DDLab Manual

Discrete Dynamics Lab
Cellular Automata - Random Boolean Networks

Andrew Wuensche
March 1996 (Copyright Andrew Wuensche 1993-96)
Santa Fe Institute
and The University of Sussex (COGS)
Email: wuensch@santafe.edu

• Overview.
  • A1. Introduction
  • A2. Network parameters
  • A3. Presentation options
  • A4. Filing and Printing
  • A5. Mutations
  • A6. Quantitative, statistical and analytical measures
  • A7. Reverse algorithms
  • A8. Sculpting attractor basins
  • A9. Hardware and software requirements
    • A9.1 DOS Platform.
    • A9.3 Mac platform.
  • A10. References
• Quick Start Instructions
  • 1 Downloading, unzipping and running.
  • 2 The user interface.
    • 2.1 Input
    • 2.2 Backtrack
    • 2.3 Changing the graphics set-up (DOS)
  • 3 Quick start examples
    • 3.1 Basin of attraction fields.
    • 3.2 ``Backwards'' space-time patterns, and state-space matrix
    • 3.3 Basins of attraction fields for a range of network sizes
    • 3.4 A single basin of attraction.
    • 3.5 A subtree
    • 3.6 Space-time pattern only, 1d
    • 3.7 Space-time pattern only, 2d (game of life).
    • 3.8 ``Screen-saver'' demo.
• Program Reference.
  • 4 Starting DDLab, memory, and the user interface.
    • 4.1 Title bar.
    • 4.2 DDLAb version, graphics and mouse status.
    • 4.3 Memory available.
    • 4.4 Virtual Memory.
    • 4.4 Prompts.
  • 5 The first prompt (and graphics setup).
    • 5.1 Field, or a run requiring a seed.
    • 5.2 Graphics set-up.
      • 5.2.1 VGA and SVGA.
      • 5.2.2 White or black background.
    • 5.3 Options.
    • 5.4 Random number seed.
    • 5.5 Exit DDLab.
  • 6 Network size, 1d.
    • 6.1 Setting range of sizes.
    • 6.2 Setting one network size.
    • 6.3 Network size limitations.
  • 7 Cell scale
  • 8 Neighbourhood.
    • 8.1 Setting neighbourhood size or mix.
    • 8.2 Setting the neighbourhood mix.
    • 8.3 Loading a neighbourhood mix file.
    • 8.4 Setting the neighbourhood mix by hand.
    • 8.5 Setting the neighbourhood at random.
    • 8.6 Reviewing the neighbourhood mix.
      • 8.6.1 Reviewing the neighbourhood mix in large networks.
      • 8.6.2 Jumping to a new cell index.
      • 8.6.3 Saving the neighbourhood mix.
      • 8.6.4 Other options to review and alter the neighbourhood mix.
  • 9 Wiring.
    • 9.1 Network geometry
    • 9.2 The pseudo-neighbourhood.
    • 9.3 Setting the wiring.
  • 10 Quick wiring settings.
    • 10.1 Loading the wiring scheme.
    • 10.2 Regular 1d wiring.
    • 10.3 Regular 2d wiring
      • 10.3.1 Conserving wiring memory in regular 2d networks
      • 10.3.2 Setting 2d network size.
    • 10.4 Random 1d wiring.
  • 11 Setting special wiring.
    • 11.1 Setting network geometry.
    • 11.2 Set special wiring.
    • 11.3 Special wiring, regular 1d (treat as random).
    • 11.4 Special wiring, regular 2d.
    • 11.5 Special wiring, random.
      • 11.5.1 Confining random wiring to a set zone.
      • 11.5.2 Self wiring.
      • 11.5.3 Distinct wiring.
    • 11.6 Wiring by hand.
      • 11.6.1 Wiring by hand in large networks.
  • 12 Reviewing Wiring.
    • 12.1 The wiring matrix, and
    • 12.2 The wiring matrix.
      • 12.2.1 Revising wiring in the wiring matrix.
      • 12.2.2 Revising by hand.
      • 12.2.3 Randomly rewiring.
      • 12.2.5 Resetting wiring options.
  • 13 Rules.
    • 13.1. The rule-table.
      • 13.1.1 The totalistic code table
      • 13.1.2 Totalistic rules.
    • 13.2 Rule table matrix.
    • 13.3 Single rule or rule mix.
