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Table of Contents
GENESIS 2.4 Reference Manual
July 2014
1.
Introduction
1.1 Getting Started with GENESIS
1.2 Credits and Copyright Notice
1.3 Reporting Bugs
2.
Changes Introduced in GENESIS 2
2.0 Changes Introduced in GENESIS 2.4
2.01 Changes Introduced in GENESIS 2.3
2.1 Changes Introduced in GENESIS 2.2
2.2 Changes Introduced in GENESIS 2.1
2.3 Changes Introduced in GENESIS 2.0
2.4 Command Names
2.5 Objects
2.6 SLI Syntax Changes
2.7 Synaptic Connections
2.8 Extended Fields
2.9 Extended Objects
2.10 Saving Simulations
2.11 Script Conversion
2.12 The Parallel Library
2.13 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
17.5
The 'chemesis' library of GENESIS objects
18.
The GENESIS Parameter Search Library
18.1 What is automated parameter searching?
18.2 The parameter searching process
18.3 The GENESIS parameter search library
18.4 Recommendations
18.5 Bug reports.
18.6 Caveats
18.7 Information about the Parameter-search (paramtable) Objects
19.
The XODUS Graphical Interface
19.1 Introduction and Overview of XODUS
19.2 Basic Widgets
19.3 Specifying Widget Geometries
19.4 The Draw Widget Family
19.5 XODUS Commands
20.
XODUS Mouse Clicks -- a summary of syntax conventions
20.1 Conventions
20.2 Overview
20.3 Graphical User Interface Actions.
20.4 Scripts and Actions: Assigning the
script
Field
20.5 Scripts and Actions: Arguments Passed to the
script
Function.
21.
Customizing GENESIS
21.1 Defining New Objects and Commands
21.3 Creating New Synaptic Objects
21.4 Creating New Synaptic Plasticity Objects
21.2 Compiling a New Version of GENESIS
22.
Converting GENESIS 1.4 Scripts to GENESIS 2.0
22.1 The Conversion Process
22.2 Using the Convert Program
22.3 Global Script Variables
22.4 Compatibility Libraries
22.5 The X1compat Library
22.6 The Connection Compatibility Library
22.7 Converting User Libraries
22.8 Convert Problem Areas
22.9 Script Callbacks
22.10 Command Options in Script Variables
22.11 Command Arguments That Look Like Options
22.12 Script Variable/Command Name Conflicts
22.13 Setting Integration Methods
22.14 Sizing of XODUS Forms
22.15 Positioning and Sizing of Widgets
23.
The Book of GENESIS
24.
GENESIS Startup Command Reference
24.1 addfunc
24.2 newclass
24.3 object
25.
GENESIS Command Reference
25.1 abort
25.2 abs
25.3 acos
25.4 addaction
25.5 addalias
25.6 addclass
25.7 addescape
25.8 addfield
25.9 addforwmsg
25.10 addglobal
25.11 addmsg
25.12 addmsgdef
25.13 addobject
25.14 addtask
25.15 argc
25.16 arglist
25.17 argv
25.18 asciidata
25.19 asin
25.20 atan
25.21 call
25.22 callfunc
25.23 cd
25.24 ce
25.25 cellsheet
25.26 check
25.27 chr
25.28 clearerrors
25.29 closefile
25.30 convert
25.31 copy
25.32 cos
25.33 countchar
25.34 countelementlist
25.35 cpu
25.36 create
25.37 createmap
25.38 debug
25.39 delete
25.40 deleteaction
25.41 deleteall
25.42 deleteclass
25.43 deletefield
25.44 deleteforwmsg
25.45 deletemsg
25.46 deletemsgdef
25.47 deletetasks
25.48 disable
25.49 echo
25.50 egg
25.51 el
25.52 enable
25.53 enddump
25.54 eof
25.55 exists
25.56 exit
25.57 exp
25.58 file2tab
25.59 fileconnect
25.60 findchar
25.61 findsolvefield
25.62 floatformat
25.63 flushfile
25.64 gaussian
25.65 gen2spk
25.66 genesis
25.67 getarg
25.68 getclock
25.69 getdate
25.70 getdefault
25.71 getelementlist
25.72 getenv
25.73 getfield
25.74 getfieldnames
25.75 getglobal
25.76 getmsg
25.77 getparamGA
25.78 getpath
25.79 getsolvechildname
25.80 getsolvecompname
