This manual describes the use of the software. To retrieve a functioning copy, you must have a copy of Microsoft QuickBASIC 4.5 to compile the source code. Proceed as follows:
- Download the source module for the main program SYNETSIM.33B into a text file, strip the HTML material above and below the two rows of "###### ..." and compile a stand-alone .EXE version using QuickBASIC version 4.5.
- Download the source module for the net compiler NET2PRM.V18 into a text file, strip the HTML material above and below the "########..." rows and compile a stand-alone .EXE version using QuickBASIC.
- Download the auxiliary page SYNETSIM-AUX into a text file and parcel the parts sandwiched between the "xxxxxxx ################# ...." delineations into separate text files named as given by the "xxxxxxx"
- You should now have the following files on your DOS disk:
- SYNETSIM.33B
- SYNETSIM.EXE
- NET2PRM.V18
- NET2PRM.EXE
- NET2MST.CNF
- NET2PRM.CNF
- NET2SBT.CNF
- SYNTEST.NET
- SYNTEST.PSP
- You should be able to run the test network as follows (see manualbelow):
- NET2PRM SYNTEST
- SYNETSIM SYNTEST
***********************************************
* *
* *
* SYNETSIM 3.3 USERS' MANUAL *
* *
* *
***********************************************
Copyright (C) 1990, 1996 by
Daniel K. Hartline
Bekesy Lab
1993 East-West Rd.
Honolulu, HI 96822
[interim version; not fully updated; use cautiously!]
SYNETSIM-3 and this manual were produced under the support of NIH grant
NS15314. NET2PRM was written by Greg Wolodkin, Dept. of Electrical
Engineering, Univ. of Maryland, College Park, MD.
The software may be used without license fees for non-profit
scientific or educational purposes only. Inquiries regarding licensing
other applications should be addressed to D. Hartline.
Copyright (C) 1990, D. Hartline
This manual is valid for SYNETSIM 3.3, revision B dated 8/23/90.
See file READ.ME for updates pertaining to subsequent releases.
TABLE OF CONTENTS
I. GENERAL INFORMATION APPENDICES
A. Overview I: Error messages
B. Hardware/Software required II: Implementation notes
C. Installation and checkout Program logic in brief
D. Common problems Hodgkin-Huxley branches
E. Availability of help Synaptic potentials
F. References Facilitation
III: User-generated additions
II. USING SYNETSIM 3.3 IV: Netlist manual
A. Startup (by Greg Wolodkin)
B. Main menu V: Input file structures
C. Output VI: SYNTEST.NET
D. End-of-run display VII: Variable list
E. SYNTEST VII: Speed tests
IX: Source listing
III. MODEL DESCRIPTION
A. Netlist structure
B. Compartmental representation of branching neurons
CMPT - Basic electrical compartment
SOMA - Spherical compartment
CYL - Cylindrical segment
INFCYL - Infinite-cylinder cable termination
C. Electrical properties
TRIGR - Trigger zone simulation
ELECTN - Electrotonic connections
DIODE - Rectifying electrical connections
SPIKE - Schmitt-trigger type spike generation
COND - Simple conductance and battery
DRIVER - Driver and plateau potentials
HHFXD - Hodgkin-Huxley kinetics with fixed time-constants
HH - Full Hodgkin-Huxley kinetics
CONNOR - Hodgkin-Huxley kinetics for crab axon A-current
SYNAPSE - Spike-generated chemical synapse
CHEMOX - Chemotonic (non-spiking) synapse
D. Pools, second messengers, and biochemistry
POOL - Basic chemical compartment
POOLK - Chemical reaction and diffusion kinetics
POOLX - Pool-dependent modulation
E. Other netlist features
.DEFINE block structure
.BLOCK block structure
.BATCH block structure
F. Data files
Synaptic transmitter file (*.PSP)
Save file (*.SAV)
Output file (*.PRN)
IV. PROGRAM COMPATIBILITY
V. PROGRAM BUGS
VI. UPDATES IN 3.0 AND 3.2
GENERAL INFORMATION
--> Persons already familiar with SYNETSIM should read the information in
the UPDATES section. A major addition in version 3.3 and later is the
"netlist compiler", written by Greg Wolodkin, which makes setting model
parameters much easier than before.
A. OVERVIEW
The SYNETSIM series of neural network models has been developed for
the realistic simulation of small networks of individually distinct
neurons using parameters measured from physiological experiment. Previous
models of the series have been limited by certain simplifications made to
facilitate derivation of model parameters, or by restrictions on computer
memory or speed. The SYNETSIM-3 versions represent a more advanced and
versatile model written in BASIC to run on various microcomputers and
capable of simulating a variety of electrical and biochemical integrative
properties of neural networks.
SYNETSIM-3 includes the following design features:
1. Compartmental structure: The network consists of an array of
compartments treated uniformly in model computations. Each is
characterized by a capacitance, a leak resistance, and a leak battery. In
addition, any number of active "branches" may be included to generate
appropriate electrical properties. Cells are constructed through
resistive coupling of appropriate compartments. Electrotonic connections
between cells are generated similarly. A separate set of "diffusionally"
connected compartments, termed "pools", is used for chemical components.
2. Current-based representations are used for synaptic interactions,
for active responses, and optionally for spike-generating regions. This
improves the physiological accuracy of the simulations compared to
voltage-based representations (e.g. SYNETSIM 2.4: Hartline 1987), although
deriving parameters is more difficult.
3. Synaptic interactions, both spike-mediated and non-spiking
chemical ("chemotonic") operate through simulation of transmitter released
and bound to postsynaptic receptors. Facilitation/antifacilitation of
spike-mediated PSPs is featured.
4. Active responses, such as plateau potentials and delaying
mechanisms are simulated (as in earlier versions) by Hodgkin-Huxley type
representations. Modular branch paradigm coding permits easy addition of
user-defined algorithms.
5. Pools can be used to simulate second messenger systems, trapping
of ions in extracellular spaces, and electrogenic pumps, as well as
biochemical reaction chains of quite general character. Modulation of any
of the parameters of any compartment can be effected through the pools.
This provides much flexibility in the integrative capabilities simulable.
6. Intracellular messengers of three kinds are simulated: a) those
produced by voltage-gated processes (e.g. Ca); b) those dependent on
transmitter (or hormone) binding; and c) those dependent on other
internal messengers (e.g. internally-released Ca; enzymatically activated
pathways).
7. The model does not directly simulate post-spike integration
effects (e.g. branch-point failure).
B. HARDWARE/SOFTWARE REQUIRED
The compiled module of SYNETSIM should run as is on an IBM PC-
compatible machine having 640K of memory. Exact memory requirements
depend on the particular net being run, but nets are likely to be limited
to only two or three cells without extended memory capabilities. The
output requires a graphics board (CGA, EGA or VGA) and monitor configured
to operate with BASIC graphics commands (SCREEN x; PSET) [default graphics
mode is CGA using SCREEN 2; color capabilities were added to version 3.3B
and are more likely to cause problems; they may also cause slowing of
execution times]. Note that the compiled version of SYNETSIM requires the
Microsoft Run-time module BRUN30, which is protected by Microsoft
copyrights. For even faster execution, you can recompile SYNETSIM.3xx.
(QuickBASIC 3 supports a math chip using BRUN3087.EXE; QuickBASIC 4 and
4.5 detect the presence of a math chip and use BRUN40.EXE or allow a
stand-alone option). Substantial speed increases can be achieved by
compiling with the debug feature deselected.
C. INSTALLATION AND CHECK-OUT (diskette distribution only)
Check to be sure the distribution package is complete. In addition
to this file (SYNETDOC.TXT), the following files should be on the
distribution diskette:
DEMO - Subdirectory with demonstration modules
HH.NET - Net file for Hodgkin-Huxley simulations
NET2PRM.BAS - Net-list compiler source code
@NET2PRM.CNF - Configuration file for NET2PRM
@NET2MST.CNF - Configuration file for NET2PRM
@NET2SBT.CNF - Configuration file for NET2PRM
@NET2PRM.EXE - Net-list compiler (compiled by QuickBASIC 4.5)
READ.ME - Update information on more recent releases, etc.
SYNETSIM.3xx - Source program (xx= version number)
*SYNETSIM.EXE - A compiled form using Microsoft's QuickBASIC 4.5
*SYNTEST.MST - Master file for test run
@SYNTEST.NET - Net file for test run
*SYNTEST.PRM - Parameter file for test run
*SYNTEST.PSP - PSP File for test run
*SYNTEST.SBT - Batch file for test run
Copy the "*" files to your logged disk area, then type:
SYNETSIM SYNTEST /B
Press the "Enter" key () when the appropriate prompt appears to test
whether the program is operating properly. The screen should plot out the
bursting trajectories shown in the SYNTEST figure at the end of Appendix
VI. To test the net-list compiler, copy the "@" files to your disk and
type:
NET2PRM SYNTEST
then proceed as above. The .MST, .PRM, and .SBT files produced by the
compiler should be identical to the ones on the distribution disk.
D. COMMON PROBLEMS
DURING STARTUP
a. "Subscript out of range in line 495": Not enough space for the
display array. The space needed can be calculated from:
(number of compartments) x XSCALE / (TINC x SKIP)
To retain the same amount of model time without changing the time
increment, increase the skip-index to skip more time between plotted
points.
DURING RUN
a. "Overflow": Time increment too large; reduce it.
b. Plotted points "blow up" ... going off scale. Problem may be too
large a time increment; also the y-scale value (VSCALE, ISCALE, etc. in
the .MASTER section of the net file) may be too small.
E. AVAILABILITY OF HELP
The file SYNETDOC.TXT [this document] contains documentation for the
version of SYNETSIM indicated on the cover page for IBM-PC and AT
compatible microcomputers. This is a program under continual development,
so parts have not been fully tested, and reliability is not guaranteed.
In case of intractable problems, call the author at (808) 956-8003 (FAX
808-956-6984). Please have hardware and software configuration
information available, including: a) make and model of your computer; b)
amount of memory; c) print-out of CONFIG.SYS. Please assure yourself that
GWBASIC works on your system (including PRINT #3, INPUT #3, SCREEN 0,
SCREEN 2, and PSET statements) and that neither the compiled
(SYNETSIM.EXE) nor the interpreted version (SYNETSIM.3xx) work. In some
cases I may be able to modify the program to fit your particular needs (no
guarantees, but I am interested in making it useful to others). Your
suggestions will be appreciated. A final caution: please note the section
PROGRAM BUGS, and please read the file READ.ME for update information not
contained herein.
F. REFERENCES
Hartline, D.K. (1976a) "Simulation of phase-dependent pattern changes
to perturbations of regular firing in crayfish stretch receptor." Brain
Res. 110: 245-257.
Hartline, D.K. (1976b) "SNAX: A language for interactive neuronal
modeling and data processing." In Brown, P.B., ed, Computer Technology in
Neuroscience, Hemisphere, Washington, D.C. pp. 41-65.
Hartline, D.K. (1979) "Pattern generation in the lobster (Panulirus)
stomatogastric ganglion. II. Pyloric network simulations." Biol.
Cybern. 33: 223-236.
Hartline, D.K. (1987) "Modeling stomatogastric ganglion" in
Selverston, A.I. and Moulins, M., eds The Crustacean Stomatogastric
System, Springer-Verlag, Berlin, pp 181-197
Hartline, D.K. (1989) "Simulation of restricted neural networks with
reprogrammable neurons" IEEE Trans. Circuits Systems 36: 653-660
Hartline, D.K.(1991) "The neuron as a reprogrammable computing
element" in Fraser, M., (ed) Advances in Control Networks and Large Scale
Parallel Distributed Processing Models, Ablex, Norwood N.J. pp. [in press]
II. USING SYNETSIM 3.3
A. STARTUP
Running this version of SYNETSIM is a two-step process. First, the
"netlist" (.NET) file, specifying the properties and connections of the
neural network to be simulated must be compiled using the program
NET2PRM.EXE. This generates three output files with default extensions of
PRM, MST, and SBT. The .PRM (parameter) file contains parameters for
properties and connections; the .MST (master) file contains parameters
related to the running of the model (integration time step, x and y
scales, colors, etc.); the .SBT (SYNETSIM batch) file allows for batch-
like operation of the various menu options at run-time. After compilation
of the netlist, SYNETSIM.EXE is run to perform the actual simulation.
After invoking SYNETSIM, the screen should display parameters from the
master file, then loading of PSPs (if any), and ending up with:
"HIT ANY KEY TO CONTINUE"
Doing so leads to the main menu (in batch mode, a sequence of menu options
will be executed: see BATCH OPERATIONS below):
B. MAIN MENU
(NO .PRN)
= RETURN TO DOS
1= FREE_RUN - Run model with no further perturbations
2= I_PULSEs - 2-pulse current injection paradigm
3= PSP_TRAIN - Fire spike train in presynaptic cell
4= Voltage clamp of a compartment [--> submenu]
5= POOL INCrement - Change level of a selected pool
6= TOXINS - Enable/disable specific branch types
7= Initiate batch mode
8= CHANGE_PARAMeters - Change selected model parameters
9= OUTPUT_PRN - Write model output to disk on next sweep
10= SAVE the model state state on a disk file
11= RESTORE previous model state from disk file
12= CHANGE_DISPLAY to output new state variable
13= Options [--> submenu]
?
Respond to this according to the following list of desired model
actions (names of parameters for menu-driven and .BATCH operation are
given in caps; names with "*" in left margin can be netlist names in
driven operation)
SELECTION 1 (Free_run) will run the main network without perturbation
for several sweeps, plotting the display-variable (default = membrane
potential; changeable with selection 12). It is often a good idea to run
the model for several sweeps to allow transients associated with non-
initialized variables to decay.
NSWEEPS = Number of sweeps to be made before returning to menu.
SELECTION 2 (I_pulse) applies a sequence of two current pulses to any
compartment: a "conditioning" pulse of arbitrary size and duration,
followed by a test pulse of arbitrary size and duration. It will also
apply a bias current that persists through subsequent sweeps. The program
will prompt you for the compartment to be perturbed, the magnitude of the
bias current (in nA: see section Model Units below), the magnitudes of the
conditioning and test pulses, and the durations of same (time to be
specified in seconds). Type the parameters on one line separated by
commas. The conditioning pulse will start with no delay at the beginning
of the sweep.
* CMPT = Compartment ID to which pulse is to be applied;
BIAS = Bias current to be applied throughout;
COND_I = Conditioning pulse magnitude;
COND_DUR = Duration of conditioning pulse (sec);
TEST_I = Test pulse magnitude;
TEST_DUR = Duration of test pulse (sec).
SELECTION 3 (PSP_train): This will produce a train of spikes of
specified frequency and duration (following a specified delay) in any unit
desired.
* SPKFLG = Spike flag ID for presynaptic spike;
RATE = Stimulation rate for presynaptic unit;
DELAY = Delay from beginning of sweep to start of PSP train;
DURATION = Duration of presynaptic train (sec).
SELECTION 4 (voltage clamp): This will clamp one specified
compartment as indicated by a submenu:
1 = HOLD - to a given hold potential for a specified number of sweeps.
* CMPT = Compartment clamped;
HOLD_V = Hold potential;
NSWEEPS = Number of sweeps hold will be applied;
SAVFILE = Name of file to save final model state.
2 = VC_CT - gives conditioning and test clamp commands as in Selection
2.
The display for the specified compartment indicates clamp
current,
rather than voltage.
* CMPT = Compartment clamped;
COND_V = Conditioning pulse level (abs mV);
COND_DUR = Duration of conditioning pulse (sec);
TEST_V = Test pulse level (abs mV);
TEST_DUR = Duration of test pulse (sec);
HOLD_V = Hold potential to be returned to after test.
3 = IV - gives runs of the condition/test type, systematically stepping
through a set of
test values, then changing the conditioning level and
rerunning.
Current at the end of each test pulse is stored in a .IV
file.
* CMPT = Compartment clamped;
COND_V = Conditioning pulse level (abs mV);
COND_DUR = Duration of conditioning pulse (sec);
COND_STEP = Increment size for conditioning pulses (mV);
NCOND = Number of conditioning pulses (minimum is 0);
TEST_V = Test pulse level (abs mV);
TEST_DUR = Duration of test pulse (sec);
TEST_STEP = Increment size for test pulses (mV);
NTEST = Number of test pulses (minimum is 1);
SAVFILE = .SAV File holding initial state;
IVFILE = File for storage of I(V) output.
SELECTION 5 (Pool_inc): This permits the abrupt increment of any
pool, permitting the effects of that pool by itself to be examined.
* POOL = ID of pool to be incremented;
INC = Increment
SELECTION 6 (Toxins) allows control of which physiological properties
are enabled. It functions like a set of specific toxins for particular
property types. Any property ("branch type" ... see below) except the
principal compartment type can be blocked by giving the property mnemonic
code and answering "B" to the input request (answer "U" to unblock a
previously blocked property).
CODENAME = Name of property to be blocked;
FLAG = B or U for blocked or unblocked
SELECTION 8 (Change_param): Model parameters are specified by a
branch code [WHICH AT THIS POINT MUST BE NUMERIC RATHER THAN MNEMONIC], a
branch number, and a parameter number. For interaction parameters (codes
3 and 21), the branch and parameter numbers are replaced with the numbers
of the two compartments or pools between which the interaction takes
place. [.BATCH mode operation of this has not yet been implemented]
SELECTION 9 (Output_prn): is used to activate output to disk for one
sweep. The status display "(NO .PRN)" on the main menu will change to
"(.PRN OUTPUT)" when this option is active. Answer the next query with
the name of a disk file, which may include a drive\directory
specification, but must not include an extension (see OUTPUT below). A
second use of selection 9 before an output run will cancel the output
mode.
PRNFILE = Output file name (.PRN will be added as extension)
SELECTIONS 10 and 11 (Save; Restore): allow storing and recalling the
model state (all state variables and the PSP summation array). This
allows saving a state just prior to a manipulation, so that several
parameters in the manipulation can be tested if desired. Note that the
model must already have the appropriate .MST, .PRM, and .PSP files in
memory.
SAVFILE = Save-file name (.SAV extension must be specified)
SELECTION 12 (Change_display): allows changing which state variables
are plotted on the screen, or written to the output .PRN file, if the
latter option has been selected. The default option is compartment
membrane potential (V). The menu selection first asks for the mnemonic
code for the branch-type of the state variable desired (e.g. "CMPT"), then
for the mnemonic for the state variable (same as the variable name given
in the parameter file block of the Model Description section)[UNTESTED]
SELECTION 13 (Options): The following options may be elected
through this selection (the assignment FLAG=ON or FLAG=OFF is used in
BATCH operations):
1= TIME_RESET - Sets U-variable [time] for reset/no reset at
beginning of sweep.
2= BELL - Turns bell on/off (beeps at end of sweep, for slow models).
3= ZERO_LINE - Turns y=zero axis plot on/off.
4= SPIKE_TIC - Turns spike plot on/off
5= Y_OFFSET - Permits the y-offset of the plot to be changed
OFFSET = offset in mV (no FLAG)
6= DEBUG_MODE - Activates/inactivates a debug mode
NSWEEPS = the number of sweeps in .BATCH mode
Following menu selections 5 and above, the model program returns to
the main menu and waits for another selection. Following menu selections
1-4, the model will plot membrane potential (or another selected display
variable), along with spikes fired, for one (or in some cases more) sweep,
before returning to Main Menu.
C. OUTPUT
To screen:
Normal output is a screen plot of a Plot Variable, initially membrane
potential (for each compartment), and modifiable by Selection 12
(=CHANGE_DISPLAY in the netlist .BATCH block) of the Main Menu. Colors
can be used with screens supporting graphics mode 9 by setting GMODE=9 in
the .MASTER block of the netlist (see MASTER BLOCK below). In the absence
of color or screen specification, SYNETSIM defaults to CGA (graphics mode
2) format. Note that the model may run a lot (e.g. 2x) slower in these
alternate screen modes!
To printer:
If the "PRINT" option is active, parameters of the run will be listed
on the printer operated by BASIC's LPRINT statement. Activation is via
menu item 13, or setting PRINT=ON in the .BATCH block, or setting PRINT=-1
in the .MASTER block.
To .PRN and .SPK files:
If output to disk is selected using main menu item 9 (=OUTPUT_PRN in
and the extensions ".PRN" and ".SPK". The .PRN file will contain Lotus 1-
2-3 compatible data columns. The first column is model time. The
subsequent columns are the display-parameter variables from selection 12
(if not left as membrane voltage). The file can be read directly into a
Lotus worksheet (using the "Import/Numbers" operations) and plotted using
the usual Lotus facilities.
The .SPK file contains two columns, Time a spike fired and Unit #
firing.