      • 13.3.1 A rule mix with just one rule.
    • 13.4 Rule mix.
    • 13.5 Rule mix options.
      • 13.5.1 Rule mix with no limit.
      • 13.5.2 By hand.
      • 13.5.3 Majority.
      • 13.5.4 Majority + end bits flipped.
      • 13.5.5 Random.
      • 13.5.6 Random + canalyzing.
      • 13.5.7 Setting a limited sub-set of rules for random selection.
    • 13.6 Setting the selection method for a singe rule (by hand).
      • 13.6.1 Methods for setting a rule.
      • 13.6.2 The rule window.
    • 13.7 Setting the majority rule
    • 13.8 Setting ``game of life'' rule.
    • 13.9 Setting the
    • 13.10 Setting the rule set at random
    • 13.11 Setting the rule as bits
      • 13.11.1 Setting bits with the mouse.
      • 13.11.2 Setting bits from the keyboard.
    • 13.12 Setting the rule in hex
    • 13.13 Repeating the last rule.
    • 13.14 Loading Rules.
      • 13.14.1 Single rule file encoding.
      • 13.14.2 Conflicts in neighbourhood size between network and file.
    • 13.15 Rule mix selection by hand.
      • 13.15.1 Changing the cell index or selection method.
      • 13.15.2 Changing the cell index.
      • 13.15.3 Changing the rule selection method.
    • 13.16 Automatic saving of last rule.
    • 13.17 Transforming the rule, and setting canalyzing inputs.
      • 13.17.1 Complimentary transformation.
      • 13.17.2 Equivalent rule by the negative transformation.
      • 13.17.3 Equivalent rule by the reflection transformation.
      • 13.17.4 Equivalent rules with a greater neighbourhood size, k.
      • 13.17.5 Setting canalyzing inputs.
      • 13.17.6 Saving the transformed rule.
  • 14 Reviewing wiring/rules.
    • 14.1 1d or 2d wiring graphic and rule scheme.
    • 14.2 Wiring graphic, 1d.
      • 14.2.1 Moving or jumping between cells, 1d wiring graphic.
    • 14.3 Wiring graphic, 2d
      • 14.3.1 Moving or jumping between cells, 2d wiring graphic.
    • 14.4 Options, 1d and 2d wiring graphic.
      • 14.4.1 Revising the wiring.
      • 14.4.2 Revising the rule.
      • 14.4.3 Computing the (weighed) average and Z parameters.
      • 14.4.4 Learning pre-images without attractor basins.
      • 14.4.5 Printing the wiring graphic window.
      • 14.4.6 Options.
    • 14.5 Revise wiring with the 1d or 2d wiring graphic.
      • 14.5.1 Changing the neighbourhood size.
      • 14.5.2 Hand rewiring.
      • 14.5.3 Random wiring.
      • 14.5.4 Random special wiring.
      • 14.5.5 Regular 1d wiring.
      • 14.5.6 Regular 2d wiring.
    • 14.6 Revise rules with the 1d or 2d wiring graphic.
    • 14.7 Rule/wiring scheme: saving, loading, or printing (to a printer or file).
      • 14.7.1 Save/load/print selection.
      • 14.7.2 Mixed rules and non-local wiring.
      • 14.7.3 One rule and non-local wiring.
      • 14.7.4 Mixed rules and local wiring.
      • 14.7.5 Printing to a printer or file.
      • 14.7.6 Wiring/rulemix file names.
      • 14.7.7 Wiring/rulemix encoding..
      • 14.7.8 Wiring/rulemix file loading conventions.
      • 14.7.9 Neighbourhood mix loading conventions.
  • 15 Seed.
    • 15.1 Setting the selection method for the seed.
    • 15.2 Seed bit pattern display.
    • 15.3 Rotating the seed.
    • 15.4 Setting the seed in decimal
    • 15.5 Setting the seed at random
    • 15.6 Setting the seed in hex
    • 15.7 Setting the seed as bits, drawing with the mouse
      • 15.7.1 1d networks (shown as 1d).
      • 15.7.2 1d networks (shown as 2d).
      • 15.7.3 2d networks.
      • 15.7.4 Setting/deleting bits with the mouse or keyboard.
    • 15.8 Repeating the seed.
    • 15.9 Loading a seed.
      • 15.9.1 Seed file encoding and loading conventions.