25.81 getstat
25.82 getsyncount
25.83 getsyndest
25.84 getsynindex
25.85 getsynsrc
25.86 h
25.87 help
25.88 initdump
25.89 initparamBF
25.90 initparamCG
25.91 initparamGA
25.92 initparamSA
25.93 initparamSS
25.94 input
25.95 isa
25.96 le
25.97 listcommands
25.98 listescape
25.99 listfiles
25.100 listglobals
25.101 listobjects
25.102 log
25.103 logfile
25.104 max
25.105 maxerrors
25.106 maxwarnings
25.107 min
25.108 move
25.109 msgsubstitute
25.110 notes
25.111 objsubstitute
25.112 openfile
25.113 planarconnect
25.114 planardelay
25.115 planardelay2
25.116 planarweight
25.117 planarweight2
25.118 plane
25.119 pope
25.120 position
25.121 pow
25.122 printargs
25.123 printenv
25.124 pushe
25.125 putevent
25.126 pwe
25.127 quit
25.128 rand
25.129 randcoord
25.130 randseed
25.131 readcell
25.132 readfile
25.133 reclaim
25.134 relposition
25.135 resched
25.136 reset
25.137 resetsynchanbuffers
25.138 restore
25.139 rotcoord
25.140 round
25.141 save
25.142 scaletabchan
25.143 setclock
25.144 setdefault
25.145 setenv
25.146 setfield
25.147 setfieldprot
25.148 setglobal
25.149 setmethod
25.150 setparamGA
25.151 setpostscript
25.152 setprompt
25.153 setrand
25.154 setrandfield
25.155 setsearch
25.156 setupNaCa
25.157 setupalpha
25.158 setupgate
25.159 setupghk
25.160 setuptau
25.161 sh
25.162 shapematch
25.163 showclocks
25.164 showcommand
25.165 showfield
25.166 showmsg
25.167 showobject
25.168 showsched
25.169 showstat
25.170 silent
25.171 simdump
25.172 simobjdump
25.173 simundump
25.174 sin
25.175 spkcmp
25.176 sqrt
25.177 stack
25.178 step
25.179 stop
25.180 strcat
25.181 strcmp
25.182 strlen
25.183 strncmp
25.184 strsub
25.185 substituteinfo
25.186 substring
25.187 swapdump
25.188 syndelay
25.189 tab2file
25.190 tan
25.191 trunc
25.192 tweakalpha
25.193 tweaktau
25.194 useclock
25.195 version
25.196 volumeconnect
25.197 volumedelay
25.198 volumedelay2
25.199 volumeweight
25.200 volumeweight2
25.201 where
25.202 writecell
25.203 writefile
25.204 xcolorscale
25.205 xgetstat
25.206 xps
25.207 xsimplot
26.
GENESIS Object Reference
26.1 Ca_concen
26.2 Kpores
26.3 Mg_block
26.4 Napores
26.5 PID
26.6 RC
26.7 asc_file
26.8 autocorr
26.9 calculator
26.10 compartment
26.11 concchan
26.12 concpool
26.13 crosscorr
26.14 ddsyn
26.15 dif2buffer
26.16 difbuffer
26.17 diffamp
26.18 difshell
26.19 disk_in
26.20 disk_out
26.21 diskio
26.22 efield
26.23 enz
26.24 event_tofile
26.25 facsynchan
26.26 fixbuffer
26.27 freq_monitor
26.28 funcgen
26.29 fura2
26.30 ghk
26.31 hebbsynchan
26.32 hh_channel
26.33 hillpump
26.34 hsolve
26.35 interspike
26.36 leakage
26.37 metadata
26.38 mmpump
26.39 nernst
26.40 neutral
26.41 paramtableBF
26.42 paramtableCG
26.43 paramtableGA
26.44 paramtableSA
26.45 paramtableSS
26.46 peristim
26.47 playback
26.48 pool
26.49 pulsegen
26.50 randomspike
26.51 reac
26.52 receptor
26.53 receptor2
26.54 script_out
26.55 sigmoid
26.56 spikegen
26.57 spikehistory
26.57.1 stdp_rules
26.58 symcompartment
26.59 synchan
26.60 synchan2
26.61 tab2Dchannel
26.62 tabchannel
26.63 tabcurrent
26.64 tabgate
26.65 table
26.66 table2D
26.67 taupump
26.68 timetable
26.69 variable
26.70 vdep_channel
26.71 xbutton
26.72 xcell
26.73 xcoredraw
26.74 xdialog
26.75 xdraw
26.76 xdumbdraw
26.77 xfastplot
26.78 xform
26.79 xgif
26.80 xgraph
26.81 ximage
26.82 xlabel
26.83 xpix
26.84 xplot
26.85 xshape
26.86 xsphere
26.87 xtext
26.88 xtoggle
26.89 xtree
26.90 xvar
26.91 xview
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