D. END-OF-SWEEP DISPLAY
At the end of the run (if not in batch mode), a "SWEEP COMPLETE:
TO MAIN MENU" message appears. At this point, the cursor keys (and
the Word-Star cursor control cluster of ^E, ^S, ^F, ^X, ^A, ^F) are
active, and permit positioning a cursor on any point of any trace. Use
the up-down arrows to switch between traces. Hold key down with
right or left arrow to make larger jumps. The key (or ^V) toggles
between the first cursor and a second one. Y and T values for both
cursors are displayed at the upper left of the screen; differences between
the two cursor values in Y and T are shown at the right. The cursors are
useful for making small numbers of quantitative measurements on model
output without having to write large files to disk. Type to return
to main menu.
III. MODEL DESCRIPTION
SYNETSIM models a set of "Compartments" each composed of "Branches"
and "Pools". Branches correspond to physiologically identifiable
contributions to the conductance and to the ionic current of a compartment
(i.e. its electrical properties). Pools deal with biochemical and
modulatory properties. The various types of branches, pools, and certain
interactions are given "Branch Codes" Except for the "Principal Branch"
(Code "CMPT" [1], specifying basic parameters for a given compartment:
capacitance, leak battery and leak conductance), there is no limit to the
number of branches of a particular type that can be associated with a
given compartment. The following describes the characteristics of each of
the branches, pools, or interactions, then describes how to specify
necessary parameters in the netlist file
A. NETLIST STRUCTURES
The first step in creating a network is producing a netlist file
(.NET extension) which describes the network desired. This file is then
compiled using the compiler NET2PRM and run as described in the STARTUP
section above. The netlist contains several sections: a parameter block
and a DEFINE block, consisting of component declaration lines which
generate a parameter file (.PRM extension); a MASTER block and a BLOCK
block, which generate a master file (.MST extension); and a BATCH block,
which generates a batch file (.SBT extension). Only the parameter and
master blocks are mandatory. These are described briefly in this section,
and the remaining block types are discussed later under SPECIAL NETLIST
FEATURES. Details of the netlist are given in Appendix IV and of each of
the input files in Appendix V.
PARAMETER BLOCK
The first line of the netlist file is a text identifier (enclosed
in quotes). What it contains is arbitrary, but it might be used to
identify the run characteristics. Following are lines laying out the
network structure, cell by cell, with properties belonging to a given cell
grouped with that cell.
The following netlist (plus a MASTER block described later) specifies
two single-compartment cells ("Drivr" and Follower"), each with a spike-
generating trigger zone. The Drivr cell bursts endogenously through a
repetitive driver potential property, and it inhibits the follower with a
spike-mediated chemical synapse. There is also a non-rectifying
electrotonic connection between Drivr and Follower (this netlist has been
written with several lines for each parameter set to keep them on the
page; in practice, only one line for each property is permitted; a less
cumbersome method for assigning property parameters is described in the
"Demo netlist"
'Code Name Parameters Connections
CELL Drivr
CMPT One (C=.005 RP=-50 GL=.2)
TRIGR (E0=0 TAUM0=0.04 PMTHR=0 KPM=2 TAUPM=.25
+ KA1=0.3 TAUA1=0.5 TAUA2=5.8 THRINF=4
+ TAUTHR=.004 DV0=-4 MAXV=-4 DTHR0=5
+ MAXTHR=5)
DRIVER (VNA=40 GBARNA=.5 V0NA=-40 MUNA=5 VK=-90
+ GBARK=.5 V0K=-40 MUK=5 GBARK1=.36 TAUK1=.4)
'
CELL Follower
CMPT One (C=.005 RP=-50 GL=.2)
TRIGR (E0=0 TAUM0=0.04 PMTHR=0 KPM=2 TAUPM=.25
+ KA1=0.3 TAUA1=0.5 TAUA2=5.8 THRINF=4
+ TAUTHR=.004 DV0=-4 MAXV=-4 DTHR0=5
+ MAXTHR=5)
HHFXD (VEQ=-90 GBAR=100 QM=1 V0M=-35 MUM=4
+ TAUMA=.005 QH=1 V0H=-70 MUH=-5 TAUH=.04)
ELECTN (GC=.1) Drivr/One
SYNAPSE (VREVS=-75 GAMMA=0.06 KDS=1 PSPSHP%=1
+ DLY=.003 A0S=.1 TAUF=0) Drivr/One/TRIGR
As can be seen from this example, each cell is declared with a CELL
reserved word, followed by a name. All components following pertain to
that cell until the next CELL declaration, or until a terminating code
(e.g. .MASTER) is encountered. A series of property declaration lines
follows (continuation lines must start with a "+"; total number of
characters in a declaration is 256). Each has three fields: the code
field, the parameter field, and the connection field.
Code field: contains one of the standard (reserved word) names of
branch types, as presented in the next section (e.g. CMPT, TRIGR, DRIVER).
In the cases of CMPT (as for CELL) there is an additional mandatory name
field after the code field (in other cases, the name, if needed, is
appended to the code field with a "/").
Parameter field: contains parameter asssignments. Parameter
assignments are indicated with "=" and those for different parameters are
separated with spaces (not commas). The assignment segment is enclosed in
(). This format is intended to follow the SPICE simulation conventions.
The order in which parameters are given does not matter, but any parameter
not assigned will be given a value of 0.
Connection field: contains sources of input from or output to other
compartments or branches. If the connection deals with a compartment,
only the full compartment name (including cell name) need be given (e.g.
the ELECTN electrotonic connection above). If it deals with a specific
property (such as the trigger zone in the SYNAPSE above), it must include
the name of the cell AND the property (if there are more than one copies
of a property-type in one compartment, they must be given unique names in
their declaration lines [e.g. TRIGR/One and TRIGR/Two] and the appropriate
one referenced by this name in the connection field).
MASTER BLOCK
The following aspects of the model are determined by assignments made
in a master block within the netlist, and reflected in entries made in the
master file (.MST extension):
PRMFILE = Name of Parameter File (less .PRM extension)
PSPFILE = Name of PSP File (less ".PSP") [defaults to "NONE"]
BATFILE = Name of batch file (less ".SBT") [defaults to "NONE"]
XSCALE = Full-scale X-axis value for screen plot (sec)
VSCALE = Full-scale Y-axis value for voltage plot (mV)
ISCALE = Full-scale Y-axis value for current plot (nA)
GSCALE = Full-scale Y-axis value for conductance plot (umho)
KSCALE = Full-scale Y-axis value for rate & binding constant plots
PSCALE = Full-scale Y-axis value for pool level plot.
Y0 = Vertical offset for plotted horizontal axis line
TINC = Integration time increment (in sec) [typical: .001]
SKIP = Plot skip index (point-plotting interval: 1=none skipped)
PSPDM = PSP duration multiplier (normally=1): scales time course
PSPL = Length of PSP table (PSPTB) [typical: 500]
SUMTBL = Length of PSP summation table (SUMTB) [typical: 500]
SPKHT = Spike height (vertical line drawn when spike fired, in mV)
ADPFLG Set = -1 to elect y=KA(E-sum A) tz option (else yinf=KA*E)
PF Set = -1 to print run protocol on printer, otherwise 0
ZPF Set = -1 to plot zero line (axis), otherwise set = 0
SPF Set = -1 to plot spikes, otherwise set = 0
The master block is indicated by a .MASTER code followed by a "(", and it
need not be contained on a single line. Continuation lines must start
with a "+". The block ends with a ")". Except for file names, parameters
omitted from the master block default to 0. PRMFILE defaults to the same
name as the netlist file. PSPFILE and BATFILE default to "NONE". An
example follows which if added to the end of the parameter block above
will allow a net to be compiled by NET2PRM and run by SYNETSIM which
serves to illustrate various points covered so far:
'
.MASTER (PSPFILE=syntest XSCALE=1 VSCALE=200 ISCALE=2000 GSCALE=10
+ KSCALE=1000 PSCALE=5 Y0=50 TINC=0.001 SKIP=5 PSPDM=1 PSPL=500
+ SUMTBL=500 SPKHT=40 ADPFLG=1 ZPF=-1 SPF=-1)
.END
B. REPRESENTATION OF BRANCHING NEURONS
Several reserved-word codes in a NET2PRM netlist generate parameter
lines in the .PRM file appropriate for the compartmental representation of
branching neurons:
CMPT - Basic electrical compartment
The basic electrical unit in the model is a compartment, consisting
of a capacitance, a resting potential, and leak conductance. The
parameters are set in the netlist using the following designations:
C - Capacitance of compartment (in uf)
VLK - Leak battery (mV absolute, e.g. -65)
GL - Leak conductance (e.g. umho; units of C/GL = sec)
The netlist line:
CELL A
CMPT Name (C=.002 RP=-50 GL=.2)
Will generate a compartment with a capacitance of 2 nf (.002 uf; see
section MODEL UNITS for discussion of units used by SYNETSIM), a leak
battery of -50 mV, and a leak conductance of 0.2 umho. Alternatively, the
same compartment could be generated with the line:
CELL A
CMPT Name (C=.002 RP=-50 GAMMA=.1)
where GAMMA is the leak conductance density in mmho/uf. In general, any
trans-membrane conductance can be given either as a straight conductance
(in umho) or as a density (in mmho/uf). In the latter case, the density
is multiplied by the capacitance (in uf) to obtain the actual value for
that conductance.
SPHERE - Spherical compartment
Instead of calculating compartment parameters for certain common cell
geometries, NET2PRM will make the calculations and produce appropriate
compartment parameters. For a spherical structure, such as a soma, the
code SPHERE, followed by the following parameter assignments will effect
this:
DIAM - Soma (e.g.) diameter (in microns)
RHOM - Specific membrane resistance (ohm-cm2)
FOLD - Infolding ratio (ratio of capacitance to that of equivalent
sphere)
RP - Resting potential (as in CMPT)
The lines:
CELL A
SPHERE SOMA (DIAM=100 RHOM=50000 FOLD=2 RP=-50)
is compiled into compartment parameters equivalent to a sherical soma with
diameter 100u, a membrane resistivity of 50kohms-cm2, an infolding ratio
of 2.0 and a resting potential of -50mV. The compartment is named
"A/SOMA".
CYL - Cylindrical segment
As for a sphere, a compartment with parameters representing a
cylindrical segment of membrane can be generated with the code CYL and the
parameter assignments:
L - Length of cylinder (e.g. axon or dendrite; in microns)
DIAM - Cylinder diameter (in microns)
RHOM - Specific resistance of membrane (ohm-cm2; as in SPHERE)
RHOI - Specific resistance of cytoplasm (ohm-cm)
FOLD - Infolding ratio (as in SPHERE)
RP - Resting potential (as in CMPT)
Compartments may be strung together using electrical connections to
produce branching cables or electrotonically-connected cells. Regular
compartments must use the ELECTN code (see below), but cylinders may
(though they need not) be connected to other compartments using the
connection field. Thus the lines:
CELL A
SPHERE SOMA (DIAM=100 RHOM=50000 FOLD=2 RP=-50)
CYL X (L=100 DIAM=10 RHOM=50000 RHOI=70 FOLD=2 RP=-50) A/SOMA
specify a cylindrical segment (named "X") connected to a sphere ("A/SOMA"
in the connection field gives the name of the compartment to which the
connection is made), and the lines:
CELL A
SPHERE SOMA (DIAM=100 RHOM=50000 FOLD=2 RP=-50)
CYL X (L=100 DIAM=10 RHOM=50000 RHOI=70 FOLD=2 RP=-50) A/SOMA
CYL Y (L=100 DIAM=5 RHOM=50000 RHOI=70 FOLD=2 RP=-50) A/X
CYL Z (L=100 DIAM=5 RHOM=50000 RHOI=70 FOLD=2 RP=-50) A/X
specify the same configuration with the addition of two cylindrical
segments, Y and Z, branching off of segment X.
CYLinders are constructed so that half of their longitudinal
resistance is on the the proximal side of the compartment, and half on the
distal side (i.e. compartment parameters are associated with the midpoint
of the cylinder). Two important restrictions result:
1. Only one explicitly-specified connection is permitted per
cylinder. This means that connections in branching trees are specified at
the proximal ends of cylindrical segments only. For connections at the
distal ends, the connection fields of other cylinders are used.
2. No more than three cylinders may join at a branch point. This
means, for example, that in the last case above, no more cylinders could
be attached to cylinder X. This is because a "Y-to-Delta" transform is
necessary to properly link cylindrical compartments, and NET2PRM can only
handle the simplest case. If multiple branches are needed from a single
point, short cylindrical pieces can be inserted between three-way
junctions, or appropriate values for standard CMPT compartments can be
calculated for the particular configuration needed.
INFCYL - Infinite-cylinder cable termination
A CYLinder with no entries in the connection field will have an
infinite termination resistance. The COND code (see below), used as one
of the components of the compartment, can provide other termination
conductances. Alternatively, the INFCYL code generates a COND code
appropriate to an infinite cylinder of specified characteristics. Thus in
the previous example, the final lines:
CYL Z (L=100 DIAM=10 RHOM=50000 RHOI=70 FOLD=2 RP=-50) A/X
INFCYL (DIAM=10 RHOM=50000 RHOI=70 FOLD=2 RP=-50)
provides a termination conductance appropriate to an infinitely extended
cable of the same diameter as the compartment. Note that there is no
connection field for INFCYL, since it is only a branch circuit on
compartment Z defined in the previous declaration line.
B. ACTIVE ELECTRICAL PROPERTIES
Special electrical branches provide characteristic electrical
properties for neurons. Among the cellular properties so represented are
various types of active conductances and simplified repetitive firing
characteristics (trigger zone kinetics). Among various types of
interactions between cells or compartments are resistive coupling
("electrotonic"), spike-mediated chemical synaptic coupling, and non-spike
chemical ("chemotonic") coupling.
CODE "COND" - Fixed conductance (Numerical code 7)
This branch type gives a fixed conductance in series with a fixed
EMF. Its intended purpose is to serve as a terminating conductance for
cables and as a target of modulation by the pools, as in simulating
second-messenger-mediated PSPs.
Parameter-field names are:
VCOND EMF
GCOND Conductance
GAMMA Capacitance-normalized conductance
As described under the CMPT code, any transmembrane conductance can be
given either as an absolute conductance (G) or as a capacitance-normalized
conductance (GAMMA). Only one of the two should be assigned in the
netlist. Example:
CELL A
SPHERE SOMA (DIAM=100 RHOM=50000 FOLD=2 RP=-50)
COND TARGET (VCOND=-75 GCOND=0)
could be a target conductance used to produce a 2nd-messenger-dependent
IPSP with a reversal potential of -75 mV (GCOND would be modulated by a
second messenger represented by a pool, as described below).
CODE "DRIVER" - Driver-potential kinetics (Numerical code 8)
This code generates active plateau-potential kinetics based on a
time-independent mixed "Na-K" conductance with sigmoidal voltage-
dependence for activation, and two slowly changing voltage-dependent K
("restoring") conductances. The voltage-dependence has the form:
ginf = gbar / (exp(-(V-Vo)/mu) + 1) (8.1)
where ginf is the steady-state conductance, gbar is the maximum
conductance, Vo is the half-activation voltage for the sigmoid and mu is
the "characteristic" voltage, defining 1/(1+e) = .27 of the full value.
The time-dependence has the form:
dg/dt = (ginf - g)/tau (8.2)
where tau is a first-order time-constant.
Parameter field:
VNA Sodium (or other inward current) reversal level
GBARNA Maximum sodium conductance
GAMMA Normalized sodium conductance
V0NA Sodium half-activation voltage
MUNA Sodium activation characteristic voltage
VK Potassium (or other outward current) reversal level
GBARK Maximum potassium conductance
GAMMAK Normalized potassium conductance
V0K Potassium half-activation voltage
MUK Potassium activation characteristic voltage
GBARK1 Restoring conductance-1 maximum conductance
GAMMAK1 Normalized maximum conductance-1
TAUK1 Restoring conductance-1 time constant
GBARK2 Restoring conductance-2 maximum conductance
GAMMAK2 Normalized maximum conductance-2
TAUK2 Restoring conductance-2 time constant
CODE "HHFXD" - HH fixed-tau kinetics (Numerical code 9)
Hodgkin-Huxley conductances with voltage-independent time constants.
For this, the activation gating variable, m, and the inactivation
variable, h, (instead of conductance) obey Eq. 8.1 and 8.2. The
conductance is then related to the gating variables in the usual way:
g = gbar * m^Qm * h^Qh (9.1)
Parameter field:
VEQ Active current reversal level
GBAR Active current maximum conductance
GAMMA Normalized maximum conductance
QM Active current activation exponent
V0M Active current half-activation voltage
MUM Active current activation characteristic voltage
TAUMA Active current activation time constant
QH Active current inactivation exponent
V0H Active current half-inactivation voltage
MUH Active current inactivation characteristic voltage
TAUH Active current inactivation time constant
CODE "HH" - Full HH kinetics (Numerical code 10) Hodgkin-Huxley type
conductances with all features, based on the differential equation for the
gating particle, x:
dx/dt = alpha (1 - x) - beta x (10.1)
in which the voltage-dependence of both alpha and beta can be described by
an equation of the form:
alpha= (a +b(V+c))/(exp(-(V+c)/d) + e) (10.2)
where a,b,c,d, and e are constants. Rate constants calculated by 10.2 are
multiplied by a scale-factor, KTEMP, to adjust for temperature.
Parameter field:
VEQHH Reversal potential (Na=55mV; K=-72; Lk=-49.387)
GBARHH Maximum conductance
GAMMA Normalized maximum g (Na=120 mmho/uf; K=36; Lk=.3)
KTEMP Rate-constant scale factor for temperature
QMHH Exponent for activation gate (Na = 3; K = 4)
QHHH Exponent for inactivation gate (Na = 1; K = 0)
AAM, BAM, CAM, DAM, EAM Constants a,b,c,d,e for alpha-m
ABM, BBM, CBM, DBM, EBM Constants a,b,c,d,e for beta-m
AAH, BAH, CAH, DAH, EAH Constants a,b,c,d,e for alpha-h
ABH, BBH, CBH, DBH, EBH Constants a,b,c,d,e for beta-h
For the Hodgkin-Huxley (1952) squid axon (6.3 degrees C, resting potential
= -60), these constants are (for rates in 1/sec):
a b c d e for Sodium
0 -100 35 10 -1 alpha-m
4000 0 60 -18 0 beta-m
70 0 60 -20 0 alpha-h
1000 0 30 10 1 beta-h
for Potassium
0 -10 50 10 -1 alpha-n
125 0 60 -80 0 beta-n
The netlist realization of a 1 nf compartment of squid membrane would
be:
CMPT SQUID (C=.001 RP=-49.387 GAMMA=0.3)
HH SODIUM (VEQHH=55 GAMMA=120 KTEMP=1 QMHH=3 QHHH=1
+ AAM=0 BAM=-100 CAM=35 DAM=10 EAM=-1
+ ABM=4000 BBM=0 CBM=60 DBM=-18 EBM=0
+ AAH=70 BAH=0 CAH=60 DAH=-20 EAH=0
+ ABH=1000 BBH=0 CBH=30 DBH=10 EBH=1)
HH POTASSIUM (VEQHH=-72 GAMMA=36 KTEMP=1 QMHH=4 QHHH=0
+ AAM=0 BAM=-10 CAM=50 DAM=10 EAM=-1
+ ABM=125 BBM=0 CBM=60 DBM=-80 EBM=0)
Note that parameters with 0 value would not have to have been explicitly
specified, this being the default value. In fact, those for potassium
inactivation have been omitted to achieve this end.
Code CONNOR - Special A-current kinetics (Numerical code 13)
Connor, Walter, and McKown (1977: Biophys. J. 18: p102) give somewhat
different empirical equations for A-current activation and inactivation
kinetics:
For steady-state gating particle concentrations (x):
xinf = (a exp [(V+b)/c]/{1+exp[(V-Vo)/mu]})q (13.1)
For gating particle time-constants:
tau = tauo + a'/{1+exp[(V-Vo)/mu'] (13.2)
Time constants are divided by a temperature coefficient. The forms of the
equations are the same for both activation and inactivation except that
the numerator of 13.1 = 1 for inactivation. The exponent, q, has the
values:
qm = 1/3 = 1/QMC for activation and
qh = 4 = QHC for inactivation.
Conductance is given by:
g = gbar mQMCh (13.3)
Parameter field:
VEQCON A reversal level
GBARCON A maximum conductance
GAMMA Normalized maximum conductance
KTEMPC Temperature factor
QMC A-activation exponent
MCA, MCB, MCC, V0MC, MUMC Constants for minf3
TMC0, TMCA, V0TM, MUTM Constants for taum
QHC A-inactivation exponent
V0HC, MUHC Constants for hinf
THC0,THCA,V0TH,MUTH Constants for tauh
The values given in Connor et al (1977) for crab axon at 18oC
translated into netlist format are:
CONNOR (VEQC=-75 GAMMA=47.7 KTEMPC=1 QMC=3
+ MCA=76.1 MCB=94.22 MCC=31.84 V0MC=-1.17 MUMC=28.93
+ TMC0=.0003632 TMCA=.001158 V0TM=-55.96 MUTM=20.12
+ QHC=4 V0HC=-53.3 MUHC=14.54
+ THC0=.00124 THCA=.002678 V0TH=-50 MUTH=16.027)
D. GRADED INTERACTIONS
These are interactions between cells or between parts of the same
cell in which the strength of the effect felt is smoothly graded as a
function of the force (membrane potential) driving the interaction.
