GENESIS Reference Manual

August 1, 1997

1. Introduction

• 1.1 Getting Started with GENESIS
• 1.2 Credits and Copyright Notice

2. Changes Introduced in GENESIS 2

• 2.1 Changes Introduced in GENESIS 2.1
• 2.2 Changes Introduced in GENESIS 2.0
• 2.3 Command Names
• 2.4 Objects
• 2.5 SLI Syntax Changes
• 2.6 Synaptic Connections
• 2.7 Extended Fields
• 2.8 Extended Objects
• 2.9 Saving Simulations
• 2.10 Script Conversion
• 2.11 The Parallel Library
• 2.12 Rallpacks Benchmarks

3. The GENESIS Script Language Interpreter

• 3.1 GENESIS Statements and Commands
• 3.2 Creating Variables
• 3.3 Functions
• 3.4 Operators
• 3.5 Control Structures

4. Basic Routines

5. Math Routines

6. String Manipulation Routines

7. Input/Output (I/O) Routines

• 7.1 Saving Simulations to a File
• 7.2 Related GENESIS Objects

8. Elements

• 8.1 Related Commands
• 8.2 Actions

9. Hierarchical Structure

• 9.1 The GENESIS Element Tree Hierarchy
• 9.2 Traversing the Element Tree
• 9.3 Pathnames and Wildcards

10. Objects

• 10.1 GENESIS Objects by Category
• 10.2 Related Commands

11. Extended Objects

• 11.1 Extending Fields
• 11.2 Extending Actions
• 11.3 Extending Message Definitions
• 11.4 Extending Classes
• 11.5 Using Extended Objects for Specialization
• 11.6 Using Extended Objects for Composition
• 11.7 Related Commands

12. Neural Simulation Routines

• 12.1 Buffer Routines
• 12.2 Compartment Routines
• 12.3 Miscellaneous Neural Routines

13. Messages

14. Synaptic Connections

15. Simulations

• 15.1 Running a Simulation
• 15.2 Simulation Clocks
• 15.3 GENESIS Jobs

16. Simulation Schedules

17. Tables and Arrays: The interpol_struct

• 17.1 Using interpol_structs

18. The XODUS Graphical Interface

• 18.1 Introduction and Overview of XODUS
• 18.2 Basic Widgets
• 18.3 Specifying Widget Geometries
• 18.4 The Draw Widget Family
• 18.5 XODUS Commands

19. XODUS Mouse Clicks -- a summary of syntax conventions

• 19.1 Conventions
• 19.2 Overview
• 19.3 Graphical User Interface Actions.
• 19.4 Scripts and Actions: Assigning the script Field
• 19.5 Scripts and Actions: Arguments Passed to the script Function.

20. Customizing GENESIS

• 20.1 Defining New Objects and Commands
• 20.2 Compiling a New Version of GENESIS

21. Converting GENESIS 1.4 Scripts to GENESIS 2.0

• 21.1 The Conversion Process
• 21.2 Using the Convert Program
• 21.3 Global Script Variables
• 21.4 Compatibility Libraries
• 21.5 The X1compat Library
• 21.6 The Connection Compatibility Library
• 21.7 Converting User Libraries
• 21.8 Convert Problem Areas
• 21.9 Script Callbacks
• 21.10 Command Options in Script Variables
• 21.11 Command Arguments That Look Like Options
• 21.12 Script Variable/Command Name Conflicts
• 21.13 Setting Integration Methods
• 21.14 Sizing of XODUS Forms
• 21.15 Positioning and Sizing of Widgets