      • 15.9.2 Seed file, 1d.
      • 15.9.3 Seed file, 2d.
    • 15.10 Saving a seed.
  • 16 Output parameters
    • 16.1 The first output parameter prompt.
      • 16.1.1 Accept all output parameter defaults.
      • 16.1.2 Space-time patters only.
      • 16.1.3 Restore all output parameter defaults, or just layout defaults.
      • 16.1.4 Jump to layout of attractor basins.
      • 16.1.5 Jump to display of attractor basins, and data
      • 16.1.6 Jump to mutation.
  • 17 Set various output parameter options.
    • 17.1 State-space matrix scatter-plot.
      • 17.1.1 Display all states.
      • 17.1.2 Display attractor states only.
      • 17.1.3 Change matrix size.
      • 17.1.4 Change start colour.
    • 17.2 In-degree frequency histogram.
      • 17.2.1 In-degree frequency cut-off.
      • 17.2.2 In-degree frequency window.
      • 17.2.3 Data shown.
      • 17.2.4 Options.
      • 17.2.5 Re-scaling the x-axis.
      • 17.2.6 Re-scaling the y-axis.
    • 17.3 States with majority of 1s or 0s.
    • 17.4 ``Screen save'' demo.
    • 17.5 Graphs: G-density, Z and ratio.
      • 17.5.1 G-density against Z and/or ratio.
      • 17.5.2 Z against ratio.
    • 17.6 ``Backwards'' space-time patterns.
    • 17.7 Scroll space-time patterns.
  • 18 Graphic conventions for attractor basins.
    • 18.1 Network states, nodes.
    • 18.2 Attractor cycles.
    • 18.3 Transient trees.
    • 18.4 Transient tree colors.
    • 18.5 Transient trees for the states all 0s or all 1s.
    • 18.6 Subtree only.
  • 19 Layout of attractor basins.
    • 19.1 The layout preview.
    • 19.2 The first layout prompt.
      • 19.2.1 Reset all layout defaults.
      • 19.2.2 Reset layout for learning.
      • 19.2.3 Basin scale, attractor radius.
    • 19.3 Basin start position.
    • 19.4 Show the field as successive basins.
    • 19.5 Basin spacing for fields.
    • 19.6 Select minimum right border width.
    • 19.7 Amend the layout after each basin or tree.
      • 19.7.1 Amend the spacing and right border after each basin.
      • 19.7.2 Amending the next position (and spacing) after each basin.
    • 19.8 Amend the spacing increase for successive fields.
    • 19.9 Revise layout parameters.
  • 20 Display of attractor basins, and data.
    • 20.1 Compression of equivalent CA dynamics.
      • 20.1.1 Suppress compression.
      • 20.1.2 Suppress copies of trees (and subtrees).
    • 20.2 Node display.
      • 20.2.1 Show bit pattern nodes for 1d networks in 2d.
      • 20.2.2 Alter node label size, decimal or hex.
      • 20.2.3 Alter node size, bits.
    • 20.3 Highlight one state in each attractor.
    • 20.4 Pause, and data.
      • 20.4.1 Data on sub-trees.
      • 20.4.2 Data on a subtree from a uniform state.
      • 20.4.3 Data on trees.
      • 20.4.4 Data on basins.
      • 20.4.5 Pause after each field.
      • 20.4.6 Pause after each basin or tree.
    • 20.5 Print data to printer.
    • 20.6 Save data to file.
    • 20.7 Format of printed or saved data.
      • 20.7.1 Network data.
      • 20.7.2 Basin field data (no tree data).
      • 20.7.3 Basin field data, including tree and subtree data.
      • 20.7.4 Single basin data file.
      • 20.7.5 Subtree data file.
  • 21 Mutation.
    • 21.1 The first mutation prompt.
    • 21.2 Flip bits.
      • 21.2.1 Alter the number of bits to flip.
      • 21.2.2 Alter the percentage of bits to flip.
    • 21.3 Special rule mutation.
      • 21.3.1 Mutate by the rule or code number.
      • 21.3.2 Assign a random rule or code number.
      • 21.3.3 Mutate by bitflip.
    • 21.4 Mutate wiring.
      • 21.4.1 Alter the number of wires to move.
      • 21.4.2 Alter the percentage of wires to move.
    • 21.5 No pause before next mutant.