CODE "ELECTN" - Electrotonic interactions (Numerical code 3)
This code type specifies two compartments which are resistively
coupled by a bi-directional coupling conductance. These use the current-
based equations:
I(i,j) = gc(i,j)[V(j)-V(i)] (3.1)
where I(i,j) is the current into compartment i from compartment j, V(i) is
the membrane potential of compartment i, and gc(i,j) is the coupling
conductance. These are summed with other sources of current to charge the
membrane capacitance. The parameter field has only one parameter, GC, the
coupling conductance (in umho). To specify a coupling between two
compartments (code CMPT) in a netlist, one is arbitrarily chosen as the
"postjunctional" compartment, and the code line placed within the domain
of that compartment. The "prejunctional" compartment name should then
appear in the connection field. Thus the lines:
CELL A
CMPT X (C=.002 VLK=-50 GL=.2)
CELL B
CMPT Y (C=.001 VLK=-60 GL=.1)
ELECTN (GC=.2) A/X
couples the two compartments X and Y with a conductance of .2 umho.
CODE "DIODE" - Rectifying electrical connection (Numerical code 4)
This code functions much the way the previous one does, but the
coupling is unidirectional. Current flows from prejunctional to
postjunctional compartment only if the membrane potential in the
prejunctional compartment is more positive (depolarized) than that in the
postjunctional one. Its method of specification is the same as for
bidirectional electrotonic connections.
CODE "CHEMOX" - Chemotonic inputs (steady state) (Numerical code 12)
In SYNETSIM 3 synapses, chemical synapses simulate the release and
binding of transmitter on the postsynaptic cell. In non-spiking chemical
transmission, transmitter release is an exponential function of
presynaptic voltage. This can occur in two ways: the steady-state value
can bear this exponential relationship (a non kinetic situation), or the
release rate can. Thus:
Xmtr= Xmtro exp(Vpre/Muc) (12.1)
dXmtr/dt= Xmtr'o exp(Vpre/Muc) (12.2)
where Xmtro and Xmtr'o are respectively the transmitter concentration or
release rate at Vpre=0, Vpre is the presynaptic voltage, and Muc is the
characteristic voltage for the release curve. Released transmitter affects
synaptic conductance according to:
g(t)= gbarc * Xmtr(t)/(Kdc + Xmtr(t)) (12.3)
where gbarc is the maximum possible conductance (saturation: all channels
open), Xmtr(t) is transmitter concentration at time t, and Kdc is the
effective dissociation constant for transmitter binding to the
postsynaptic receptor. Synaptic current (I) is then calculated as for all
other ionic currents:
I(t)=g(t)(V-Vrevc) (12.4)
where Vrevc is the reversal potential for this particular synapse.
Parameter field:
VREVC Chemotonic reversal potential
GBARC Maximum chemotonic conductance
GAMMA Normalized maximum conductance
KDC Dissociation constant for transmitter binding
S0C Transmitter release at 0 mV presynaptic voltage
MUC Presynaptic voltage giving release of S0C * e
KS Decay time-constant of transmitter
If KS=0, then a steady state situation is simulated.
Presynaptic compartments are specified in the connection field of the
netlist. Thus the lines:
CELL A
CMPT X (C=.002 VLK=-50 GL=.2)
CELL B
CMPT Y (C=.001 VLK=-60 GL=.1)
CHEMOX (VREVC=-75 GBARC=.2 KDC=1 S0S=.1 MUC=15 KS=.01) A/X
would use the voltage in cell A compartment X to release transmitter onto
cell B compartment Y.
Note that the transmitter pools pertaining to spikes and those
pertaining to chemotonic interactions are separate. This may be
physiologically inaccurate since a given synapse could well operate in
both modes, and this would produce errors in calculation of receptor-
saturation proportions.
E. SPIKE-FLAG-RELATED PROPERTIES
Spike flags allow for simulations in which the crossing of threshold
by membrane potential generates a spike, which in turn can activate a
synapse, releasing transmitter onto a postsynaptic cell. The same
processes can be simulated using the HH properties to simulate spike
generation and the CHEMOX properties to generate synaptic potentials, but
the simulations, while physiologically more correct, require much more
computer time.
CODE "TRIGR" - Trigger-zone kinetics (Numerical code 2)
This property provides repetitive firing kinetics using the "active
pacemaker model" of Hartline 1976a. It operates by setting a "spike flag"
when threshold conditions have been met, and this spike flag can be used
to drive other spike-flag-sensitive properties (i.e. SYNAPSE-type
synapses) It gives a nearly linear pacemaker response relation (f-I
curve), with up to three components of adaptation. The present
implementation approximates the trigger zone of SYNETSIM 2.4. [WARNING:
There is a known flaw in this module which renders the simulation
quantitatively inaccurate, though qualitatively acceptable; further,
various programming relics of version 2.4 have not yet been removed, and
not all features of the SNAX version 2.4 are included in SYNETSIM-3]. The
trigger zone is driven by the voltage of the parent compartment, and
providing they are given uniques names, there may be more than one trigger
zone in each compartment. The SYNETSIM 3 versions to date have no
feedback to the parent compartment (e.g. simulating spike-
invasion/shunting or loading phenomena). Use Code HHFXD type branches for
this. Loading may be added in future versions.
The kintics of SYNETSIM trigger zones are discussed in Hartline
(1989) and the reader is referred to this source for details. Parameter
names are as follows:
Parameter field:
E0 Base excitation
TAUM0 Base level membrane time constant
PMTHR Threshold for active pacemaker response
KPM Pacemaker sensitivity factor
TAUPM Pacemaker response increase time constant
KCOND Spike conductance sensitivity factor
TAUCOND Spike conductance time constant
KAR Resting-potential adaptation sensitivity factor
TAUAR Resting-potential adaptation time constant
KA1 Adaptation component 1 sensitivity factor
TAUA1 Adaptation component 1 time constant
KA2 Adaptation component 2 sensitivity factor
TAUA2 Adaptation component 2 time constant
THRINF Asymptotic spike threshold value
KTHR Spike threshold sensitivity factor
TAUTHR Spike threshold time constant
DV0 Base increment in membrane voltage
MAXV Maximum membrane voltage reset level
DG0 Base increment in spike conductance
MAXG Maximum spike conductance
DAR0 Base resting-potential adaptation increment
MAXAR Maximum resting-potential adaptation level
DA10 Base adaptation 1 increment
MAXA1 Maximum adaptation 1 level
DA20 Base adaptation 2 increment
MAXA2 Maximum adaptation 2 level
DTHR0 Base threshold increment
MAXTHR Maximum threshold
(Note that not all TRIGR parameters have been implemented as modulation
targets yet)
CODE "SPIKE" - Spike flag (Numerical code 5)
This branch type generates a "Schmidt trigger" type of spike when the
voltage in its compartment exceeds an "on" threshold; it is "refractory"
until voltage goes below an "off" threshold. The intended use is to allow
Hodgkin-Huxley spikes to set spike flags.
Parameter field:
ONTHR On-threshold (mV absolute)
OFFTHR Off threshold (mV absolute)
Synapses are linked to both of these spike generators (TRIGR and SPIKE)
through their connection field in the netlist (see below).
CODE "SYNAPSE" - Spike-mediated PSP inputs (Numerical code 11)
In SYNETSIM 3, spikeflag-produced PSP time-courses are computed by
tabular interpolation to obtain the time-course of transmitter
concentration. Transmitter is accumulated separately at each synapse.
Concentration is assumed to be additive (not a valid assumption under some
conditions). The amplitude function, representing intrinsic synaptic
strength and facilitation effects, is computed as described in Hartline
(1989) and yields a transmitter release coefficient. Conductance and
current are calculated as they are for chemotonic inputs.
Parameter field:
VREVS PSP reversal potential
GBARS Maximum synaptic conductance
GAMMA Normalized maximum conductance
KDS Dissociation constant for transmitter binding
PSPSHP PSP shape # (sequence number during .PSP file read-in)
DLY Synaptic delay
A0S Base amount of transmitter release
------------------[ repeating unit] ------------
TAUF Facilitation time-constant
NF Facilitation exponent
C2F Base facilitation increment
C1F Facilitation increment factor
------------------------------------------------
The repeating facilitation unit permits several facilitation "pools" to be
associated with a single synapse. SYNETSIM continues to read in
facilitation blocks until it encounters a TAUF=0.
Presynaptic "units" in the model refer to the spike flag name in the
netlist. Thus the lines:
CELL A
CMPT X (C=.002 VLK=-50 GL=.2)
SPIKE/1
CELL B
CMPT Y (C=.001 VLK=-60 GL=.1)
SYNAPSE/i (VREVS=-75 GBARS=.2 KDS=1 PSPSHP%=1 A0S=.1) A/X/SPIKE/1
would use spikes generated by the Schmidt-trigger generator in cell A
compartment X to generate PSPs in cell B compartment Y. Note that the
full name of the spike source must be given, including the name of the
property (SPIKE) generating it. The synapse in this example has been
given an optional name ("i") by which can be referenced (see Pool Type 1
example, below)
STIM reserved word
This word used in a connection field specifies the need for a spike
flag that has not been attached to either a TRIGR branch or a SPIKE
branch. It would then be available for use in the "PSP_train" option of
the main menu (option 3). If it is given a name (e.g. STIM/electrode1),
then several different synapses could be acitvated by the same stimulator.
The flag number will be printed out on the screen by NET2PRM when the
netlist is compiled. This number must be used when specifying the
spikeflag in menu option 3.
F. POOLS, SECOND MESSENGERS, AND BIOCHEMISTRY
Non-electrical neuronal properties (e.g. biochemically derived) are
simulated through a set of POOLS. Each pool has an amount of material
(Xpool) contained in a specific volume (XVOL parameter in netlist). In
addition, each pool potentially has an additive base level (XPOOL0 in the
netlist) which is not subject to "diffusion" and "degradation". This can
be used to bias the level of modulation produced in target parameters, if
desired. (Note: in Hartline 1989, different symbols were used: S=Xmtr,
P=Xpool, Po=Xpool0, R=Xtarg, and Ro=Xtarg0.)
For the netlist, the pool type is specified by a TYPE=__ assignment,
assignments for XVOL and XPOOL0, and several type-specific assignments as
delineated below. The pool specifications (as for other compartmental
components) must be grouped under the compartment definition line.
CODE "POOL" - Pool definition (Numerical code 20)
Pool types are defined using this code. Four types of pools can be
specified according to the rules for their filling and emptying:
TYPE 1: Bound transmitter pool. Pool level is proportional to the
concentration of bound transmitter at a synapse:
Xpool= C * Xmtr/(Kd + Xmtr) (20.1)
where C is a constant of proportionality and Kd is the dissociation
constant for transmitter binding. The synapse must be one of the Code
"SYNAPSE" (=11) synapses, but this can be made to have no PSP (if desired)
by setting GBARS=0. Note that the dissociation constant controlling the
pool can in general be different from that for the Code SYNAPSE synapse
The netlist line is of the form:
POOL[/Name] (TYPE=1 XVOL=xx XPOOL0=xx KD=xx C=xx) SynapseName
The connection field contains the full name of the synapse associated with
the pool. An example:
POOL/cAMP (TYPE=1 XVOL=1 XPOOL0=0 KD=1 C=.005) B/Y/SYNAPSE/i
where the synapse is the one given above for SYNAPSE.
TYPE 2: Filling rate proportional to bound transmitter.
dXpool/dt = C1 * Xmtr/(Kd + Xmtr) - C2 * Xpool (20.2)
where terms are analogous to type 1. This can be used to simulate
activation of an enzyme producing second messenger at a rate proportional
to bound transmitter.
The netlist line is similar to that for Type 1:
CELL A
CMPT X
POOL[/Name] (TYPE=2 XVOL=xx XPOOL0=xx KD=xx C1=xx C2=xx)
CELL/CPT/SYNAPSE/ID
TYPE 3: Filling rate proportional to ionic current, with first order
decay.
dXpool/dt = C1 * I(k,j) - C2 * Xpool (20.3)
where I(k,j) is the current flowing in the kth branch of type code j.
This can be used to simulate entry of ions through channels, e.g. Ca.
The netlist line is of the form:
POOL[/Name] (TYPE=3 XVOL=xx XPOOL0=xx K=xx J=xx C1=xx C2=xx)
Note that the K and J specified must correspond to values assigned in the
parameter file. To find those values, the netlist must be compiled twice,
the first time with dummy K,J's (e.g. 1,1). [THIS NEEDS TO BE CHANGED TO
PERMIT NAMED SOURCES IN THE CONNECTION FIELD]
TYPE 4: Constant filling rate with first-order decay.
dXpool/dt = F - K * Xpool (20.4)
where F is the filling rate and K the rate constant for decay. This can
be used to simulate a substance which is synthesized and degraded, rates
of which can then be modulated by other pools, e.g. enzymatic regulation
of synthesis and degradation.
The netlist form is:
POOL[/Name] (TYPE=4 XVOL=xx XPOOL0=xx F=xx K=xx)
Additional pool types can be added as needed. Pool-defining
("spring") subroutines must be added starting at line 11340. Follow the
format for existing types.
TYPE 5: Bound transmitter from CHEMOX branch. Essentially a Type 1
pool for CHEMOX.
Xpool= C * Xmtr/(Kd + Xmtr) (20.5)
POOL[/Name] (TYPE=5 XVOL=xx XPOOL0=xx KD=xx C=xx) ChemoxName
CODE "POOLK" - Inter-pool diffusion (Numerical code 21)
All pools are potentially interconnected by first-order "diffusional"
rate constants:
dXpool(k)/dt = SUM{K(k,j) Xpool(j)/Xvol(j)} (21.1)
- SUM{K(j,k)} Xpool(k)/Xvol(k)
where K(k,j) is the first-order rate constant into pool k from pool j.
Note that the rate constants in the two directions need not be equal.
This can be used to simulate not only diffusion within and between
compartments and cells (in which intrinsic rate constants in the two
directions would be equal), but also first-order chemical reactions.
Netlist format is:
POOLK[/Name] (K=xx) SourcePoolName
The pool k of eq. 21.1 is the pool under which the definition line
appears. The connection field gives the full name of pool j. For
example, a situation for a modulator-activated cAMP pool diffusing away
from the site of origin into the interior of the cell might be represented
by the following netlist:
POOL/cAMP1 (TYPE=2 XVOL=1 XPOOL0=0 KD=1 C1=5) A/X/SYNAPSE/e
POOLK (K=.1) POOL/cAMP2
POOL/cAMP2 (TYPE=4 XVOL=1)
POOLK (K=.1) POOL/cAMP1
CODE "POOLX" - Pool interactions (Numerical code 22)
Pool levels can affect various "targets": other pools and compartment
parameters of the model. Seven types of interaction have been programmed
(in the following, Xpool refers to the sum of the calculated pool level
plus a base level, Xpool0, which can be specified with the Code POOL
parameters). A base level of interaction in the presence of 0 control-
pool levels (Xtarg0) is set automatically for any non-zero value in the
input (.PRN) file.
Netlist interaction entries must follow after the pool-definition
line for the pool controlling (driving) the interaction. The name of the
target (a pool or a parameter) is specified in the interaction fields.
The name structure for a pool target is:
[Cell-name/Compartment-name/]POOL/Pool-name
and for a parameter:
[Cell-name/Compartment-name/]CODE/Branch-name/Parameter-name
Note the "/"s are required between cell and compartment names in this
structure. The cell and compartment names may be omitted (indicated by
[]) if they are the same as for the compartment generating the
interaction. As an example, the target name for the maximum synaptic
conductance (GBARS) in Cell B of the SYNAPSE example given below would be:
B/Y/SYNAPSE/i/GBARS
TYPE 1: Direct proportionality. The value of the target is a
constant multiple of the pool value plus a base level:
Xtarg = C Xpool + Xtarg0 (22.1)
where Xtarg is the value of the target, C is a constant, and Xtarg0 is the
value of Xtarg if Xpool = 0.
Netlist declaration line:
POOLX (TYPE=1 C=1) Target
where Target is the name of either a pool or of a parameter to be
modulated.
Example:
CELL A
CMPT X (C=.002 VLK=-50 GL=.2)
SPIKE/1 (ONTHR=-30 OFFTHR=-40)
CELL B
CMPT Y
SYNAPSE/i (VREVS=-75 GBARS=.2 KDS=1 PSPSHP%=1 A0S=.1) A/X/SPIKE/1
POOL/cAMP1 (TYPE=2 XVOL=1 XPOOL0=0 KD=1 C1=5) SYNAPSE/i
POOLX (TYPE=1 C=1) A/X/GL
In this case, the target was a model parameter instead of a pool.
TYPE 2: Equilibrium receptor binding. The value of the target above
base is proportional to the binding of the control pool to a receptor:
Xtarg = C Xpool/(Kd + Xpool) + Xtarg0 (22.2)
Netlist declaration line:
POOLX (TYPE=2 C=1 KD=1) Target
TYPE 3: Bimolecular reaction with pseudo first-order kinetics. The
rate of change in target value is proportional to the difference in rates
of forward and backward reaction of the form:
A + Xpool <---> Xtarg
dXtarg/dt = alpha * Xpool(A0-Xtarg) - beta * Xtarg (22.3)
where alpha and beta are the two rate constants and A0 is the total amount
of the limiting reactant (Xpool is assumed not to change as a result).
This can be used, for example, to simulate the kinetics of receptor
binding, or enzymatic phosphorylation of a channel. Note that for the
steady state:
Xtarg = A0/(1 + beta/alpha/Xpool) (22.4)
Netlist declaration line:
POOLX (TYPE=3 ALPHA=xx BETA=xx A0=xx) Target
TYPE 4: Ionic battery interaction. The target value is related to
the pool level by the Nernst equation:
Xtarg = 26 * ln (Xpool/Conc) (22.5)
where Conc is the concentration of ion on the other side of the membrane.
In conjunction with a Type 3 pool, trapping of ions in extracellular
spaces can be simulated.
Netlist declaration line:
POOLX (TYPE=4 CONC=xx) Target
TYPE 5: Modulation of target synthesis. The rate of change of the
target is proportional to pool value:
dXtarg/dt = C * Xpool (22.6)
This can be used to simulate the enzymatically-limited synthesis of a
compound from a large substrate pool. It can also be used as an
alternative to Type 3 to simulate the production of a second messenger at
a rate proportional to bound transmitter.
Netlist declaration line:
POOLX (TYPE=5 C=xx) Target
TYPE 6: Modulation of coupling conductance. The target conductance
is proportional to the controlling pool:
GC(Post, Pre) = C * Xpool + Xtarg0 (22.7)
Netlist declaration line:
POOLX (TYPE=6 C=xx) PostTargetCmpt PreTargetCmpt
Since electrotonic interactions involve two compartments, specifying one
for modulation requires two names in the interaction field, one for the
post- and one for the prejunctional compartment.
TYPE 7: Modulation of diffusion rate constant between pools. The
target constant is proportional to the controlling pool:
K(Post, Pre) = C * Xpool + Xtarg0 (22.8)
This can be used to simulate the effect of changing enzyme concentrations
on the rates of first-order reactions.
Netlist declaration line:
POOLX (TYPE=7 C=xx) PostTargetPool PreTargetPool
As with type 6, this interaction requires two connection-field entries.
Other interaction types can be added. Appropriate subroutines should
be inserted beginning at line 12800.
G. SPECIAL NETLIST FEATURES
".DEFINE" BLOCKS
A standard parameter set for any type of branch can be defined in a
DEFINE line and assigned a unique name, by which it can be invoked. This
name is then placed just prior to the parameter-assignment segment. This
has the effect of setting default template values for all branch
parameters. Only those parameters that differ from this template then
need be assigned in the assignment segment.