22. The Book of GENESIS

23. GENESIS Startup Command Reference

• 23.1 addfunc
• 23.2 newclass
• 23.3 object

24. GENESIS Command Reference

• 24.1 abort
• 24.2 abs
• 24.3 acos
• 24.4 addaction
• 24.5 addalias
• 24.6 addclass
• 24.7 addescape
• 24.8 addfield
• 24.9 addforwmsg
• 24.10 addmsg
• 24.11 addmsgdef
• 24.12 addobject
• 24.13 argc
• 24.14 arglist
• 24.15 argv
• 24.16 asciidata
• 24.17 asin
• 24.18 atan
• 24.19 call
• 24.20 callfunc
• 24.21 cd
• 24.22 ce
• 24.23 check
• 24.24 chr
• 24.25 clearerrors
• 24.26 closefile
• 24.27 convert
• 24.28 copy
• 24.29 cos
• 24.30 countchar
• 24.31 cpu
• 24.32 create
• 24.33 createmap
• 24.34 debug
• 24.35 delete
• 24.36 deleteaction
• 24.37 deleteall
• 24.38 deleteclass
• 24.39 deletefield
• 24.40 deleteforwmsg
• 24.41 deletemsg
• 24.42 deletemsgdef
• 24.43 echo
• 24.44 egg
• 24.45 el
• 24.46 enddump
• 24.47 exists
• 24.48 exit
• 24.49 exp
• 24.50 file2tab
• 24.51 findchar
• 24.52 findsolvefield
• 24.53 floatformat
• 24.54 flushfile
• 24.55 gaussian
• 24.56 genesis
• 24.57 getarg
• 24.58 getclock
• 24.59 getdate
• 24.60 getdefault
• 24.61 getelementlist
• 24.62 getenv
• 24.63 getfield
• 24.64 getfieldnames
• 24.65 getmsg
• 24.66 getpath
• 24.67 getsyncount
• 24.68 getsyndest
• 24.69 getsynindex
• 24.70 getsynsrc
• 24.71 h
• 24.72 help
• 24.73 initdump
• 24.74 input
• 24.75 le
• 24.76 listcommands
• 24.77 listescape
• 24.78 listfiles
• 24.79 listglobals
• 24.80 listobjects
• 24.81 log
• 24.82 logfile
• 24.83 max
• 24.84 maxerrors
• 24.85 maxwarnings
• 24.86 min
• 24.87 move
• 24.88 notes
• 24.89 openfile
• 24.90 planarconnect
• 24.91 planardelay
• 24.92 planardelay2
• 24.93 planarweight
• 24.94 planarweight2
• 24.95 plane
• 24.96 pope
• 24.97 position
• 24.98 pow
• 24.99 printargs
• 24.100 printenv
• 24.101 pushe
• 24.102 putevent
• 24.103 pwe
• 24.104 quit
• 24.105 rand
• 24.106 randseed
• 24.107 readcell
• 24.108 readfile
• 24.109 reclaim
• 24.110 reset
• 24.111 resetsynchanbuffers
• 24.112 restore
• 24.113 rotcoord
• 24.114 round
• 24.115 save
• 24.116 scaletabchan
• 24.117 setclock
• 24.118 setdefault
• 24.119 setenv
• 24.120 setfield
• 24.121 setfieldprot
• 24.122 setmethod
• 24.123 setprompt
• 24.124 setupalpha
• 24.125 setupgate
• 24.126 setuptau
• 24.127 sh
• 24.128 showclocks
• 24.129 showcommand
• 24.130 showfield
• 24.131 showmsg
• 24.132 showobject
• 24.133 silent
• 24.134 simdump
• 24.135 simobjdump
• 24.136 simundump
• 24.137 sin
• 24.138 sqrt
• 24.139 stack
• 24.140 step
• 24.141 stop
• 24.142 strcat
• 24.143 strcmp
• 24.144 strlen
• 24.145 strncmp
• 24.146 strsub
• 24.147 substring
• 24.148 swapdump
• 24.149 syndelay
• 24.150 tan
• 24.151 trunc
• 24.152 tweakalpha
• 24.153 tweaktau
• 24.154 useclock
• 24.155 version
• 24.156 volumeconnect
• 24.157 volumedelay
• 24.158 volumeweight
• 24.159 where
• 24.160 writecell
• 24.161 writefile
• 24.162 xcolorscale
• 24.163 xgetstat

25. GENESIS Object Reference

• 25.1 Ca_concen
• 25.2 Kpores
• 25.3 Mg_block
• 25.4 Napores
• 25.5 PID
• 25.6 RC
• 25.7 asc_file
• 25.8 compartment
• 25.9 ddsyn
• 25.10 diffamp
• 25.11 disk_in
• 25.12 disk_out
• 25.13 diskio
• 25.14 efield
• 25.15 enz
• 25.16 funcgen
• 25.17 hebbsynchan
• 25.18 hh_channel
• 25.19 hsolve
• 25.20 leakage
• 25.21 metadata
• 25.22 nernst
• 25.23 neutral
• 25.24 playback
• 25.25 pool
• 25.26 pulsegen
• 25.27 randomspike
• 25.28 reac
• 25.29 receptor
• 25.30 receptor2
• 25.31 script_out
• 25.32 sigmoid
• 25.33 spikegen
• 25.34 spikehistory
• 25.35 symcompartment
• 25.36 synchan
• 25.37 synchan2
• 25.38 tab2Dchannel
• 25.39 tabchannel
• 25.40 tabgate
• 25.41 table
• 25.42 variable
• 25.43 vdep_channel
• 25.44 xbutton
• 25.45 xcell
• 25.46 xcoredraw
• 25.47 xdialog
• 25.48 xdraw
• 25.49 xdumbdraw
• 25.50 xform
• 25.51 xgif
• 25.52 xgraph
• 25.53 ximage
• 25.54 xlabel
• 25.55 xpix
• 25.56 xplot
• 25.57 xshape
• 25.58 xsphere
• 25.59 xtext
• 25.60 xtoggle
• 25.61 xtree
• 25.62 xvar
• 25.63 xview