  • 22 Run backwards for subtree, or forwards for a single basin.
    • 22.1 Subtree: Run forwards before running backwards.
    • 22.2 Single basin repeat check limit.
      • 22.2.1 Alter repeat check limit, or forwards only.
  • 23 Final options: subtree, single basin or basin of attraction field.
    • 23.1 Local wiring.
    • 23.2 Non-local wiring.
    • 23.3 Partial pre-image stack, local wiring.
    • 23.4 Partial pre-image histogram, non-local wiring.
    • 23.5 The exhaustive testing reverse algorithm.
      • 23.5.1 Load exhaustive pairs.
      • 23.5.2 Computing exhaustive pairs.
      • 23.5.3 Saving exhaustive pairs.
  • 24 Final options for space-time patterns (forwards only).
    • 24.1 Color cells by value or neighbourhood.
    • 24.2 Pause when screen full.
    • 24.3 Frozen generation size.
    • 24.4 Analysis.
      • 24.4.1 Pattern density.
      • 24.4.2 Lookup frequency and entropy.
    • 24.5 Analysis generation size.
    • 24.6 State-space matrix scatter-plot (forwards only).
  • 25 Changing settings ``on the fly'' (attractor basins).
    • 25.1 Interrupting attractor basins.
      • 25.1.1 Backtrack through prompts.
      • 25.1.2 Abandoning a tree and continuing with the next tree.
      • 25.1.3 Other options.
    • 25.2 Key hit attractor basin options.
    • 25.3 Attractor basin complete options.
    • 25.4 Further attractor basin complete options.
      • 25.4.1 Rule options.
      • 25.4.2 Seed options.
  • 26 Changing settings ``on the fly'' (space-time patterns only).
    • 26.1 The ``Interrupt Key Index'' (space-time patterns only).
      • 26.1.1 change rule table
      • 26.1.2 change wiring
      • 26.1.3 change seed/size
      • 26.1.4 presentation
      • 26.1.5 2d-space-time pattern
      • 26.1.6 highlight frozen cells
      • 26.1.7 analysis
      • 26.1.8 state-space matrix
      • 26.1.9 index, pause, quit
    • 26.2 The ``Interrupt Key Index``, some further details.
      • 26.2.1 change rule table
      • 26.2.2 change wiring
      • 26.2.3 2d-space-time pattern
      • 26.2.4 highlight frozen cells
      • 26.2.5 analysis
    • 26.3 Pause space-time pattern.
    • 26.4 Rule details (space-time patterns only).
    • 26.5 Further space-time pattern options.
      • 26.5.1 Screen options.
      • 26.5.2 Rule options.
      • 26.5.3 Seed options.
      • 26.5.4 Other options.
      • 26.5.5 Further options, first backtrack.
  • 27 Learning, forgetting, and highlighting.
    • 27.1 Highlighting states.
    • 27.2 Default attractor basin layout for learning.
    • 27.3 Selecting the wiring graphic.
    • 27.4 Selecting the learn/highlight window.
    • 27.5 Select the ``target'' state.
    • 27.6 Select a set of states as pre-images.
      • 27.6.1 An arbitrary list of aspiring pre-images.
      • 27.6.2 Pre-images according to Hamming distance.
      • 27.6.3 Range of decimal equivalents.
      • 27.6.4 Odd or even parity.
      • 27.6.5 Repeat previous selection.
    • 27.7 Review target state and aspiring pre-images.
    • 27.8 Learn, forget, or highlight only.
      • 27.8.1 Highlighting only.
    • 27.9 Learning/forgetting by wire moves or bit-flips.
      • 27.9.1 Learning/forgetting by bit-flips.
      • 27.9.2 Learning/forgetting by wire-moves.
    • 27.10 Highlighting options.
    • 27.11 Learning complete.
  • 28 Filing
    • 28.1 File types, default extensions and filenames
    • 28.2 Saving and Loading
    • 28.3 Changing the directory
    • 28.4 List files
    • 28.5 File encoding
      • 28.5.1 SCREEN (image)
      • 28.5.2 N'HOOD MIX
      • 28.5.3 WIRING ONLY, RULE SCHEME ONLY, WIRING-RULE SCHEME
      • 28.5.4 SINGLE RULE
      • 28.5.5 SEED
    • 28.5.6 DATA
    • 28.5.7 EXHAUSTIVE (pairs)