For example, a neuron represented as a spherical soma with a 5-
segment 5 micron diameter two-times infolded uniform axon which could be
represented by the netlist:
CELL X
SPHERE SOMA (DIAM=60 RHOM=50000 FOLD=5 RP=-50)
CYL AXON1 (L=100 DIAM=5.0 RHOM=50000 RHOI=50 FOLD=2 RP=-50) X/SOMA
CYL AXON2 (L=200 DIAM=5.0 RHOM=50000 RHOI=50 FOLD=2 RP=-50) X/AXON1
CYL AXON3 (L=300 DIAM=5.0 RHOM=50000 RHOI=50 FOLD=2 RP=-50) X/AXON2
CYL AXON4 (L=400 DIAM=5.0 RHOM=50000 RHOI=50 FOLD=2 RP=-50) X/AXON3
CYL AXON5 (L=500 DIAM=5.0 RHOM=50000 RHOI=50 FOLD=2 RP=-50) X/AXON4
could be more clearly and efficiently represented by:
CELL X
SPHERE SOMA (DIAM=60 RHOM=50000 FOLD=5 RP=-50)
CYL AXON1 AXON (L=100) X/SOMA
CYL AXON2 AXON (L=200) X/AXON1
CYL AXON3 AXON (L=300) X/AXON2
CYL AXON4 AXON (L=400) X/AXON3
CYL AXON5 AXON (L=500) X/AXON4
.DEFINE CYL AXON (DIAM=5.0 RHOM=50000 RHOI=50 FOLD=2 RP=-50)
".BLOCK" BLOCKS
Physiological properties can be blocked with a set of toxin flags,
one for each property type (=branch code). These flags may be set during
run time using main menu option 6 (or an equivalent .BATCH block call).
Initial values are also set by the master file, which in turn is
automatically written by NET2PRM so that any branch codes found in the
declaration lines will be unblocked, and those missing will be blocked.
However, this latter default can be overridden by including the branch
code in the parameter field of a .BLOCK statement, e.g.:
.BLOCK (ELECTN HHFXD POOLK)
in SYNTEST.NET blocks these three properties.
BATCH BLOCKS and BATCH OPERATIONS
If a .BATCH block is present in the netlist, and a "/B" switch is
used in invoking SYNETSIM (e.g. "SYNETSIM SYNTEST /B "), normal menu-
driven input from the keyboard will be suspended and command sequences and
parameters will be taken from the batch file (in the example just given,
this would default to the file SYNTEST.SBT, which is also the default name
of the file generated by NET2PRM for SYNTEST.NET; the third file given in
the command lines for both NET2PRM and SYNETSIM is assigned to the batch
file, if this is to be different from the default name). The batch file
consists of lines of numbers or strings which would be normally the
responses to INPUT prompts.
The batch file is generated from a .BATCH block in the netlist which might
contain something like:
.BATCH HOLD (CMPT=1/1 HOLD_V=-100 NSWEEPS=20 SAVFILE=FILE.SAV)
IV (CMPT=1/1 COND_V0=-100 NCOND=1 TEST_V0=-60 SAMPLE_T=.006
TEST_STEP=10 NTEST=13 SAVFILE=FILE.SAV IVFILE=FILE.IV)
.ENDBATCH
This would generate a file with the lines:
SYNETSIM 3.3.2
4,1,1,-100,20,FILE.SAV,0
4,3,1,-100,0,0,1,-60,.006,10,13,FILE.SAV,FILE.IV,0
7
The first line is a format check line; the next two are the numbers that
must be entered to guide the SYNETSIM menu system through a hold-potential
voltage clamp run followed by an I(V) curve run. The last line ("7")
terminates the batch mode, and is generated by the mandatory ".ENDBATCH"
directive in the netlist.
It will be seen that the batch mode allows using names for the
various parameters that must be given to SYNETSIM to set up a given run
(the same names appear in the screen prompts of the menu mode). Any
numerical parameters not assigned will be set (effectively) to zero. If
file names are to be omitted, the assignment (file)NAME = NONE must be
made.
Batch mode also allows using netlist names for compartments
(parameter name "CMPT"), spikeflags ("SPKFLG"), pools ("POOL"), pool
targets ("TARGET"), and toxin and display-variable names ("CODENAME"). In
addition, the parameter "FLAG" can be set equal to "ON" (=-1 or true) or
"OFF" (=0 or false). See NET2SBT.CNF discussion in the Appendix.
Batch block parameter names are listed in the description of the main
menu above.
H. DATA FILES
SYNAPTIC TRANSMITTER FILE (PSPFILE$.PSP)
This file contains time-course data for all PSPs. It must be
constructed with an editor, word processor, or user-generated program.
Two formats for specifying the data are possible. In one, the PSP is
given as transmitter-level and time pairs. In the other, the PSP
transmitter level is calculated as an analytic function. The choice is
specified by the entries in the file. The first three entries are:
STITLE$ Title of PSP file
SFIDD$ SYNETSIM 3.0.1 (12/25/87 file format code)
NPSP% Number of PSP's in file (any number of PSPs can be
contained in a file, but only the first NPSP% of
those will be read in)
Subsequent entries are specific to the two formats. Formats can be
intermixed:
Format 1:
In the first format, entries consist of of alternating time (T3) and
value (V3) (transmitter level) entries in sequential order but no
specified interval. The latter should be normalized to a peak
concentration of 1.0. Each PSP must begin with the pair 0,0, which also
serves as the termination code for the preceding PSP. Each PSP must
extend beyond the end of the PSP storage array (PSPTB), this being
accomplished, for example, by having a final T,V pair = 1000,0. The final
PSP must have a 0,0 termination pair at its end.
4: 0
5: 0
6,8,... T1, T2 ... Tm-1, 1000 Time of points on 1st PSP.
7,9,... V1, V2 ... Vm-1, 0 Value of points on 1st PSP.
n-1: 0 End code
n: 0
Format 2:
For PSPs calculated from an equation, the first entry must be a
negative number, the magnitude of which specifies which of various
analytic functions is to be used for the calculation. In SYNETSIM 3.3,
only an instantaneously rising, exponentially decaying function is
implemented, but other formats are readily programmed (see line 685 ff).
For this "Type -1" PSP, the second entry is the decay time constant of
transmitter (sec). Example:
-1,0.07
specifies a sharp-rise transmitter release with a decay of 70 msec.
SAVE FILE (*.SAV; set as File#1)
When option 10 of the Main Menu is selected to save the model state,
it writes a file having the following format [.SAV is a suggested, though
not mandatory, extension]:
PFILE$ - Parameter file format code
U - Model time
SUMTB0% - Pointer to current place in psp summation array
V(i)s - Membrane potentials for all compartments (1 to N%)
{j%, k%, s.v} - Indices and state-variable for branch (j%,k%)s
[j%=1 to 12 (excl 3); k%=1 to N%(j%)]
XPOOL(k%)s Pool values for all pools (1 to N%(POOL%))
0,0 Block termination
SUMTB(j%,t%)s Synaptic transmitter concentrations for all synapses
"END" End-code
SAMPLE NETWORKS
SYNTEST 2-CELL NET
The SYNTEST network consists of a circuit of two cells ("Drivr and
"Follower": see wiring diagram in Appendix IV). This network features an
endogenously bursting network-driver neuron which inhibits and is
inhibited by the follower. Drivr is electrotonically coupled to Follower
by a rectifying connection. In addition to the spike-mediated synapses,
there is a blocked reciprocal chemotonic inhibition between Drivr and
Follower that can be unblocked (set toxin flag CHEMOX = "U" with menu
option 6) as a demonstration of the chemotonic feature of the model. In
addition, transmitter released by Drivr activates the synthesis of a
"second messenger" pool in Follower which induces a voltage-dependent
inward current in the cell, causing it to produce plateau potentials. For
purposes of demonstration a second pool is "diffusionally connected" to
the second messenger one if the "diffusion" property is enabled (set toxin
flag POOLK to "U" using menu option 6). This could represent "buffering"
of the second messenger, or its reversible inactivation through a chemical
reaction. In the SYNTEST net, only codes TRIGR, ELECTN, DRIVER, SYNAPSE,
POOL, and POOLX (=2,3,8,11,20,22) are unblocked (spikes, electrotonic
connections, plateaus, spike-mediated synapses, pools and pool targets).
The resulting output is plotted using LOTUS in the figure accompanying
Appendix IV.
See APPENDIX VI for an annotated listing of the SYNTEST parameter
file, and output plots.
SQUID AXON
A 1-compartment cell with parameters appropriate for a .001 cm2 patch
of space-clamped Hodgkin-Huxley squid axon is also provided. The
parameters are for an axon at 6.3oC as specified in J. Physiol. 117: 500-
544 (1952), using a resting potential of -60 mV. To utilize this, run
NET2PRM and then SYNETSIM using HH in the command line. Choose menu
selection 1 for several sweeps to let the state variables settle, then use
selection 2 with Compartment=1, Bias=0, Cond_I=0, Test_I=900, 150, 70, and
60 (nA/nf=uA/cm2) in sequence, Cond_durn=0.001, and Test_durn=0.0001 to
generate Fig. 12 of HH '52 (be sure to allow several recovery sweeps
between stimuli).
DEMONSTRATION MODULES
A set of demonstration modules is included which is suitable for
training students in the application and properties of various SYNETSIM
branch types and the physiological phenomena they represent. See the
separate description SYNETDEM.TXT.
MISCELLANEOUS
PROGRAM COMPATIBILITY
The current version of SYNETSIM is completely compatible (to the best
of my belief) with QuickBASIC 3.0. The source code provided in
SYNETSIM.3xx is intended to be mostly GWBASIC compatible as well. In
recompiling it with QuickBASIC, comment out line 50 (GWB%=-1). Small
networks (<=3 branches per compartment) can be run under GWBASIC. In
transporting it to a foreign version of BASIC a problem may be encountered
owing to the frequent use of the same name for an array and for a standard
variable. Thus N% is the number of compartments in the model, whereas
N%(i) is the number of branches having code i. Also, T is a scratch time
variable whereas T% is a time index for an array. GWBASIC permits these,
but other BASICs (e.g. BetterBASIC) may not.
MODEL UNITS
The basic unit of time in SYNETSIM is the second. Thus time
increments (TINC), display X-axis length (XSCALE) and stimulus durations
(from Main Menu) must be given in this unit.
The basic unit of voltage is the millivolt. This is the unit for
activation voltages, reversal potentials, etc. There is no absolute
voltage reference built into the model. The demonstration models (e.g.
SYNTEST) use the external bath potential as the zero reference, but one
could as well use resting potential.
Other units in the model (current, conductance, capacitance,
concentrations, binding constants) are arbitrary, but must be kept
consistent with the time and voltage units. In SYNTEST and most
demonstration modules, current has been given in nA, making resistance
units = Mohms, conductance units = umho, and capacitance units = uf. To
bring specific conductances into line with current usage, these (i.e.
GAMMAs) are given in mmho/uf. One can use other units, but keep in mind
that membrane conductances in the model are calculated from densities with
the equation G = GAMMA/(1000*C).
PROGRAM BUGS
TRIGR inaccuracies: The present version still has the known
inaccuracy in the spike calculation routine of 3.0, which renders it
inaccurate, though usable.
Type 3 pool interaction: There is a known minor inaccuracy in this
interaction in line 12310.
SYNAPSE facilitation: reported not to work (S. Lin, personal comm.)
Untested options: Not all options have been tested. The following
sections, in particular, have NOT been tested in the current version and
may be particularly prone to errors:
Code TRIGR details, including RP adaptation; spike resets; threshold-
crossing corrections; handling of excitatory drive.
Code POOL pools of types 2 and 3
Code POOLK (inter-pool diffusion)
Code POOLX pool interactions of types 4,6,7, and 8
DIMension limitations: The model as it stands does not DIMension
many arrays, giving them default dimensions of 10. If more than 10
branches are required, DIM statements will have to be added after line 63,
and MAXBR% in line 60 must be changed to the new maximum number of
branches.
Despite every attempt to minimize them, errors are inevitable.
Your help in drawing attention to such will be greatly appreciated.
OTHER NOTES
Interpreted-mode: If need be, a truncated version of the source
program (SYNETSIM.3xx, where xx=version and revision #) can be run in
interpreted mode with GWBASIC (or BASICA), although much more slowly (see
Speed tests, Appendix V). The "comment" mark (') must be removed from
line 50 before attempting this. The program itself must also be
shortened, and unnumbered lines must be deleted. It is suggested that
lines 13000 to the end be deleted and that pool interactions be blocked.
UPDATES IN 3.0 AND 3.2
This release of SYNETIM has several changes from the two previous
releases (3.0D and 3.2C), primarily in the implementation of Greg
Wolodkin's net-list compiler, NET2PRM. This is reflected in the rewritten
descriptions of network properties above, and in separate sections on
NET2PRM (see also the NET2PRM manual in Appendix V).
A. Modifications of the Parameter File (.PRM)
The parameter file is now created from the netlist file. Old
parameter files must be translated into the new form. As an aid, empty
templates for each v3.0 and 3.2 SYNETSIM property are given below as
which must be inserted: see NET2PRM documentation):
"Netlist title (1 line of text enclosed in quotes)"
'Code Name Parameters (changes) Connections
'-------------------------------------------------------------------------
----
.DEFINE CMPT x (C= RP= GL= )
.DEFINE TRIGR x (E0= TAUM0= PMTHR= KPM= TAUPM=
+ KCOND= TAUCOND= KAR= TAUAR= KA1= TAUA1=
+ KA2= TAUA2= THRINF= KTHR= TAUTHR= DV0=
+ MAXV= DG0= MAXG= DAR0= MAXAR= DA10=
+ MAXA1= DA20= MAXA2= DTHR0= MAXTHR= )
.DEFINE ELECTN x (GC= )
.DEFINE SPIKE x (ONTHR= OFFTHR= )
.DEFINE COND x (VCOND= GCOND= )
.DEFINE DRIVER x (VNA= GBARNA= V0NA= MUNA= VK=
+ GBARK= V0K= MUK= GBARK1= TAUK1= GBARK2=
+ TAUK2= )
.DEFINE HHFXD x (VEQ= GBAR= QM= V0M= MUM=
+ TAUMA= QH= V0H= MUH= TAUH= )
.DEFINE HH x (VEQHH= GBARHH= KTEMP=1 QMHH= QHHH=
+ AAM= BAM= CAM= DAM= EAM=
+ ABM= BBM= CBM= DBM= EBM=
+ AAH= BAH= CAH= DAH= EAH=
+ ABH= BBH= CBH= DBH= EBH= )
[NOTE that this property contains the additional parameter KTEMP, for
temperature scaling, which cannot be defaulted to 0 and hence atleast
a value of 1 must be inserted in any v3.3 netlist]
.DEFINE SYNAPSE x (VREVS= GBARS= KDS= PSPSHP%= DLY=
+ A0S= TAUF= )
.DEFINE CHEMOX x (VREVC= GBARC= KDC= S0= MUC= )
[NOTE: "S0" replaces "XMTR0C"]
.DEFINE POOL x (TYPE=1 XVOL= XPOOL0= KD= C= )
.DEFINE POOL x (TYPE=2 XVOL= XPOOL0= KD= C1= C2= )
.DEFINE POOL x (TYPE=3 XVOL= XPOOL0= C1= C2= )
.DEFINE POOL x (TYPE=4 XVOL= XPOOL0= F= K= )
.DEFINE POOLK x (K= )
.DEFINE POOLX x (TYPE=1 XVOL= XPOOL0= C= )
.DEFINE POOLX x (TYPE=2 XVOL= XPOOL0= C= KD= )
.DEFINE POOLX x (TYPE=3 XVOL= XPOOL0= ALPHA= BETA= A0= )
.DEFINE POOLX x (TYPE=4 XVOL= XPOOL0= CONC= XBRN%= XPRM%= )
.DEFINE POOLX x (TYPE=5 XVOL= XPOOL0= C= XBRN%= XPRM%= )
.DEFINE POOLX x (TYPE=6 XVOL= XPOOL0= C= )
.DEFINE POOLX x (TYPE=7 XVOL= XPOOL0= C= )
Specific changes which have been made in parameter file structure are:
1. HH parameter lines add KTEMP after GBAR (normally = 1), the
temperature-dependent rate-constant scale factor (added to 3.2.4, v3.2D).
2. Omitted parameters are no longer allowed in parameter lines (e.g.
omitting the exponent in HH lines to abort the further read-in of non-
utilized activation or inactivation properties). This is to maintain
compatibility with NET2PRM, which, except for certain special exceptions,
expects a fixed parameter line format.
3. DIODE branch replaces "ELECTN" for unidirectional connections;
ELECTN is reserved only for bidirectional ones. Branch Code for DIODE is
4; SPIKE has been reassigned code 5.
4. Conductance densities. Version 3.3 adds the option of
conductance densities (per uf of capacitance) to be specified in place of
conductances, wherever they appear in the old parameter set. If only a
single conductance is present for a particular property, the density is
simply called "GAMMA" in the netlist. Where several conductances appear,
the density for the first is GAMMA, and in the remainder, "GBAR" is
replaced by "GAMMA" in the name (e.g. the density for GBARK1 is GAMMAK1 in
DRIVER).
B. Master File (.MST) is replaced by .MASTER block:
The master file is now created from a .MASTER block in the netlist
file. Old master files must be translated into the new form. As an aid,
the .MASTER block-equivalents for SYNTEST.MST is given for version 3.0 and
3.2C:
Version 3.0D:
.MASTER (PRMFILE=SYNTEST PSPFILE=SYNTEST
+ XSCALE=1 VSCALE=50 TINC=.002 SKIP=1 PSPDM=1 PSPL=500 SUMTBL= 500
+ SPKHT=15 ADPFLG=-1
+ ZPF=-1 SPF=-1)
.BLOCK (ELECTN HHFXD CHEMOX POOLK)
Note that the plot switches (PLTSW%) of v3.0D have been eliminated except
for the zero-line plot (ZPF) and the spike-tic plot (SPF) [the original
plot switches have been replaced by plot variables: see main menu
selection 12; note that this replaces main menu option 6]. All switches
and flags have been converted to a Boolean form (i.e. using -1 instead of
1). The header information for the master file is generated automatically
by NET2PRM.
Version 3.2D:
.MASTER (PRMFILE=SYNTEST PSPFILE=SYNTEST
+ XSCALE=1 VSCALE=100 ISCALE=2000 GSCALE=10 KSCALE=1000 PSCALE=5 Y0=50
+ TINC=.002 SKIP=1 PSPDM=1 PSPL=500 SUMTBL=500
+ SPKHT=20 ADPFLG=-1
+ ZPF=-1 SPF=-1)
.BLOCK (ELECTN HHFXD CHEMOX POOLK)
The master file for v3.3B also includes the parameter BATFILE (for batch
file operation) and the flag PF (for protocol printout), which default to
NONE and 0, respectively, if they are left unassigned.
C. Additional features of 3.2 and 3.3:
1. Voltage-clamp conditions can be applied to a single compartment
at a time (Main Menu option 4; options 4 & 5 renumbered). see Main Menu
section (3.2).
2. A cursor-supplied screen display, useful for making measurements
on simulation runs, has been added. It automatically comes up at the end
of each run (3.2). See End-of-Run Display section.
3. Three new branch types have been added. "SPIKE" (code 4)
branches generate spikes from membrane potential via a "Schmidt trigger",
so that Hodgkin-Huxley branches can be linked to synapses (3.2). "COND"
(code 7) branches give fixed conductances which can be modulated by second
messengers to simulate slow PSPs (3.2). "CONNOR" (code 13) branches
specify HH-type rate constants for A-current as developed by Connor et al
(3.3).
D. Bugs corrected
HH Branch line 5020 incorrectly read IF EAM(K%)=-1 ..." It has been
corrected to read "IF EBM(K%)=-1 ...". The only situation in which this
gave much of a problem was in voltage clamp with a hold potential of -60
(which is when V=-CBM) (corrected in 3.3).
E. Demonstration package for 3.2 and 3.3
Several modules which illustrate model features are included in this
release (see DEMO subdirectory and SYNETDEM documentation). Some modules
require SYNTEST.PSP.
=============================================================================
APPENDIX I
ERROR MESSAGES
230: BAD MASTER FILE Need: x Have y
Discrepancy in .MST file format code. Program expects format
code x but found code y.
360: BAD PARAMETER FILE: Need: x Have: y
Discrepancy in .PRM file format code.
465: .PRM FILE FRAMING ERROR
Program failed to find termination sequence "0,0,END" at the
end point in the .PRM file. One likely cause is an
incorrect number of parameters for one of the branch types.
530: BAD PSP FILE: Need: x Have: y
Discrepancy in .PSP file format code.
680: ILLEGAL PSP TYPE
Invalid type-code (<-1) encountered in PSP file.
1520: WRONG SAVE FILE
.PRM format code on the model-state file being loaded does not
correspond to the
current .PRM file in use.
1585: SAVE FILE END ERROR
Expected "END" not found at end of .SAV file
5300: ILLEGAL BRANCH CODE CALL IN KINETICS
An illegal branch-type code was encountered in doing update kinetics.
INDICATES
PROBABLE MODEL BUG.
6190: INPUT CODE x NOT IMPLEMENTED
An illegal branch-type code was encountered in the .PRM file.
14950: TARGET-FETCH CALLED ILLEGAL BRANCH CODE x
An illegal branch-type code was encountered while retrieving a pool-
target parameter.
14960: TARGET-FETCH INVALID TARGET PARAMETER prm OF BRANCH i INTERACTION k
In a type k pool interaction, a legal branch type, i, was found with
a parameter-
number (prm) outside the valid range for that branch. Some
parameters for some of
the branches have not been implemented yet, but can readily be by
following the
format laid down in this section of the program.
