Discrete Dynamics Lab Cellular Automata - Random Boolean Networks. Andy Wuensche wuensch@santafe.edu March 1996 ----------------------------------------------------------------------- DDLab (first announced Dec 94, updated Jul 95) is now available for UNIX/XWindows, as well as an updated version for DOS. See below for details and download instructions. ----------------------------------------------------------------------- Attractor basins of discrete dynamical networks are objects in space-time that link network states according to their transitions. Access to these objects provides insights into complexity, chaos and emergent phenomena in cellular automata. In less ordered networks (as well as CA), attractor basins show how a network is able to categorize its state space, explaining what it is that constitutes memory in a network. DDLab is an interactive graphics program for research into the dynamics of finite binary networks, relevant to the study of complexity, emergent phenomena, neural networks, and aspects of theoretical biology such as gene regulatory networks. A network can be set up with any architecture between regular CA (1d or 2d) and "random Boolean networks" (networks with arbitrary connections and heterogeneous rules). The network may also have heterogeneous neighborhood sizes. The program iterates the network forward to display space-time patterns, and also runs the network "backwards" to generate a pattern's predecessors and reconstruct its branching sub-tree of all ancestor patterns. For smaller networks, sub-trees, basins of attraction or the whole basin of attraction field can be reconstructed and displayed as a directed graph or set of graphs in real time. The network's parameters, and the graphics display and presentation options, can be flexibly set, reviewed and altered, including changes (mutations) "on the fly". Various statistical measures and data are available. Learning/forgetting algorithms allow "sculpting" attractor basins to approach a desired scheme of hierarchical categorization. ------------------------------------------------------------------------- DDLab update March 1996 ----------------------- The UNIX/XWindows version is compiled for the Sun OS 4.1. The DOS version is for a 386 or higher, with VGA or SVGA graphics, maths co-processor, mouse, extended memory recommended -- ideally a fast 486 or higher with 8MB RAM. Downloading DDLab and documentation ----------------------------------- The latest version of DDLab is available from http://alife.santafe.edu/alife/software/ddlab.html the DDLab page on Alife Online, or directly by ftp://alife.santafe.edu/pub/SOFTWARE/ddlab Files to download ----------------- * this text file (uncompressed): download "ddlab.txt" * The DDLab manual: download "ddman_20.zip", at present the DDLab reference manual is only available as an un-illustrated Word for Windows file. *DDLab for DOS: download "ddlab_20.zip" *DDLab for UNIX/X Windows: download "ddlabx_20.tar.gz" downloading by FTP ------------------ If you wish to download DDLab using FTP, follow these instructions: ftp alife.santafe.edu name: anonymous password: (your complete email address) ftp>cd pub/SOFTWARE/ddlab (note "SOFTWARE" is upper case) for "ddlab.txt", type: ftp>asc ftp>get ddlab.txt and for the executable and the doc, type: ftp>bin ftp>get ddlab_20.zip (for DOS) or ftp>get ddlab_20.tar.gz (for UNIX/XWindows) or ftp>get ddman_20.zip (for the manual in Word for Windows format)> ftp>quit Unzipping and running. --------------------- DDLab Documentation ------------------- "ddman_20.zip" will unzip to give the following files: "ddman.doc" a Word for Windows file with the (un-illustrated) reference manual. "ddlab.txt" this text file, uncompressed. DOS program files ----------------- "ddlab_20.zip" will unzip to give the following files: "ddlab.exe" the program "dos4gw.exe" the DOS extender, giving access to extended memory. "dd-bh.map, dd-bl.map, dd-wh.map, dd-wl.map" 4 image files for titles some extra files listed below Keep these files in the same directory. To run the program in DOS, enter "ddlab" plus the optional program parameters -b (black background) and -h (svga resolution), i.e. for a black background in svga enter "ddlab -b -h". The "DOS extender" banner will briefly appear, and the program will start. Note that DDLab may also be set up and run as a non-Windows application under Microsoft Windows. UNIX/XWindows program files --------------------------- To uncompress ddlabx.tar.gz into a tar archive, type:gunzip ddlab_20.tar.gz. Now, to unpack the tar archive, type:tar -xf ddlab_20.tar This will create a new directory called "ddlabx_20", and place the following files into it: "ddlabx" the program some extra files listed below Keep these files in the same directory. To run the program in UNIX?X Windows, enter "ddlab" plus the optional program parameters -b (black background). extra files common to both DOS and UNIX/XWindows ----------------------------------------------- Files with "complex" 1d CA rules which feature interacting gliders: "glider5.r_s" about 60 complex 5-neighbour rules. "glider6.r_s" about 5 complex 6-neighbour rules. "glider7.r_s" about 10 complex 7-neighbour rules. "pento.eed" the "rpentomeno" 2d pattern, which seeds interesting "game-of-life" dynamics. I am grateful to Simon Fraser for helping to perfect the XWindows version and for porting DDLab to the Mac (a preliminary version of this is available from him, at smfr@santafe.edu. DDLab is at present free for non-commercial research or educational use only. For any other use of DDLab contact the author to arrange for a licensing agreement. References ---------- Wuensche,A., and M.J.Lesser. "The Global Dynamics of Cellular Automata: An Atlas of Basin of Attraction Fields of One-Dimensional Cellular Automata", Santa Fe Institute Studies in the Sciences of Complexity, Reference Vol.I, Addison-Wesley, 1992. (this is a book IBSN 0-201-55740-1) Wuensche.A.,"The Ghost in the Machine: Basins of Attraction of Random Boolean Networks", in Artificial Life III, Santa Fe Institute Studies in the Sciences of Complexity, Addison-Wesley, 1994. Wuensche.A., "Complexity in One-D Cellular Automata: Gliders, Basins of Attraction and the Z parameter", Santa Fe Institute working paper 94-04-025, 1994. Wuensche.A., "The Emergence of Memory; Categorisation Far From Equilibrium", Cognitive Science Research Paper 346, University of Sussex, 1994. To appear in "Towards a Scientific Basis for Consciousness" eds SR Hameroff, AW Kaszniak, AC Scot, MIT Press.