain: Domains
• interface direction: Domains
• interface name: Domains
• interface type: Domains
• invalid amino acid sequence: Biological Inspiration
• irreversibility: Biological Inspiration
• Jacques Monod: Introduction
• LBDE: Domains
• LBDR: Domains
• license: Contributing to Monod
• license: Orientation
• LID: Domains
• ligand: The Incubator Design Pattern
• ligand --- semantically terminating: Some Definitions
• ligand --- terminating: Some Definitions
• ligand binding domain with extraction: Domains
• ligand binding domain with remapping (LBDR): Domains
• ligand binding projection: The Incubator Design Pattern
• lock and key: The Swarm Design Pattern
• logging: Logging
• logical integration domain (LID): Domains
• Makefiles: Compilation
• marker: The Swarm Design Pattern
• matcher: The Incubator Design Pattern
• matching: The Swarm Design Pattern
• membrane transport: Biological Inspiration
• milestones: Future
• molecular computing: Molecular Computing
• molecular recognition: The Swarm Design Pattern
• Monod Cell: The Design Stack
• Monod Culture: The Design Stack
• Monod, Jacques: Introduction
• name --- interface: Domains
• OCaml: OCaml
• ocamldoc: Source Code Documentation
• operation --- domain: Domains
• operation --- domain assembly: Protein Construction and Properties
• output history: Protein Construction and Properties
• Pandemonium: The Swarm Design Pattern
• parallelization: The Incubator Calculator Example
• predictable behavior function: Protein Construction and Properties
• primed Incubator: Some Definitions
• probabilistic matching: The Swarm Design Pattern
• processing unit: The Incubator Design Pattern
• program --- behaved: Some Definitions
• program --- deterministic: Some Definitions
• program --- well-grounded: Some Definitions
• program for Incubator: Some Definitions
• projection: The Swarm Design Pattern
• projection sites --- domain: Domains
• projection, ligand binding: The Incubator Design Pattern
• projection, structural binding: The Incubator Design Pattern
• protein folding: Biological Inspiration
• protein synthesis: Biological Inspiration
• randomness: The Hive Design Pattern
• randomness: The Swarm Design Pattern
• reaction-diffusion systems: Biological Inspiration
• release: Release
• release: Biological Inspiration
• resident: The Hive Design Pattern
• reversibility: Biological Inspiration
• Selfridge's Pandemonium: The Swarm Design Pattern
• semantically terminating ligand: Some Definitions
• shelter: The Hive Design Pattern
• shifting an operation history: Protein Construction and Properties
• Shortcomings of Contemporary Programming: To Study the Future of Computation
• simple ligand binding domain (SLBD): Domains
• Simulation of a Turing machine: Turing Soup
• Slashdot: History
• SLBD: Domains
• snippet: The Incubator Design Pattern
• social life: History
• source code: Source Code Structure
• source code: Source Code Documentation
• SourceForge: Contributing to Monod
• SourceForge: Orientation
• SourceForge: Source Code Structure
• spacing an operation history: Protein Construction and Properties
• spacing independent behavior function: Protein Construction and Properties
• stabilizing domain assembly: Protein Construction and Properties
• stack, design: The Design Stack
• state --- domain assembly: Protein Construction and Properties
• state history: Protein Construction and Properties
• structural binding projection: The Incubator Design Pattern
• Swarm: The Design Stack
• Swarm: The Swarm Design Pattern
• terminating ligand: Some Definitions
• testing: Contributing to Monod
• testing: Test Suite
• thrashing: Biological Inspiration
• threading: The Hive Design Pattern
• topological structure: Biological Inspiration
• Turing / von Neumann model: To Study the Future of Computation
• Turing machine --- simulating: Turing Soup
• Turing soup: Turing Soup
• type --- interface: Domains
• well-defined domain assembly: Protein Construction and Properties
• well-grounded Incubator program: Some Definitions