16950: TARGET-SAVE CALLED ILLEGAL BRANCH CODE x
See 14950
16960: TARGET-SAVE ILLEGAL TARGET PARAMETER prm OF BRANCH i INTERACTION k
See 14960
=============================================================================
APPENDIX II
IMPLEMENTATION NOTES
A. PROGRAM LOGIC, IN BRIEF
The Initializations and Parameter Input Calls section does the usual
set-up of special constants, reading of parameter files, checking formats,
and printing out diagnostic information. Branch codes, identified in the
program by the index J% and decoded/encoded from their ASCII form via the
surboutine array following location 100, direct the calling of appropriate
subroutines for reading in parameters and making model calculations. The
Branch-data Input Loop uses a simple ON {Branch Type} GOSUB to read
appropriate parameters from the parameter file, keeping track of the
maximum index number of each branch type with the array N%(j%). When a
branch-type of 0 is encountered, it should be the end of the list, in
which case another 0 and a string "END" is expected, or a framing error
has occurred. A minor loop at 475 sets to 1 those pool volumes not set by
input data, to prevent later division by 0. The PSP Shape Table Input
Loop tests data for PSP format. For a tabulated PSP, (time,value) pairs
are read in and intermediate values at equal time increments are
calculated by interpolation, to be stored in the PSP table, VPSP(K%,T%).
For calculated PSPs, a mathematical computation of the functional form of
the PSP replaces the interpolation, but either way, the PSPs end up as
functions tabulated at intervals of the integration time step. Voltage
values are initialized to resting potential, and base levels (XTARG0) for
targets of modulation by pools are set to the initial levels taken from
the parameter file.
NETST Section: Model Run Options operates the main menu. This is a
straight forward ON {Menu Selection} GOTO switch which executes the
selection, then returns to line 815 or 820 to clear the screen and
redisplay the menu. Programming for most is uncomplicated. For selection
2 (current pulse), the start and end times are requested, and the model-
call loop includes testing of current time so that a current is applied
through the variable IM0(UNIT%) to compartment UNIT% during the interval.
Saving and restoring the model state (selections 10 and 11) involves a ON
{Branch Type} GOSUB switch to subroutines at 7000+NAME%*10 and
7500+NAME%*10 to write/read corresponding state variables to/from disk,
followed by a write/read of the SUMTB(J%,T%) array. Additional conditions
for the model can be programmed by following the pattern set by menu
selections 2 and 3. The key line to insert is:
GOSUB 1800: IF X=0 THEN GOTO 815
This executes one time-increment of the model, plots results, and clears
any spike flags that have been set. If you need the spike flag
information, use GOSUB 3000 to run the model and GOSUB 2000 to plot, deal
with the flags yourself, and test for X=0 to see if the sweep is finished.
The return to 815 clears previous disk-write modes. Return to 820 to
avoid this.
NETWRK Subroutine (at line 3000) is the heart of the model. The
first part, PATCH, calculates the sum of all ionic currents (II(I%)) and
conductances (GI(I%)) from each branch for each compartment. It adds the
currents to those from other compartments using the coupling conductances
GC(I%,J%) or GC(J%,I%). Which is used is determined by the sign of the
voltage difference between the two compartments, hence allowing for
rectifying connections (line 3160). Total currents are used to calculate
the change in compartment voltage, DV(k%), due to the charging of the
compartment's capacitance. The second part, Branch 2 Updates, applies
the membrane voltage minus the leak battery (VA(I%)) to the trigger zone
subroutine at 4070 and updates its state variables. If a spike is fired,
the SPIKE subroutine at 4600 is called to reset trigger zone variables
appropriately. The third section, PATCHI, does the updates on all of the
other electrical branch codes (7-13), using the ON {Code} GOSUB switch in
line 3400. These call subroutines at 4000+NAME%*100 which contain
appropriate kinetics for each branch type. Most of these are straight
forward, but special notes on some are given below. This results in new
values for the conductance G(K%,J%) and the ionic current I(K%,J%) for
each branch K% of each code J%. The fourth part involves producing pool
interactions (subroutine at 12000). Targets are located, a minus flag
being used to tag a compartmental parameter as a target, and the lack of
the flag being used to specify a pool as a target. The variable K is used
as temporary storage for the value of this target parameter. The type of
operation performed is determined by the type-specifier XINTYP%, which
controls the GOSUB switch in line 12080. The new value for the target
parameter is returned to the target variable via K. Following this, pools
are updated by the Inter-pool Diffusion subroutine at location 11000,
which includes a type-specific pool "spring" to fill them. Fluxes are
computed to and from other pools, based on the first-order rate constants
K(L%,K%), as well as pool "degradation" (specified by the rate constant
K(0,K%)), and net pool changes (DPOOL(K%)) are calculated. Upon return,
compartmental voltages are incremented by DV (line 3600), pools are
incremented (line 3700), and pool values are printed at the top of the
screen. Finally, the the current location in the transmitter summation
table is zeroed and the location pointer, SUMTB0%, is incremented.
PLOTS: Returning from the NETWRK subroutine, the PLOTS subroutine is
called. First, a skip-count (SKPCNT%) is tested. This allows skipping
the plotting and writing of time points to make output files more
manageable. If the count is 0, a subroutine at 2200 is called which
writes the time on the .PRN file, then tests switch options, and plots and
writes appropriate variables. Next, if any of the spike flags are set,
spike tics are generated, spikes are sent to the .SPK file, if
appropriate, and spike perturbations (vertical lines of height SPKHT) are
generated on the voltage plots and .PRN file.
Cursor-accessed display: The final test is whether the sweep limit
on the screen has been exceeded, in which case the run is done, and a
"SWEEP COMPLETE" message is generated (line 2125). If batch file
operations or multiple-run conditions pertain, the program returns for the
next sweep. Otherwise, it enters the display mode loop at 2130 which
tests for keyboard input and interprets the ASCII codes in terms of curor
manipulations on the screen. An key returns control to the main
menu.
B. HODGKIN-HUXLEY BRANCHES
The equations given by Hodgkin and Huxley (1952) for the gating
particles have been placed in a uniform format, specified by 5 constants,
a,b,c,d,e (see Code 10 description). This form reduces to 0/0 when a=0,
e=-1 (i.e. for alpha-m; alpha-n) and V+c=0. By applying l'Hospital's
rule, alpha = b*d at this point. The program tests for the condition and
uses this alternate calculation if needed. It should also be noted that
the voltage variable, V, given in the H&H paper is with respect to rest,
and represents outside minus inside, instead of the currently used inside
minus outside. Thus for their "V", -(V+60) must be substituted, where the
new V is absolute membrane potential (-60 is the average squid axon
resting potential).
C. SYNAPTIC POTENTIALS
Version 3 reads in each synaptic potential from the .PSP file and
converts it to a sequence of values at equal time increments corresponding
to the integration increment (TINC) in the array VPSP(K%,T%). At run
time, the index K% is used to retrieve a particular shape when needed.
Each synapse (indexed by K%) has a PSP summation array, SUMTB(K%,L%),
which accumulates the transmitter released. The array is "circular" for
loading or read-out, meaning that it "wraps around" and the point
following L%=SUMTBL% (the upper limit) is L%=0. During a simulation, the
pointer variable SUMTB0% gives the starting L% index for all SUMTBs. This
index is incremented by 1 each integration cycle, picking off synaptic
input values at progressively later times as model time increases. When a
spike fires in a presynaptic unit, points from the corresponding
VPSP(K%,T%), scaled according to amplitude calculations, are added to
SUMTB, commencing at index SUMTB0%, wrapping around, and ending at
L%=SUMTB0-1.
D. FACILITATION
Each spike-mediated synaptic input branch (Numerical code 11) can
have several facilitation pools associated with it, the number being held
in the variable NF%(K%) for the K%th branch. These NF% pools are
represented by consecutive indices, L%, of the various facilitation
parameters (TAUF(L%), NF(L%), C2F(L%), C1F(L%)) and the pool variable,
XF(L%). For the K%th branch, the index L% starts at FLOC%(K%). To
calculate transmitter release, the facilitation pools are first calculated
by exponentially decaying their value after the previous spike in the
presynaptic unit. These numbers are raised to the appropriate power (see
Hartline 1988) and all summed to give the net facilitation factor, which
(as 1+F) multiplies transmitter released. Increments to each facilitation
pool are then calculated and the storage variable for the previous spike
on this input branch, TPREV(K%) is updated to the current model time (U).
E. TARGETS OF MODULATION
Targets are specified by an integer (XTARG%()) in the parameter
block. If the integer is positive, it is taken as the number of the pool
which is the target. If the integer is negative, its absolute value
specifies a branch type code. The particular branch number and the
particular parameter of that branch which will be the target are specified
by the additional line entries XBRN%() and XPRM%() respec- tively. NOTE
THAT NOT ALL PARAMETERS ARE LEGAL TARGETS. In particular, indices and
other integers are usually not. These are recognized (by a non-standard
name, such as one ending if "%") and skipped over by NET2PRM in
calculating XPRM%. THE APPROPRIATE TARGET PARAMETER SPECIFIER for XPRM%
is given following the parameter name in the Parameter File Block lists.
"*" targets (coupling and diffusion) are handled by special interactions
(Types 6 and 7). The POOL which controls the interaction is specified by
XSRC%() [generated by NET2PRM from the preceding pool-definition line],
and the interaction type by XINTYP%() [taken from the TYPE= assignment].
=============================================================================
APPENDIX III
USER-GENERATED ADDITIONS
A. ADDITION OF MAIN MENU OPTIONS
1. Changes in source file (SYNETSIM.3xx). Additions to the main
menu can be made readily by adding selections to the NETST section
starting at line 1750. Follow the format of existing selections.
2. Changes in NET2SBT.CNF. To add changes made in the main menu
(and any sub-menus added) to the batch capability, additional lines
corresponding to the menu selction(s) and input parameters needed must be
added to this file. Follow the examples given in the listing of the file
(Appendix __).
B. ADDITION OF PHYSIOLOGICAL PROPERTIES (branch codes)
1. Changes to source file (SYNETSIM.3xx). Intentional gaps have been
left in the branch coding for later additions. Codes 17 - 19 are reserved
for user-generated functions. Each new branch code must have a parameter
input section (lines 6160- 6589 reserved). The input section commences
with the third parameter (usually the compartment assignment), since the
calling code reads the branch code and index. The new code must also be
provided with a branch update section commencing at line 5700, 5800, or
5900 for codes 17, 18, and 19, respectively (accessed through the switch
in line 3400). HIBR% will need to be set to the highest code number used
under 20 in line 53. If the parameters of the new branch type are to be
modulated by pools, appropriate subroutines for accessing branch
parameters must be added to the FETCH BRANCH PARAMETER VIA K (line 13000
ff) and SET BRANCH PARAMETER FROM K (line 16000 ff) sections (follow the
examples already there). If preloading and saving of state variables from
the new branch type are required, appropriate subroutines must be written
to read and write them on sequential files, starting at lines 8700, 8800,
and 8900 for codes 17, 18, and 19 respectively, again following the
existing form.
2. Changes to NET2PRM.CNF: For each new property added, a new
parameter-configuration line must be added to this file specifying the new
code, the names of its parameters, and their order in the parameter file.
Read the description of the file in Appendix V (NET2PRM Manual) and follow
the examples for other codes.
3. CHECKLIST for addition of branch codes to SYNETSIM:
a. Add NAME% to line 52
b. Add IF J$=NAME$ THEN J%=NAME% to line 100+NAME%.
c. Add ON J% GOTO .... XXX .... to line 150
d. Change LOWBR% or HIBR% in line 54
e. Add kinetic calculations in lines 4000 + 100*NAME%
f. Add INPUT #1, CP%(K%, NAME%, prm1(K%), .:RETURN in 6000+NAME%*10
g. Add PRINT #1, vrbl1(K%), vrbl2(K%),.... :RETURN in 7000+NAME%*10
h. Add INPUT #1, vrbl1(K%), vrbl2(K%),.... :RETURN in 7500+NAME%*10
For addition of parameters to an existing branch code, as well as
adding new branch codes:
i. Add a line NAME%, NAME, name-prm1, name-prm2, ...,END to
NET2PRM.CNF
j. Add ON XPRM% GOTO beginning at line 13000+NAME%*100
k. Add K=prm(XBRN%) line blocks in the appropriate space following
l. Add ON XPRM% GOTO 16x05 at line 16000+NAME%*100
Add prm(K%) = K line blocks in the appropriate space following
APPENDIX IV
NETLIST MANUAL
by Greg Wolodkin
Dept. of Electrical Engineering
University of Maryland
College Park, MD
A. STRUCTURE OF THE NETLIST
Net2prm reads in a netlist containing information about a compartmental
structure which represents some physiological system. The basic structure
consists of compartments (which make up cells) and cells (which make up
the network). While an essay on compartmental modeling is certainly
beyond the scope of this manual, some introduction is necessary to make
sense of the format of the netlist. With that in mind, the basic
structure is this:
CELL is the largest 'object' or structure within the netlist.
A cell can be composed of one compartment, or many. All
compartments which are listed underneath of a CELL belong
to that CELL. The beginning of a cell is marked by a
CELL declaration line, consisting of the reserved word CELL
as the first word on the line, followed by a cell name. The
cell name must be unique. The end of a cell is marked by the
beginning of a new cell, or the end of the netlist, whichever
occurs first. An example of a proper cell declaration is this:
CELL PD
.
.
which defines a cell named 'PD' and assigns any items under
it to belong to 'PD'.
The CELL structure is not used by SYNETSIM, but is rather a
human concern. As we observe networks in the form of cells,
we would like our model to also represent the various cells
observed.
CMPT is the real building block of the compartmental model. As
mentioned above, cells can be constructed of one CMPT, or
of many. CMPT declarations work identically to cell declarations,
in that the beginning of a CMPT is marked by the reserved word
"CMPT" as the first word on a line, followed by a compartment
name. Compartment names must be unique only within the cell.
(Two cells could have compartments in them with matching names,
as long as the cells had unique names themselves.) The CMPT
declaration must also include a parameter set, which follows
the compartment name. For now, we will represent the parameter
set by the label '[parameter set]'. Its form in the netlist will
be discussed later. A legal CMPT declaration would be:
CMPT Soma [parameter set]
.
.
Furthermore, to define a cell with one compartment, we could
combine the two examples to form:
CELL PD
CMPT Soma [parameter set]
.
.
The indentation here helps to show that the CELL is made up of
any number of CMPTs, and the CMPT Soma as shown belongs to the
CELL PD.
These two structures (CELL and CMPT) allow us to build the
skeleton of a compartmental model. To reference this skeleton,
we need a naming convention. Electrical circuits are typically
referenced by node number, as in the circuit simulator SPICE.
In the compartmental model, each compartment is connected at
two nodes. One connection represents ground, and all
compartments share a common ground. The other connection
or node represents the membrane voltage, inside the membrane.
Since the compartmental model involves dividing a length of
membrane into compartments, each compartment has associated
with it the membrane voltage for a particular segment of the
membrane. Thus each compartment represents a node in the
circuit.
We have chosen to reference these nodes by name, and this name
is formed by the combination cell/compartment. Notice that
each cell has a unique name, and each compartment has a unique
name within the cell. With this in mind, then, each node has
a unique name. For the example above, the node would be named
PD/Soma
Each compartment MUST have a name, and all compartments must
belong to a cell. Each cell MUST have a name.
ELECTN The electrical coupling of compartments is accomplished via the
DIODE codes ELECTN and DIODE. These can be pictured as resistances
which passively connect one node to another. This adds another
field to our netlist form, that being the connection field.
A proper ELECTN declaration involves two nodes or compartments,
one which the ELECTN belongs to, and the other which is
specified in the connection field. The example below shows
two compartments which are connected electrotonically.
CELL PD
CMPT Soma [parameter set]
ELECTN [parameter set] Axon
CMPT Axon [parameter set]
.
.
where again the [parameter set] will contain information
regarding the specifics of each declaration.
Notice that the connection field for ELECTN above contains
'Axon', the name of the node to which it connects. It could
just as well have contained 'PD/Axon', as that is the FULL
name of the node. Since compartment names are unique within
a cell, however, we can omit the cellname and call it by 'Axon'.
The following example has an identical effect.
CELL PD
CMPT Soma [parameter set]
CMPT Axon [parameter set]
ELECTN [parameter set] Soma
.
.
For a DIODE, which represents a rectifying connection, the
direction of current flow (positive ions) is always INTO the
parent compartment, FROM the connection field. For the ELECTN
or bi-directional connection, the specification is not
important.
These four structures (CELL CMPT ELECTN DIODE) are enough
to build a passive membrane, consisting of resistances,
capacitances, and DC voltage sources. Other properties
can be added quite easily, as described below.
B. COMPONENTS WITHIN THE STRUCTURE [to be continued]
C. CONFIGURATION FILES
The .CNF files used by NET2PRM specify the names and orders for parameters
appearing in various input files for synetsim.
1. NET2PRM.CNF ---> contains information concerning the codes available
in the current version of synetsim.
- Lines which begin with a single quote ( ' ) are comments.
- Blank lines (along with comment lines) are ignored.
- The first line of the file represents the synetsim file format.
It is of the form:
SYNETSIM 3.3.2
and must match with the current version of synetsim. The compiler
passes this string on to any .PRM file which it creates. Upon
execution of synetsim, a fatal error will result if this string
doesn't match with synetsim's internal format. This is necessary,
as the .CNF file contains the order in which to pass parameters to
the .PRM file.
- All information following the first line must be of the form:
CODENUMBER, CODENAME, [parameter list], END
where CODENUMBER represents the number which synetsim uses to
index codes, CODENAME represents the name of the code,
[parameter list] represents a series of strings, separated by
commas, which correspond to synetsim parameters and compiler
reserved-words. END is used to mark the end of a parameter list,
and the beginning of a new code definition.
CODENUMBERS must go in sequence, starting with one.
Valid items in the parameter list include:
PNAME - a alphabetic string represents a parameter which is
to be input from the netlist. It will be found in
the netlist in the form (PNAME=34), and the
value 34 will be passed to synetsim.
PNAME% - a string ending with % indicates a value that will
be dependent on the structure of the netlist. The
compiler keeps track of these (cmpt number, branch
number, etc...) and passes them to the model quietly.
no effort is needed on the part of the user to set
these "structural" parameters.
membrane t.c. = 25 msec)
CMPT,1,1,DRIVER, .005,-50,.2 -- Network driver neuron
CMPT,2,2,FOLLOWER,.005,-50,.2 -- Network follower neuron
Branch Type Code TRIGR (or 2): Trigger zone parameters
| This trigger zone should fire a spike train with a sensitivity of
| ca 8 Hz/nA, adapting to ca 70% of its original frequency with a
| timeconstant of 500 msec (see Hartline 1979).
|
| K% - Branch index
| | CP%(K%,2) - Compartment assignment for branch
| | | E0(K%) - Base excitation
| | | | TAUM0(K%) - Base level membrane time constant (sec)
| | | | | PMTHR(K%) - Pacemaker response thresh (mV rel. to rest)
| | | | | | KPM(K%) - PM response excitation (EX) sensitivity fctr
| | | | | | | TAUPM(K%) - Pacemaker response time constant (sec)
| | | | | | | | KCOND(K%) - Spike conductance EX-sensitivity fctr
| | | | | | | | | TAUCOND(K%) - Spike-conductance time constant
| | | | | | | | | | KAR(K%) - "RP" adaptation EX-sensitivity fctr
| | | | | | | | | | | TAUAR(K%) - "RP" adaptation time constant
| | | | | | | | | | | | KA1(K%) - Adapt'n 1 EX-sensitivity fctr
| | | | | | | | | | | | | TAUA1(K%) - Adapt'n 1 t.c. (sec)
| | | | | | | | | | | | | | KA2(K%) - Adapt'n 2 EX-sens factor
| | | | | | | | | | | | | | | TAUA2(K%) - Adaptation 2 t.c.
| | | | | | | | | | | | | | | | THRINF(K%) -Thresh asymp (mV)
| | | | | | | | | | | | | | | | | KTHR(K%) - Thresh-EX fctr
| | | | | | | | | | | | | | | | | | TAUTHR(K%) - Thresh t.c.
| | | | | | | | | | | | | | | | | | |
TRIGR,1,1, 0,.04,0,2,.25,0,0,0,0,.30,.5,0,5.8,4,0,.004
TRIGR,2,2, 0,.04,0,2,.25,0,0,0,0,.30,.5,0,5.8,4,0,.004
DV0(K%) - Base reset-increment in trigger-zone voltage (mV)
| MAXV(K%) - Maximum membrane pot'l spike-reset level (mV relative rest)
| | DG0(K%) - Base spike conductance increment (rest units)
| | | MAXG(K%) - Maximum spike conductance level (rest units)
| | | | DAR0(K%) - Base "RP" adaptation spike-increment (mV)
| | | | | MAXAR(K%) - Maximum "RP" adaptation level (mV relative to rest)
| | | | | | DA10(K%) - Base adaptation 1 increment (mV)
| | | | | | | MAXA1(K%) - Maximum adaptation 1 level (mV)
| | | | | | | | DA20(K%) - Base adaptation 2 increment
| | | | | | | | | MAXA2(K%) - Maximum adaptation 2 level
| | | | | | | | | | DTHR0(K%) - Base threshold increment (mV)
| | | | | | | | | | | MAXTHR(K%) - Maximum thresh (mV relative)
| | | | | | | | | | | |
-4,-4,0,0,0,1000,0,1000,0,1000,5,5
-4,-4,0,0,0,1000,0,1000,0,1000,5,5
Type Code ELECTN (or 3): Inter-compartmental electrotonic connections
| These parameters provide for a rectifying electrotonic connection
| between cells 1 and 2 (DRIVER and FOLLOWER). Conductance is low
| (.01 umho) going from DRIVER to FOLLOWER, but large (.1 umho) in
| the reverse direction.
| I% - Postjunctional compartment for low-resistance direction
| | J% - Prejunctional compartment for low-resistance direction
| | | GC(I%,J%) - Coupling conductance (umho)
| | | |
ELECTN,1,2,.01
ELECTN,2,1,.1
Branch Type Code DRIVER (=8): Driver potential
| This parameter set gives plateau and endogenous burst properties to
| the DRIVER cell, and voltage-dependent outward-currents to the
| FOLLOWER. With induction of inward current (through synaptic input
| from DRIVER) FOLLOWER can also generate plateaus. In addition,
| there are slow restoring conductances in both cells which decay with
| a time constant of 400 msec.
| K%
| CP%(K%,8) - Compartment assignment
| | | VNA(K%) - I-in reversal potential (mV, abs)
| | | | GBARNA(K%) - I-in maximum conductance (umho)
| | | | | V0K(K%) - I-in half-activation voltage (mV, abs)
| | | | | | MUNA(K%) - I-in characteristic width (mV)
| | | | | | | VK(K%) - I-out reversal potential (mV abs)
| | | | | | | | GBARK(K%) - I-out maximum conductance (umho)
| | | | | | | | | V0K(K%) - I-out half-activation V (mV)
| | | | | | | | | | MUK(K%) - I-out characteristic V (mV)
| | | | | | | | | | | GBARK1(K%) - Restoring g-max (umho)
| | | | | | | | | | | | TAUK1(K%) - K1 decay t.c
| | | | | | | | | | | | | GBARK2(K%)
| | | | | | | | | | | | | | TAUK2(K%)
| | | | | | | | | | | | | | |
DRIVER,1,1,40,.50,-40,5,-90,.50,-40,5,.36,.4,0,1
DRIVER,2,2,40, 0,-40,5,-90,.50,-40,5,.36,.4,0,1
Branch Type Code HHFXD (=9): Fixed tau active HH current
| These parameters specify a hyperpolarization deinactivated,
| depolarization activated "A"-type conductance in both network cells.
| K%
| | CP%(K%,9)
| | | VEQ(K%) - Active current reversal level (mV abs)
| | | | GBAR(K%) - Maximum conductance (umho)
| | | | | QM(K%) - Activation variable (m) exponent
| | | | | | V0M(K%) - m half-activation voltage (mV, abs)
| | | | | | | MUM(K%) - m characteristic voltage (mV)
| | | | | | | | TAUMA(K%) - m time-constant (sec)
| | | | | | | | | QH(K%) - Inactivation variable (h) exponent
| | | | | | | | | | V0H(K%)
| | | | | | | | | | | MUH(K%)
| | | | | | | | | | | | TAUH(K%)
| | | | | | | | | | | | |
HHFXD,1,1,-90,100,1,-35,4,.005,1,-70,-5,.04
HHFXD,2,2,-90,200,1,-35,4,.005,1,-70,-5,.04
Branch Type Code HH (=10): Hodgkin-Huxley kinetics (in file HH.PRM)
| K%
| | CP%(K%,10)
| | | VEQHH(K%) - Equilibrium potential for ion
| | | | GBARHH(K%) - Maximum conductance (umho)
| | | | | QMHH(K%) - Exponent for activation variable
| | | | | | QHHH(K%) - Exponent for inactivation variable
| | | | | | | xAM(K%) | xBM(K%) | xAH(K%) | xBH(K%)
| | | | | | | A B C D E A B C D E A B C D E A B C D E
| | | | | | | | | | | | | | | | | | | | | | | | | | |
HH,1,1,+55,120, 3,1,0,-100,35,10,-1,4000,0,60,-18,0,70,0,60,-20,0,1000,0,30,10,1
HH,2,1,-72, 36, 4,0,0, -10,50,10,-1, 125,0,60,-80,0
The file HH.PRM also has the following Principal Compartment parameters:
1,1,1,SQUID,.001,-49.387
which corresponds to Table 3 of HH '52.
Branch Type Code SYNAPSE (=11): Conventional PSP
| These PSPs are all based on equal amounts of transmitter released
| (A0S= 0.1x Kd) with differences in intrinsic strength deriving from
| differences in maximum conductance (GBARS: .1 and .3 for synapses 1
| and 2 respectively). PSPs rise with 10 msec to peak (Shape 1 from the
| SYNTEST.PSP file; shape 2 is a slowly-rising PSP for comparison).
| K%
| | CP%(K%,11) - Postsynaptic compartment
| | | VREVS(K%) - Revrsl pot'l for synaptic ionic battery (mV, abs)
| | | | GBARS(K%) - Saturation conductance level (umho)
| | | | | KDS(K%) - Dissoc. constant for xmtr-receptor binding
| | | | | | CPS%(K%) - Presynaptic compartment
| | | | | | | PSPSHP%(K%) - PSP shape index
| | | | | | | | DLY(K%) - Synaptic delay (sec)
| | | | | | | | | A0S(K%) - Base peak xmtr conc (Kd units)
| | | | | | | | | | TAUF(FLOC%) - Facil time constant (0=none)
| | | | | | | | | | |
SYNAPSE,1,2,-75,.1,1,1,1,.003,.1,0 -Synapse 1: weak inhib of FFR by DRIVER
SYNAPSE,2,1,-75,.3,1,2,1,.003,.1,0 -Synapse 2: strong inhib of DRVR by FFR
SYNAPSE,3,1,+50,.2,1,3,1,.003,.1,0 -Synapse 3: EPSP to DRVR from input #3.
Branch Type Code CHEMOX (=12): Chemotonic exponential interaction
| Reciprocal chemotonic interactions between FOLLOWER and DRIVER
| are included for demonstration purposes. They can be activated
| by setting Toxin Flag CHEMOX = "U" using the Main Menu option 6.
| K%
| | CP%(K%,12) - Postsynaptic compartment
| | | VREVC(K%) - Reversal potential (mV, abs)
| | | | GBARC(K%) - Saturation conductance (umho)
| | | | | KDC(K%) - Dissoc. const. for trnsmttr (arbitrary units)
| | | | | | CPC%(K%) - Presynaptic compartment
| | | | | | | XMTR0C(K%) - Transmitter conc at 0 mV (arb. units)
| | | | | | | | MUC(K%) - Characteristic V for release curve (mV)
| | | | | | | | |
CHEMOX,1,2,-75, 5,1,1,1,10
CHEMOX,1,1,-75, 5,1,2,1,10
Branch Type Code POOL (=20): Pool type
| Two types of pools are included. The bound transmitter one (XTYPE%
| = 1) is proportional to synapse 1 (PPRM1: DRIVER to FOLLOWER) trans-
| mitter binding (proportionality constant = 1: PPRM2) and has a Kd of
| 1 (PPRM3). The two second messenger pools (XTYPE%=4) are synthesized
| at "fixed rates", but this base rate (PPRM1) is zero (input in this
| case will come from interactions and diffusion). One (pool 2) decays
| with a time constant of 1 sec (1/PPRM2), while the other (pool 3)
| does not decay.
| K%
| | CP%(K%,20) - Compartment assignment
| | | XTYPE%(K%) - Pool type (1-4)
| | | | 1= Value : bound transmitter
| | | | 2= Filling rate : bound transmitter
| | | | 3= Ionic current
| | | | 4= Constant filling, first-order decay
| | | | XNAME$(K%) - Pool name
| | | | | XVOL(K%) - Pool volume (arbitrary units)
| | | | | | XPOOL0(K%) - Base pool level
| | | | | | | Pool: 1 2 3
| | | | | | | PPRM1(K%) PreCpt F F
| | | | | | | | PPRM2(K%) C K K
| | | | | | | | | PPRM3(K%) Kd -- --
| | | | | | | | | | PPRM4(K%) -- -- --
| | | | | | | | | | |
POOL,1,2,1,"BOUND TRANSMITTER",1,0,1,1,1,0 Type 1: Xpool=C*Xmtr/(Kd+Xmtr)
POOL,2,2,4,"2ND MESSENGER A", 1,0,0,1,0,0 Type 4: dXpool/dt= F - K*Xpool
POOL,3,2,4,"2ND MESSENGER B", 1,0,0,0,0,0 Type 4: " "
Branch Type Code POOLK (=21): Pool Diffusion/Reaction
| For demonstration purposes, a bidirectional "diffusion" between
| pools 2 and 3, with time constant of 100 msec, can be activated by
| setting Toxin Flag POOLK = "U" using option 6 of the main menu.
| K% - Recipient pool #
| | L% - Source pool #
| | | K(K%,L%) Diffusion/Reaction rate constant (1/sec)
| | | |
POOLK,2,3, 1
POOLK,3,2, 1
Branch Type Code POOLX (=22): Pool Interactions
| The first line sets up pool 2 as a target (XTARG%) of a "Type 5"
| interaction (XINTYP%) controlled by pool 1 (XSRC%). This means
| that the synthesis rate of pool 2 is proportional to the level
| of pool 1. This, in effect, makes synthesis rate dependent on
| bound transmitter at the DRIVER to FOLLOWER synapse. The second
| line gives the maximum conductance of compartment 2, GBARNA (case 2
| of branch type 8, second parameter) a "Type 5" dependence on pool 2.
| This means that GBARNA will change according to pseudo first-order
| kinetics with rate constant proportional to pool 2 level.
| K%
| | XTARG%(K%) - Target pool (if >0) or branch parameter (if <0)
| | | XSRC%(K%) - Source pool exerting the interaction
| | | | XINTYP%(K%) - Interaction type (1-7)
| | | | | 1= Direct proportionality
| | | | | 2= Steady state 2nd messenger bound to receptor
| | | | | 3= Pseudo first-order kinetics
| | | | | 4= Ionic battery
| | | | | 5= Modulation of target synthesis rate
| | | | | 6= Modulation of electrotonic connection
| | | | | 7= Modulation of inter-pool diffusion
| | | | | Interaction: 1 2
| | | | | XPRM1(K%) C alpha
| | | | | | XPRM2(K%) -- beta
| | | | | | | XPRM3(K%) -- A0
| | | | | | | | XPRM4(K%) -- --
| | | | | | | | | XBRN%(K%) - Target branch
| | | | | | | | | | XPRM%(K%) - Target parameter in branch
| | | | | | | | | | |
POOLX,1, 2,1,5, 1,0, 0,0 Type 5: target= pool 2; dXpool/dt=C*Xpool(1)
POOLX,2,-8,2,3,20,1,.8,0,2,2 Type 3: GBARNA=alpha*Xpool(2)
| | | *(A0-GBARNA) - beta*GBARNA
target: Code 8 (DRIVER) | Pool 2
Branch #2
0,0,END (Termination set)
=============================================================================
APPENDIX VII
SPECIAL VARIABLE ASSIGNMENTS
(excluding those listed above):
BIAS: Bias current on cell, menu selection 2 (960)
CURRENT: Pulse stimulus magnitude, menu sel. 2 (960)
DBGI%: Debug loop count (1825)
FLOC%: Pointer to facilitation compartment array
G(K%,J%): Conductance of K%th branch of type J%
GC(I%,J%): Coupling conductance from cmpt J% to cmpt I%
GI(I%): Total conductance of I%th compartment
I(K%,J%): Current in the K%th branch of type J%
II(I%): Total ionic current in compartment I% (sum of all
branches)
IM(I%): Imposed external membrane current through compartment
I%
IM0(I%): Biasing offset current to compartment I%
N%: Total number of cells (Type 1 codes)
N%(J%): Tally of number of branches of code type J%
NCODE%: Number of branch codes (set in 60)
NF(K%): Number of facilitation compartments for synapse K%
NPSP%: Tally of number of PSP shapes
POOLINC: Pool increment, menu sel. 4 (1050)
SUMTB(I%,T%+SUMTB0%): Summed PSPs for cell I% (time point T%)
SUMTB0%: Starting point in SUMTB for synaptic input
SWP%: Sweep count, menu sel. 1 (900)
T%: Time index for PSP shape calculation
TINC: Time increment for integration (msec)
T1,T2,T3 Special-use PSP shape variables
U: Time
UEND: Time of end of stimulus period, menu sels. 2,3 (990
ff)
UNEXT: Time of next stimulus event, menu sels. 2,3,4 (990 ff)
UNIT%: Stimulated unit, menu sels. 2,3,4 (960, 1010, 1050)
VPSP(I%,T%) Converted PSP shape for I%th PSP
V1,V2,V3 Special use PSP transmitter value variables
X: X-axis variable for plot
Y: Y-axis variable for plot
***** STATE VARIABLES (SNAX name) ***************
(C# = code pertaining to variable)
A1(I%): C2 Adaptation 1 (ADPT)
A2(I%): C2 Adaptation 2 (ADPT2)
AR(I%): C2 Resting-potential adaptation (RPADPT)
EI(I%): C2 Current (I)
GK1(K%): C8 Restoring conductance 1
GK2(K%): C8 Restoring conductance 2
GE(I%): C2 External conductance (CONDCT)
GS(I%): C2 Spike-dependent conductance (COND)
H(K%): C9 Inactivation variable
HHH(K%): C10 Inactivation variable
J(I%): C2 Current excitation (CURX)
M(K%): C9 Activation variable
MHH(K%): C10 Activation variable
P(I%): C2 Pacemaker response (PM)
THR(I%): C2 Spike threshold (THR)
TPREV(K%): C11 Time of previous spike firing, synapse K%
V(I%): C1 Absolute membrane potential (ACTV + RP)
VA(I%): C2 active voltage from non tz sources: V - RP (ACTV)
VM(I%): C2 Membrane potential at trigger zone (VM)
W(I%): C2 Perturbation (PTB)
XF(L%): C11 Facilitation in f-pool L%
XSS(I%): C2 Excess of threshold above membrane potential (THR-
VM)
***** FLAGS (see also Master File Format ********
SPKFLG%(I%): Spike-fired flag for presynaptic unit I%
(=branch index for corresponding Code 2
branch)
TRGFLG%: Trigger flag: If <0, skip prefiring of spikes
PLTSW%(I%): Plot switch, specifying which variables will be
plotted
***** TEMPORARY VARIABLES ***********************
CHI: C2 chi in paper (excitation less adaptation if ADPFLG=0)
(ETOT)
DJ: C2 change in current excitation (4240)
DPG, DPH, DPL: C2 variables used in threshold-crossing correction
DPM: C2 change in PM (4270)
EX: C2 X in paper (total excitation) (ETOT$)
GM: C2 total membrane conductance (= GE()+GS()+1)
PM: C2 pacemaker response
PMTHR: C2 pacemaker threshold (4090)
V: C1 membrane potential
XMTR: C12 transmitter concentration (5460)
XX: C2 time-increment fragments for threshold crossing (4420)
YY: C2 see XX (4420)
*****INDEX VARIABLES ****************************
I%: Cell #/Cmpt #/Other
J%: Branch type code
K%: Branch number
L%: Sub-index within a branch: facilitation, PSP time index etc
T%: Quantized time index: PSP input and summations
***** SCRATCH VARIABLES *************************
A 5300
F 5260
G 4610
H
L 4380
T 4620
XXX Plots
YYY Plots
========================================================================
APPENDIX VIII
EXECUTION SPEEDS ON VARIOUS COMPUTERS
Execution time (min:sec) for one sweep of SYNTEST:
Machine GWBASIC Compiled
Compiled
(- math chip) (+
math chip)
Zenith Z158 25: -- 2:10
8 MHz
IBM PC/AT 1:13
8 MHz
IBM AT clone 8:34 1:06
10 MHz (Standard)
Compaq 386/20 0:14.5
20 MHz
===============================================================================
APPENDIX IX
SOURCE LISTING
10 ID$ = "SYNETSIM 3.3B 8/24/90": PRINT ID$
12 MFID$="SYNETSIM 3.3.2": PFID$="SYNETSIM 3.3.2": SFID$="SYNETSIM 3.0.2"
14 PRINT "(C) COPYRIGHT D.K. HARTLINE 1987, 1988, 1989, 1990."
16 PRINT "SEE SYNETSIM.TXT FOR OPERATING INSTRUCTIONS"
18 PRINT " BRUN3087 (C) COPYRIGHT MICROSOFT CORP. 1982, 1983, 1984"
20 PRINT " 1985, 1986, 1987"
35 'NEEDS MODULATION TARGETS FOR GAMMAS
36 '3.3B (.33B 8/21/90): Conductance AND density (gamma); color traces
37 '3.3A (.33A 8/3/90): Conductance density parameters
38 '3.2D (.32D 7/9/90): Greg's changes: command line; cursor; mid-swp interrupt
39 ' 7/23 DIODE addition; 7/24 multiple clamp runs
40 '3.2C (.32C 4/4/90): save refixed; Boolean flags; SPIKE; COND branches
41 '3.2B (.32B 11/28/89): V-clamp version; cursor fxd; save/restore fxd; CMB3
42 '3.2A (.32A 9/12/89): ACNLSPDPM version; String codes; Cursor; CMC12
43 '3.1 (.Q3D 9/2/88): INNS version; minor error correction; CMC11
44 '3.0C (.Q3C 12/25/87): IEEE version; CMC10
45 '3.0 (.Q3B 11/87) = Original Soc Neurosci version; Numerical codes; CMC9
47 ' ##############################################
48 '################ INITIALIZATIONS AND PARAMETER INPUT CALLS ########
49 ' ##############################################
50 'GWB%=-1 'FOR GWBASIC # Branches<=3; COMMENT OUT FOR QuickBASIC
51 CMPT%=1: TRIGR%=2: ELECTN%=3: DIODE%=4: SPIKE%=5 'BRANCH TYPE CODES
52 COND%=7: DRIVER%=8: HHFXD%=9: HH%=10: SYNAPSE%=11: CHEMOX%=12
53 CONNOR%=14: POOL%=20: POOLK%=21: POOLX%=22
60 LOWBR%=7: HIBR%=14: FRCT%=10 'CONDUCTANCE-BRANCH CODE RANGE
65 DSPLYB%=1: D$(0)="V": D$(1)="I": D$(2)="G" 'INVARIANT DISPLAY CHARACTERS
70 mdly=20 'seconds to elapse before continuing batch mode.
75 NCODE%=22: IF GWB% THEN MAXBR%=3 ELSE MAXBR%=15
80 DIM TXFLG%(NCODE%), N%(NCODE%), CP%(MAXBR%, NCODE%), G(MAXBR%, 14), I(MAXBR%, 14)
85 FLOC%=1 'INITIAL LOCATION FOR FACILITATION PARAMETERS
90 RST%=-1 'Reset to zero initial conditions every sweep
98 GOTO 199
99 '************** Subroutine for decoding/encoding Branch Codes ***** 100
IF J$="CMPT" THEN J%=CMPT%: GOTO 149
102 IF J$="TRIGR" THEN J%=TRIGR%: GOTO 149
103 IF J$="ELECTN" THEN J%=ELECTN%: GOTO 149
104 IF J$="DIODE" THEN J%=DIODE%: GOTO 149
105 IF J$="SPIKE" THEN J%=SPIKE%: GOTO 149
107 IF J$="COND" THEN J%=COND%: GOTO 149
108 IF J$="DRIVER" THEN J%=DRIVER%: GOTO 149
109 IF J$="HHFXD" THEN J%=HHFXD%: GOTO 149
110 IF J$="HH" THEN J%=HH%: GOTO 149
111 IF J$="SYNAPSE" THEN J%=SYNAPSE%: GOTO 149
112 IF J$="CHEMOX" THEN J%=CHEMOX%: GOTO 149
114 IF J$="CONNOR" THEN J%=CONNOR%: GOTO 149
120 IF J$="POOL" THEN J%=POOL%: GOTO 149
121 IF J$="POOLK" THEN J%=POOLK%: GOTO 149
122 IF J$="POOLX" THEN J%=POOLX%: GOTO 149
140 J%=VAL(J$)
149 RETURN
150 ON J% GOTO 151,152,153,189,189,189,189,158,159,160,161,162,189,164,189,189,189,189,189,170,171,172: GOTO 189
151 J$="CMPT": GOTO 180 '(Access from 1920,...
152 J$="TRIGR": GOTO 180
153 J$="ELECTN": GOTO 180
154 J$="DIODE": GOTO 180
155 J$="SPIKE": GOTO 180
157 J$="COND": GOTO 180
158 J$="DRIVER": GOTO 180
159 J$="HHFXD": GOTO 180
160 J$="HH": GOTO 180
161 J$="SYNAPSE":GOTO 180
162 J$="CHEMOX": GOTO 180
164 J$="CONNOR": GOTO 180
170 J$="POOL": GOTO 180
171 J$="POOLK": GOTO 180
172 J$="POOLX": GOTO 180
180 RETURN
189 J$="": GOTO 180
199 '*************** Master file input
'----
if command$<>"" THEN
cm$=command$
sp%=instr(cm$,"/") 'detect a single switch SW$
if sp%>0 then
ep%=instr(sp%,cm$," ")
if ep%=0 then ep%=len(cm$)+1
sw$=mid$(cm$,sp%+1,ep%-sp%-1)
cm$=left$(cm$,sp%-1)+right$(cm$,len(cm$)-ep%+1)
end if
end if
while left$(cm$,1)=" " 'remove excess spaces fore and aft
cm$=right$(cm$,len(cm$)-1)
wend
while right$(cm$,1)=" "
cm$=left$(cm$,len(cm$)-1)
wend
if cm$<>"" then
sp%=instr(cm$," ")
if sp%=0 then sp%=len(cm$)+1
cm$=left$(cm$,sp%-1)
sp%=instr(cm$,".")
if sp%=0 then sp%=len(cm$)+1
mfile$=left$(cm$,sp%-1)
else
200 INPUT "INPUT MASTER FILE (no ext)[use for test mode]"; MFILE$
205 IF MFILE$ = "" THEN MFILE$ = "SYNTEST"
end if
210 OPEN "I", #3, MFILE$ + ".MST" 'OPEN AND PROCESS MASTER FILE
215 INPUT #3, MTITLE$, MFIDD$, PFILE$, PSPFILE$, BAT$, XSCALE, VSCALE, ISCALE, GSCALE
217 INPUT #3, KSCALE, PSCALE, Y0, TINC, SKIP%, PSPDM, PSPL%, SUMTBL%
220 IF SW$="B" OR SW$="b" THEN GOTO 228
222 IF SW$<>"" THEN PRINT "Invalid switch /";SW$;" ignored.";CHR$(7): GOTO
228
224 BATFILE$=BAT$ 'save name of BAT file in case of menu#7 selection.
226 BAT$="none" 'force model to ignore BAT file.
228 IF BAT$<>"NONE" AND BAT$<>"none" THEN OPEN "I",#5,BAT$ ELSE BAT$=""
230 YSCALE=VSCALE
232 IF GWB% THEN SUMTBL%=200: PSPL%=200
233 ' 'CHECK FORMATS OF DATA FILES
234 IF MFID$<>MFIDD$ THEN PRINT "230: BAD MASTER FILE: Need: "; MFID$; " Have: "; MFIDD$: END
236 INPUT #3, SPKHT, ADPFLG%: IF ADPFLG%<>0 THEN ADPFLG%=-1 'BOOLEAN FLAG
240 REM 10 -1
250 INPUT #3, PF%,ZPF%,SPF% 'PRINT, PLOT FLAGS: ZERO, SPIKES
252 input #3, gmode%, ncol%, zcol%, scol%, icol%, vcol% 'enhanced graphics mode
254 if gmode%=0 or gmode%=2 then gmode%=2: scx%=639: scy%=199: GOTO 260
256 if gmode%=9 then scx%=639: scy%=349 'Enhanced EGA
259 REM color 0 is black... not real desirable.
260 if ncol%=0 then ncol%=15
262 if zcol%=0 then zcol%=15
264 if scol%=0 then scol%=15
266 if icol%=0 then icol%=15
268 if vcol%=0 then vcol%=15
270 FOR I%=2 TO NCODE% '"TOXIN" BRANCH FLAGS
272 INPUT #3, L%: IF L%<>0 THEN L%=-1
274 TXFLG%(I%)=L%
276 NEXT I%
278 IF PF% THEN LPRINT ID$; " **** RUN DATE: ";DATE$;" AT ";TIME$;" ****"
290 PRINT "MASTER FILE= "; MFILE$ + ".MST: "; MTITLE$: IF PF% THEN LPRINT "MASTER FILE= "; MFILE$ + ".MST: "; MTITLE$
300 PRINT "TINC="; TINC; " SKIP INDEX="; SKIP%: IF PF% THEN LPRINT "TINC="; TINC; " SKIP%="; SKIP%; "PSP-DURN-MPYR="; PSPDM
310 PRINT "ADPFLG%="; ADPFLG%
320 IF PF% THEN LPRINT "SPKHT="; SPKHT; " ADPFLG%="; ADPFLG%
330 GOSUB 1900 'PRINT FLAGS/SWITCHES
339 '*************** Parameter file input
340 OPEN "I", #1, PFILE$ + ".PRM" 'OPEN AND CHECK PARAMETER FILE
350 INPUT #1, PTITLE$, PFIDD$
360 IF PFID$ <> PFIDD$ THEN PRINT "360: BAD PARAMETER FILE: Need: "; PFID$; " Have: "; PFIDD$: END
370 PRINT "PARAMETER FILE= "; PFILE$ + ".PRM: "; PTITLE$: IF PF% THEN LPRINT "PARAMETER FILE= "; PFILE$ + ".PRM: "; PTITLE$
410 '***************** BRANCH-DATA INPUT LOOP *****
420 INPUT #1, J$, K% 'BRANCH TYPE, BRANCH INDEX
425 GOSUB 100 'DECODE BRANCH CODE
430 IF J%=0 THEN GOTO 465 'END INPUT LIST?
435 rem PRINT "J%=";J%,"K%=";K%
440 IF K%>N%(J%) THEN N%(J%)=K% 'UPDATE BRANCH CODE MAX INDEX
445 ON J% GOSUB 6010, 6020, 6030, 6040, 6050, 6060, 6070, 6080, 6090, 6100, 6110, 6120, 6130, 6140, 6150, 6160, 6170, 6180, 6190, 6200, 6210, 6220
450 ' Code: 1 2 3 4 7 8 9 10 11 12 13 20 21 22
455 GOTO 420
460 RETURN 'USED FOR BLANK INDICES
465 INPUT #1, ID$: IF ID$<>"END" THEN PRINT "465: .PRM FILE FRAMING ERROR. Code:";J$: STOP
466 CLOSE #1
470 N% = N%(1)
475 FOR L% = 1 TO N%(POOL%)
480 IF XVOL%(L%) = 0 THEN XVOL(L%) = 1
485 NEXT L%
490 DIM SUMTB(N%(11), SUMTBL%) '1 SUMTB SLOT EA SYNAPSE
495 L%=XSCALE/TINC/SKIP%+3: DIM Y(N%,L%)
496 PRINT "Y DIM=(";N%;",";L%;")"
500 '***************** PSP SHAPE TABLE INPUT LOOP ********
505 IF PSPFILE$="NONE" THEN TXFLG%(SYNAPSE%)=1: GOTO 720
510 OPEN "I", #2, PSPFILE$ + ".PSP"
520 INPUT #2, STITLE$, SFIDD$, NPSP%: DIM VPSP(NPSP%, PSPL%)'NUMBER OF PSP SHAPES
530 IF SFID$ <> SFIDD$ THEN PRINT "530: BAD PSP FILE: Need: "; SFID$; " Have: "; SFIDD$: END
540 PRINT "PSP FILE= "; PSPFILE$ + ".PSP: "; STITLE$: IF PF% THEN LPRINT "PSP FILE= "; PSPFILE$ + ".PSP: "; STITLE$
550 FOR K%=1 TO NPSP%
560 PRINT "LOADING PSP"; K%
570 INPUT #2, T1 'TIME
580 INPUT #2, V1 'VALUE
590 IF T1<>0 OR V1<>0 THEN IF T1>=0 THEN GOTO 570 ELSE GOTO 680'GET BEGIN
600 T2=TINC: T%=1 'TABULATED PSP (NOTE VPSP(K%,0)=0)
610 INPUT #2, T3 'TIME
620 INPUT #2, V3 'VALUE
630 T3=T3*PSPDM 'SCALE TIME BY PSPDM
640 VPSP(K%,T%) = V1+(V3-V1)*(T2-T1)/(T3-T1)'INTERPOLATION FORMULA
650 T%=T%+1
660 T2=T2+TINC
665 IF T%>PSPL% THEN GOTO 700
670 IF T2<=T3 THEN GOTO 640
675 T1=T3: V1=V3: GOTO 610
680 IF T1<>-1 THEN PRINT "680: ILLEGAL PSP TYPE": STOP 'COMPUTED PSP
685 FOR T%=0 TO PSPL%
690 VPSP(K%,T%) = EXP(-TINC*T%/V1) 'V1 IS DECAY TIME-CONSTANT
695 NEXT T%
700 NEXT K%
710 CLOSE #2
715 '***** Initialize state variables **************
720 FOR I%=1 TO N%: V(I%)=VLK(I%): NEXT I% 'PRELOAD V'S
725 FOR I%=2 TO NCODE%
726 IF N%(I%)=0 THEN TXFLG%(I%)=-1
727 NEXT I%
730 FOR K%=1 TO N%(POOLX%) 'BASE LEVELS FOR MODULATION TARGETS = INITIAL VALUES
735 XTARG%=XTARG%(K%)
740 IF XTARG%<0 THEN I%=-XTARG%: XBRN%=XBRN%(K%): XPRM%=XPRM%(K%): GOSUB 13000: XTARG0(K%) = K: GOTO 760
750 XTARG0(K%)=XPOOL(XTARG%)
760 NEXT K%
765 PRINT "HIT ANY KEY TO CONTINUE";
while inkey$=""
wend
770 GOTO 800
790 RETURN '(used by ON x GOSUB)
793 '
795 ' #######################################
797 '################ NETST SECTION: MODEL RUN OPTIONS ####################
799 ' #######################################
800 U=0
810 X=0
812 FOR I%=1 to N%(DSPLYB%): Y(I%,0)=0: NEXT I% 'store YSCALES here later
815 CLOSE #2: CLOSE #3: IF SF% THEN SF%=0 'RESET DISK-STORE-FLAG
820 IF RST% THEN X=0: U=0 'RESET U IF RESET-FLAG SET
821 SCREEN 0: CLS
822 IF BAT$<>"" THEN INPUT #5,MM$: GOTO 855
825 PRINT "MAIN MENU": IF SF% THEN PRINT "(.PRN OUTPUT)" ELSE PRINT "(NO
827 IF DBF%<>0 THEN PRINT "DEBUG MODE ON"
830 PRINT " = END"
831 PRINT " 1= FREE_RUN"
832 PRINT " 2= I_PULSE - Current pulses to a compartment"
833 PRINT " 3= PSP_TRAIN from presynaptic cell"
834 PRINT " 4= Voltage clamp of a compartment"
835 PRINT " 5= POOL_INCrement"
836 PRINT " 6= TOXINS changed"
837 PRINT " 7= Batch operation"
838 PRINT " 8= CHANGE PARAMeters"
839 PRINT " 9= OUTPUT_PRN next sweep"
840 PRINT " 10= SAVE model state"
841 PRINT " 11= RESTORE previous model state"
842 PRINT " 12= CHANGE_DISPLAY variable"
843 PRINT " 13= Options"
850 INPUT MM$
855 MM%=VAL(MM$)
860 SCREEN GMODE%
865 if gmode%=9 then color ncol% 'default text color.
870 ON MM% GOTO 900, 925, 970, 1000, 1090, 1100, 1195, 1200, 1300, 1400, 1500, 1680, 1700
875 IF PF% THEN LPRINT CHR$(12)
880 CLOSE: END
898 '
899 '***************** 1: Network free run **************************
900 IF BAT$<>"" THEN INPUT #5, SWEEP0%: GOTO 904
901 INPUT "NUMBER OF SWEEPS";SWEEP0%
904 SWP%=SWEEP0%
905 CLS: PRINT "SWEEP=";SWEEP0%-SWP%+1;" length=";XSCALE;" sec; YSCALE=";YSCALE
910 GOSUB 1800
'mid-sweep interrupt... space bar followed by "I" for interrupt.
i$=inkey$
if i$=" " then
do
g$=inkey$
loop while g$=""
if g$="i" or g$="I" then
x=0 : x%=0 'plot positions
swp%=0 'force final sweep
end if
end if
915 IF X<>0 THEN GOTO 910
920 SWP%=SWP%-1
922 IF SWP%<=0 THEN GOTO 815 ELSE GOTO 905
923 '
924 '**************** 2: Single-cell current pulses ****************
925 PRINT "CURRENT PULSE"
929 IF BAT$<>"" THEN INPUT #5,CPT%,BIAS,COND,UCEND,TEST,UEND: GOTO 932
930 INPUT "COMPARTMENT, BIAS-I, COND-I, COND DURN, TEST-I, TEST DURN"; CPT%,BIAS,COND,UCEND,TEST,UEND
932 IF CPT%=0 THEN GOTO 820
935 IF PF% THEN LPRINT "CURRENT PULSE TO CMPT "; CPT%;" BIAS=";BIAS;" COND-I=";COND;" DURN=";UCEND;" TEST-I=";TEST;" DURN=";UEND
940 UCEND=UCEND+U: UEND=UEND+UCEND: CLS: IM0(CPT%)=COND
945 GOSUB 1800: IF X=0 THEN GOTO 815 'COND PULSE
950 IF U"" THEN INPUT #5,UNIT%, PSPF, UNEXT, UEND: GOTO 976
975 INPUT "UNIT#, PSP RATE (HZ), START DELAY, TRAIN DURN"; UNIT%, PSPF, UNEXT, UEND
976 UNEXT=UNEXT+U: UEND=UEND+UNEXT
977 IF UNIT%=0 THEN GOTO 820
980 IF PF% THEN LPRINT "UNIT# "; UNIT%; " RATE "; PSPF; " FROM "; UNEXT; " TO "; UEND
985 CLS : TXFLG%(SYNAPSE%)=0: X=0: GOTO 995
990 UNEXT=UNEXT+1/PSPF
995 GOSUB 1800: IF X=0 THEN GOTO 815 '1 MODEL STEP
996 IF U>UNEXT AND U"" THEN INPUT #5, VCMODE$: GOTO 1011
1002 PRINT " - RETURN
1005 PRINT " 1 - HOLD level run"
1007 PRINT " 2 - VC_CT: Single condition-test run"
1008 PRINT " 3 - IV: Multiple condition-test runs with file storage"
1010 INPUT VCMODE$
1011 VCMODE%=VAL(VCMODE$): IVFILE$="": VCF%=-1: SWP%=0
1012 ON VCMODE% GOTO 1015, 1030, 1040
1013 VCF%=0: GOTO 820
1014 ' ---------- Hold run ---------------
1015 IF BAT$<>"" THEN INPUT #5,CPT%,HOLD,SWEEP0%,LOD$: GOTO 1019
1016 INPUT "COMPARTMENT, HOLD-V, # HOLD SWEEPS"; CPT%,HOLD,SWEEP0%
1017 IF CPT%=0 THEN GOTO 1000
1018 INPUT "SAVE TO FILE";LOD$
1019 IF PF% THEN LPRINT "VCLAMP OF CMPT "; CPT%;" HOLD=";HOLD;" FOR ";SWEEP0%;"SWEEPS; SAVED TO: ";LOD$
1020 U=0: X=0: X%=0: VC=HOLD: V(CPT%)=VC: SWEEP%=SWEEP0%: SWP%=2 '(FLG)
1022 IF SWEEP%>0 THEN GOTO 1024 ELSE IF LOD$<>"" OR LOD$<>"NONE" THEN GOSUB 1410: GOTO 1000 ELSE GOTO 1000
1024 CLS: PRINT "SWEEP";SWEEP0%-SWEEP%+1;" length=";XSCALE;"sec";"ISCALE=";ISCALE;"YSCALE=";YSCALE: GOSUB 1800
1026 GOSUB 1800: IF X<>0 THEN GOTO 1026
1028 SWEEP%=SWEEP%-1: GOTO 1022
1029 ' ------------ Single C-T paradigm --------
1030 IF BAT$<>"" THEN INPUT #5,CPT%,COND0,UCEND,TEST0,UEND,HOLD: GOTO 1035
1032 INPUT "COMPARTMENT TO CLAMP, COND-V, COND DURN, TEST-V, TEST DURN, HOLD-V"; CPT%,COND,UCEND,TEST,UEND,HOLD
1035 IF PF% THEN LPRINT "CMPT= ";CPT%;" COND-V=";COND;" DURN=";UCEND;"TEST-V=";TEST;" DURN=";UEND;" HOLD-V=";HOLD
1037 CLS: SWP%=1: UEND=UEND+UCEND: GOSUB 1070: CLS: GOTO 1000
1039 ' ------------ Multiple C-T paradigm ---------
1040 IF BAT$<>"" THEN INPUT #5,CPT%,COND0,UCEND,DCOND,NCOND%,TEST0,UEND,DTEST,NTEST%,LOD$,IVFILE$: GOTO 1045
1041 INPUT "COMPARTMENT TO CLAMP, INITIAL COND-V, COND DURN, COND-INC, #-COND";CPT%,COND0,UCEND,DCOND,NCOND%
1042 INPUT "INITIAL TEST-V, SAMPLE TIME, TEST-INC, #-TEST"; TEST0,UEND,DTEST,NTEST%
1044 INPUT ".SAV-FILE NAME (incl ext), STORAGE FILE NAME (or 'NONE')";LOD$,IVFILE$
1045 IF IVFILE$<>"NONE" AND IVFILE$<>"none" THEN OPEN "O",#4,IVFILE$: PRINT#4,CHR$(34);IVFILE$;" from ";LOD$;" using ";PFILE$;CHR$(34);CPT%;UCEND;UEND
1047 SWP%=2
1048 IF PF% THEN LPRINT "MULTIPLE CT RUN TO COMPARTMENT";CPT%;
1050 IF PF% THEN LPRINT " COND-V0=";COND0;"COND-DUR=";UCEND;"COND-STEP=";DCOND;"NCOND=";NCOND%;
1051 IF PF% THEN LPRINT "TEST-V0=";TEST0;"SAMPLE TIME=";UEND;"TEST_STEP=";DTEST;"#-TEST=";NTEST%
1052 IF PF% THEN LPRINT ".SAV FILE=";LOD$;" IV-FILE=";IVFILE$
1054 UEND=UEND+UCEND
1055 CLS: COND=COND0: TEST=TEST0
1056 FOR VCNT1%=1 TO NCOND%
1057 FOR VCNT2%=1 TO NTEST%
1058 GOSUB 1515: GOSUB 1070 'RESTORE INITIAL STATE & OUTPUT PULSE SEQ
1060 IF IVFILE$<>"NONE" AND IVFILE$<>"none" THEN PRINT #4, COND,TEST,II(CPT%)-IM(CPT%)
1061 TEST=TEST+DTEST
1062 NEXT VCNT2%
1064 COND=COND+DCOND: TEST=TEST0
1066 NEXT VCNT1%
1067 CLOSE #4
1068 IF BAT$="" THEN GOSUB 2100: CLS: GOTO 1000 ELSE CLS: GOTO 1000
1069 '----------- Output of 1 C-T episode -------------
1070 X=0: U=0: X%=0: VC=COND: V(CPT%)=VC
1071 CLS: LOCATE 1,1: PRINT "COND=";COND;" TEST=";TEST;" HOLD=";HOLD;" "
1072 GOSUB 1800: IF X=0 THEN PRINT "PREMATURE END": SWP%=0: RETURN 'COND
1076 IF U"" THEN INPUT #5,CPT%,POOLINC: GOTO 1092
1091 INPUT "POOL#, INCREMENT"; CPT%, POOLINC
1092 IF CPT%=0 THEN GOTO 820
1094 IF PF% THEN LPRINT "POOL INCREMENT IN POOL "; CPT%; " BY"; POOLINC
1096 XPOOL(CPT%)=XPOOL(CPT%)+POOLINC
1098 GOTO 815
1099 '**************** 6: Toxin selection ****************************
1100 IF BAT$<>"" THEN INPUT #5, J%,TXFLG%(J%): PRINT "TOXIN:";J%;TXFLG%(J%):GOTO 820
1101 PRINT "UNBLOCKED CODES: ";
1102 FOR J%=2 TO NCODE%
1104 IF NOT TXFLG%(J%) THEN GOSUB 150: PRINT J$;" ";
1105 NEXT J%: PRINT
1110 INPUT "TOXIN (TRIGR, ELECTN, HH, etc.):";J$: IF J$="" THEN GOTO 820
1112 GOSUB 100
1115 IF TXFLG%(J%) THEN PRINT "BLOCKED: "; ELSE PRINT "UNBLOCKED: ";
1120 INPUT "INPUT 'U' TO UNBLOCK, 'B' TO BLOCK";TXFLG$
1122 IF TXFLG$="b" OR TXFLG$="B" THEN TXFLG%(J%)=-1: GOTO 1125
1123 IF TXFLG$="u" OR TXFLG$="U" THEN TXFLG%(J%)=0 ELSE PRINT "BAD RESPONSE": GOTO 1120
1125 IF PF% THEN LPRINT "TOXIN "; J$; "= "; TXFLG$
1130 GOTO 820
1194 '*********** 7: **************
1195 IF BAT$ <>"" THEN BAT$="": CLOSE #5: GOTO 820 'Turn off batch mode if on
1196 PRINT "BATCH FILE (";BATFILE$;")"; : INPUT BAT$ : IF BAT$="" THEN BAT$=BATFILE$
1197 OPEN "I", #5, BAT$
1198 GOTO 820
1199 '**************** 8: Change parameters *************************
1200 IF BAT$<>"" THEN INPUT #5,J$,XBRN%,XPRM%: GOTO 1205
1201 INPUT "CHANGE PARAMETER: BRANCH TYPE, BRANCH #, PARAMETER #";J$,XBRN%,XPRM%
1203 IF J$="" THEN GOTO 820
1205 GOSUB 100 : I% = J%
1210 IF J%=ELECTN% THEN K=GC(XBRN%,XPRM%): GOTO 1250 'CODES ELECTN & POOLK SPECIAL
1230 IF J%=POOLK% THEN K=K(XBRN%,XPRM%): GOTO 1250
1240 GOSUB 13000: IF ER% THEN GOTO 1290 'FETCH PARAMETER IN K
1250 PRINT "OLD VALUE =";K;
1252 IF BAT$<>"" THEN INPUT #5,K ELSE INPUT "NEW VALUE =";K
1255 IF PF% THEN LPRINT "PARAMETER ";:LPRINT J$;: LPRINT USING "## ";XBRN%;XPRM%;: LPRINT " NEW VALUE=";K
1260 IF J%=ELECTN% THEN GC(XBRN%,XPRM%)=K: GOTO 820
1270 IF J%=POOLK% THEN K(XBRN%,XPRM%)=K: GOTO 820
1280 GOSUB 16000 'SAVE NEW VALUE
1290 IF ER% THEN ER%=0: INPUT " TYPE ANY KEY";A$
1295 GOTO 820
1298 '
1299 '**************** 9: Output file set-up subroutine *************
1300 IF BAT$<>"" THEN INPUT #5,OFILE$: SF%=-1: GOTO 1325
1305 IF SF% THEN SF%=0: GOTO 820 ELSE SF%=-1 'TOGGLE DISK OUTPUT FLAG
1310 IF SF% THEN INPUT "OUTPUT FILE NAME (no .EXT)"; OFILE$
1320 IF OFILE$ = "" THEN SF%=0: GOTO 820
1325 OPEN "O",#2, OFILE$+".PRN": IF PF% THEN LPRINT "OUTPUT FILES: "; OFILE$; ".PRN+.SPK"
1330 OPEN "O", #3, OFILE$ + ".SPK"
1335 IF PF% THEN LPRINT "OUTPUT START TIME =";U
1340 GOTO 820
1398 '
1399 '**************** 10: Save state ********************************
1400 IF BAT$<>"" THEN INPUT #5,LOD$: GOTO 1405
1401 INPUT "SAVE STATE AS FILE"; LOD$: IF LOD$ = "" THEN GOTO 820
1405 GOSUB 1410: GOTO 820
1409 '----------------- Subroutine entry (from 1022) ----------
1410 OPEN "O", #1, LOD$: LOD0$=LOD$
1412 PRINT #1, CHR$(34); PFILE$; CHR$(34); ","; '.PRM FILE NAME
1415 PRINT #1, U; SUMTB0%
1420 FOR I%=1 TO N%: PRINT#1, V(I%);: NEXT I%: PRINT#1, "" ' SAVE CMPT V'S
1425 FOR J% = 1 TO HIBR% 'SAVE STATE VARIABLES
1430 IF J% = TRIGR% THEN GOTO 1460
1435 IF N%(J%)=0 THEN GOTO 1460
1440 FOR K% = 1 TO N%(J%)
1445 IF CP%(K%, J%) = 0 THEN GOTO 1455
1447 PRINT #1, J%; K%;
1450 ON J% GOSUB 7010,7020,7030,7040,7050,7060,7070,7080,7090,7100,7110,7120,7130,7140,7150,7160,7170,7180,7190,7200,7210,7220
1453 PRINT #1, ""
1455 NEXT K%
1460 NEXT J%
1462 IF N%(POOL%)=0 THEN GOTO 1464
1463 FOR K%=1 TO N%(POOL%): PRINT #1,"POOL,";K%;",";XPOOL(K%): NEXT K% 'SAVE POOLS
1464 PRINT#1,"0,0" 'BLOCK TERM.
1465 IF N%(SPIKE%)=0 THEN GOTO 1475
1470 FOR K%=1 TO N%(SPIKE%):PRINT#1,REFR%(K%);:NEXT K%:PRINT #1,"" 'SPIKE REFRs
1475 IF N%(SYNAPSE%)=0 THEN GOTO 1490
1478 FOR J%=1 TO N%(SYNAPSE%) 'SAVE PSP'S
1480 FOR T%=0 TO SUMTBL%
1482 PRINT #1, SUMTB(J%, T%);
1484 NEXT T%: PRINT #1, ""
1486 NEXT J%
1490 PRINT#1,"END": CLOSE #1
1495 RETURN
1499 '**************** 11: Restore state variables *****
1500 IF BAT$<>"" THEN INPUT #5, LOD$: GOTO 1507
1501 PRINT "RESTORE FROM FILE (default=";LOD0$;: INPUT "):";LOD$
1505 IF LOD$ = "" THEN LOD$=LOD0$
1507 LOD0$=LOD$: IF LOD$="NONE" THEN GOTO 820
1510 GOSUB 1515
1513 GOTO 820
1514 '----------- Restore subroutine entry (called by 1057 and 1510) ------
1515 OPEN "I", #1, LOD$
1518 INPUT #1, PFILEE$
1520 IF PFILEE$ <> PFILE$ THEN PRINT "1520: WRONG SAVE FILE":CLOSE #1:LOD$ = "": return
1525 INPUT #1, U, SUMTB0%
1530 FOR I%=1 TO N%: INPUT#1, V(I%): NEXT I% 'COMPARTMENT VOLTAGES
1535 INPUT #1, J%, K% 'BRANCH TYPE, BRANCH INDEX
1540 IF J%=0 THEN GOTO 1560
1545 ON J% GOSUB 7510,7520,7530,7540,7550,7560,7570,7580,7590,7600,7610,7620,7630,7640,7650,7660,7670,7680,7690,7700,7710,7720
1550 GOTO 1535
1560 IF N%(SPIKE%)=0 THEN GOTO 1570
1565 FOR K%=1 TO N%(SPIKE%): INPUT#1, REFR%(K%): NEXT K% 'LOAD SPIKE REFR%s
1570 IF N%(SYNAPSE%)=0 THEN GOTO 1585
1572 FOR J%=1 TO N%(SYNAPSE%) 'LOAD PSP'S
1574 FOR T%=0 TO SUMTBL%
1576 INPUT #1, SUMTB(J%, T%)
1578 NEXT T%
1580 NEXT J%
1585 INPUT#1, A$: IF A$<>"END" THEN PRINT "1585: SAVE FILE END ERROR"
1590 CLOSE #1
1595 RETURN
1598 '****************** 12: Display-parameter handling *****
1599 ' (accessed by 1696 and 2220)
1600 ON DSPLYB% GOTO
1610,1620,1679,1679,1679,1679,1679,1630,1640,1650,1660,1665
1605 IF DSPLYB%=20 THEN Y=POOL(K%): YSCALE=PSCALE: RETURN ELSE PRINT "BAD BRANCH REQ:";DSPLYB%: RETURN
1610 ON DSPLYV% GOTO 1613,1614 'CMPT
1612 Y=V(K%): YSCALE=VSCALE
IF VCF% AND K%=CPT% THEN 'Voltage clamp shows current
Y=II(K%)-IM(K%) 'in clamped compartment.
YSCALE=ISCALE
PCOL%=ICOL%
RETURN
ELSE
PCOL%=VCOL%
RETURN 'if DSPLYV%=0, display voltage
END IF
1613 Y=II(K%): YSCALE=ISCALE: RETURN
1614 Y=GI(K%): YSCALE=GSCALE: RETURN
1620 ON DSPLYV% GOTO 1622,1623,1624,1625,1626,1627,1628 'TRIGR
1621 GOTO 1679
1622 Y=I(K%,TRIGR%): YSCALE=ISCALE: RETURN
1623 Y=G(K%,TRIGR%): YSCALE=GSCALE: RETURN
1624 Y=VM(K%): YSCALE=VSCALE: RETURN
1625 Y=EX(K%): YSCALE=VSCALE: RETURN
1626 Y=W(K%): YSCALE=VSCALE: RETURN
1627 Y=P(K%): YSCALE=VSCALE: RETURN
1628 Y=THR(K%): YSCALE=VSCALE: RETURN
1630 ON DSPLYV% GOTO 1632,1633,1634,1635,1636,1637 'DRIVER
1631 GOTO 1679
1632 Y=I(K%,DRIVER%): YSCALE=ISCALE: RETURN
1633 Y=G(K%,DRIVER%): YSCALE=GSCALE: RETURN
1634 Y=GNA(K%): YSCALE=GSCALE: RETURN
1635 Y=GK(K%): YSCALE=GSCALE: RETURN
1636 Y=GK1(K%): YSCALE=GSCALE: RETURN
1637 Y=GK2(K%):SCALE=GSCALE: RETURN
1640 ON DSPLYV% GOTO 1642,1643,1644,1645 'HHFXD
1641 GOTO 1679
1642 Y=I(K%,HHFXD%): YSCALE=ISCALE: RETURN
1643 Y=G(K%,HHFXD%): YSCALE=ISCALE: RETURN
1644 Y=M(K%): YSCALE=1: RETURN
1645 Y=H(K%): YSCALE=1: RETURN
1650 ON DSPLYV% GOTO 1652,1653,1654,1655,1656,1657,1658,1659 'HH
1651 GOTO 1679
1652 Y=I(K%,HH%): YSCALE=ISCALE: RETURN
1653 Y=G(K%,HH%): YSCALE=GSCALE: RETURN
1654 Y=MHH(K%): YSCALE=1: RETURN
1655 Y=ALPHAM(K%): YSCALE=KSCALE: RETURN
1656 Y=BETAM(K%): YSCALE=KSCALE: RETURN
1657 Y=HHH(K%): YSCALE=1: RETURN
1658 Y=ALPHAH(K%): YSCALE=KSCALE: RETURN
1659 Y=BETAH(K%): YSCALE=KSCALE: RETURN
1660 ON DSPLYV% GOTO 1662,1663 'SYNAPSE
1661 GOTO 1679
1662 Y=I(K%,SYNAPSE%): YSCALE=ISCALE: RETURN
1663 Y=G(K%,SYNAPSE%): YSCALE=GSCALE: RETURN
1665 ON DSPLYV% GOTO 1667,1668 'CHEMOX
1666 GOTO 1679
1667 Y=I(K%,CHEMOX%): YSCALE=ISCALE: RETURN
1668 Y=G(K%,CHEMOX%): YSCALE=GSCALE: RETURN
1679 PRINT "BAD DISPLAY PARAMETER REQUEST: BRANCH=";DSPLYB%;" PARAMETER=";DSPLYV%: RETURN
1680 IF BAT$<>"" THEN INPUT #5,DSPLYP%,DSPLYV%,Y0: GOTO 820
1681 INPUT "BRANCH-TYPE TO DISPLAY (CMPT, TRIGR, DRIVER, HHFXD, HH, SYNAPSE); OFFSET";J$,Y0
1682 GOSUB 100 : DSPLYB%=J% : ON DSPLYB% GOTO
1683,1684,1697,1697,1697,1697,1688,1689,1690,1691,1692
1683 J%=2: GOTO 1695 'CMPT
1684 D$(3)="VM": D$(4)="EX": D$(5)="W": D$(6)="P": D$(7)="THR": J%=7: GOTO
1695 'TRIGR
1688 D$(3)="GNA": D$(4)="GK": D$(5)="GK1": D$(6)="GK2": J%=6:GOTO 1695 'DRIVER
1689 D$(3)="M": D$(4)="H": J%=4: GOTO 1695 'HHFXD
1690 D$(3)="ALPHAM": D$(4)="BETAM": D$(5)="ALPHAH": D$(6)="BETAH": J%=6: GOTO 1695 'HH
1691 J%=2: GOTO 1695 'SYNAPSE
1692 J%=2: GOTO 1695 'CHEMOX
1695 PRINT J$;: FOR I%=1 TO J%: PRINT USING "; ##=";I%;: PRINT D$(I%);: NEXT I%: INPUT DSPLYV%
1696 GOSUB 1600 : GOTO 820
1697 PRINT "ILLEGAL BRANCH TYPE": GOTO 1680
1699 '**************** 13: Options *********
1700 IF BAT$<>"" THEN INPUT #5, OM%,J%: GOTO 1760 ELSE PRINT "OPTIONS MENU"
1701 PRINT " 1=TIME RESET: Change U-variable reset flag"
1702 PRINT " 2=BELL: Turn bell on/off"
1703 PRINT " 3=ZERO-PLOT: Turn plot on/off"
1704 PRINT " 4=SPIKE-TIC: Turn on/off"
1705 PRINT " 5=Y_OFFSET: new value"
1706 PRINT " 6=DEBUG_MODE: turn on/off"
1707 PRINT " 7=PRINT protocol flag on/off"
1710 INPUT OM%
1711 ON OM% GOTO 1722,1724,1726,1728,1730,1732,1734
1719 '---
1722 IF RST% THEN A$="ON" ELSE A$="OFF"
1723 PRINT "U-RESET IS ";A$;C$="; NEW STATUS (ON/OFF)": GOTO 1750
1724 IF BLF% THEN A$="ON" ELSE A$="OFF"
1725 PRINT "BELL IS ";A$;"; NEW STATUS (ON/OFF)": GOTO 1750
1726 IF ZPF% THEN A$="ON" ELSE A$="OFF"
1727 PRINT "ZERO-PLOT IS ";A$;"; NEW STATUS (ON/OFF)": GOTO 1750
1728 IF SPF% THEN A$="ON" ELSE A$="OFF"
1729 PRINT "SPIKE-PLOT IS ";A$;"; NEW STATUS (ON/OFF)": GOTO 1750
1730 PRINT "Y0=";Y0;"; NEW Y0": GOTO 1750
1732 IF DBF% THEN A$="ON" ELSE A$="OFF"
1733 PRINT "DEBUG FLAG IS ";A$;"; NEW STATUS (ON/OFF)": GOTO 1750
1734 IF PF% THEN A$="ON" ELSE A$="OFF"
1735 PRINT "PLOT FLAG IS ";A$;"; NEW STATUS (ON/OFF)": GOTO 1750
1749 '---
1750 INPUT A$
1755 IF A$="ON" OR A$="on" THEN J%=-1 ELSE J%=0
1759 '--- (BAT$ reentry)
1760 ON OM% GOTO 1762,1764,1766,1768,1770,1772: GOTO 820
1762 RST%=J%: GOTO 820
1764 BLF%=J%: GOTO 820
1766 ZPF%=J%: GOTO 820
1768 SPF%=J%: GOTO 820
1770 Y0=VAL(A$): GOTO 820
1772 DBF%=J%: IF BAT$<>"" THEN INPUT #5,DBGI%: ELSE INPUT "DEBUG ITERATIONS:";DBGI%: GOTO 820
1773 GOTO 820
1774 PF%=J%: GOTO 820
1799 '**************** ONE TIME INCREMENT OF MODEL *******
1800 GOSUB 3000: IF VCF% THEN V(CPT%)=VC 'KINETIC CALCULATIONS
1805 GOSUB 2000 'PLOTS
1810 FOR I%=1 TO NSPF%: SPKFLG%(I%)=0: NEXT I% 'CLEAR SPIKE FLAGS
1820 if inkey$=chr$(27) then end
1830 RETURN
1899 '**************** Flag/Switch print-out subroutine ***********
1900 PRINT "UNBLOCKED BRANCH TYPES: "; :IF PF% THEN LPRINT "UNBLOCKED BRANCH TYPES: ";
1910 FOR J%=2 TO NCODE%
1920 IF NOT TXFLG%(J%) THEN GOSUB 150: PRINT J$;" ";: IF PF% THEN LPRINT J$;" ";
1930 NEXT J%: PRINT : IF PF% THEN LPRINT
1940 J%=DSPLYB%: GOSUB 150
1950 PRINT "DISPLAY/WRITE BRANCH-TYPE & VARIABLE:";J$;"/";D$(DSPLYV%)
1960 IF SF% AND PF% THEN LPRINT ".PRN FILE COLUMNS (Branch-type & variable):";J$;"/";D$(DSPLYV%)
1990 RETURN
1995 ' ###############
1996 '####################### PLOTS #####
1997 ' ###############
2000 SKPCNT%=SKPCNT%+1: IF SKPCNT%=SKIP% THEN SKPCNT%=0
2005 IF SKPCNT%=0 THEN GOSUB 2200 'PLOT EVERY SKIPCOUNT
2015 IF N%(TRIGR%)=0 OR TXFLG%(TRIGR%) THEN GOTO 2050
2020 FOR I%=1 TO N%(TRIGR%) 'PLOT TRIGR SPIKES
2025 J%=CP%(I%,TRIGR%)
2030 IF SPKFLG%(I%) THEN LINE (XXX, J%*(SCY%+1)/(N%+1)) - (XXX, 5+J%*(SCY%+1)/(N%+1)),scol%
2035 IF SPKFLG%(I%) AND SF% THEN PRINT #3, I%; X 'WRITE TIME TO .SPK FILE
2040 IF SPKFLG%(I%) AND SPF% THEN V(J%)=V(J%)+SPKHT: GOSUB 2200: V(J%)=V(J%)-SPKHT: GOSUB 2200: X%=X%-2
2045 NEXT I%
2050 IF N%(SPIKE%)=0 OR TXFLG%(SPIKE%) THEN GOTO 2075 'PLOT CODE SPIKE% SPIKES
2055 FOR I%=1 TO N%(SPIKE%)
2060 J%=CP%(I%,SPIKE%)
2065 IF SPKFLG%(SPF%(I%)) AND SPF% THEN V(J%)=V(J%)+SPKHT: GOSUB 2200: V(J%)=V(J%)-SPKHT: GOSUB 2200: X%=X%-2
2070 NEXT I%
2075 IF N%(POOL%)=0 THEN GOTO 2080
2076 LOCATE 1,1: PRINT USING "T= ##.### ";U;
2077 FOR K%=1 TO N%(POOL%): PRINT "POOL(";K%;:PRINT USING ")= ##.#####";XPOOL(K%);: NEXT K%: PRINT " "
3078 PRINT " ";: FOR K%=1 TO N%(POOLX%): PRINT "TARG(";K%;:PRINT USING ")= ##.###; ";TARG(K%);: NEXT K%: PRINT " "
2080 U= U+TINC: X=X+TINC 'INCREMENT MODEL TIME
2085 IF X1 THEN RETURN 'ABORT END-OF-RUN DSPLY ON MULTIPLE SWPS
if bat$<>"" THEN
locate 24,1
print "Press any key to display cursor.";
st=timer
foo%=0
do
ft=timer
A$=inkey$
if A$<>"" THEN 'go to cursor display if keypress
locate 24,1
print space$(40);
foo%=-1
end if
if (ft-st)>mdly then RETURN 'RETURN if too much time
loop while not foo% 'elapses
end if
2096 IF BLF% THEN PRINT CHR$(7);CHR$(7);CHR$(7);CHR$(7);
2099 '**************** End-of-run cursor-accessed display **************
2100 I%=1: XXX=0: YYY=0: F%=2: M%=1: XF%=1: YF=0 'F%,M%=FIXED,MVBL CURSORS
2105 for k% = 1 to n%(dsplyb%) 'load appropriate Yscales.
gosub 1600
yscale(k%) = YSCALE
pcol%(k%) = pcol%
next k%
2109 locate 24,1: print space$(79);: locate 24,1
2110 PRINT "SWEEP COMPLETE: TO MAIN MENU";
2130 A$ = INKEY$ 'Key-based cursor read-out mode
2135 IF A$ = "" THEN GOTO 2130 'I%= Trace#; X%= TimePoint#
2137 A$=RIGHT$(A$,1) 'Lop off possible space character
2138 A%=ASC(A$)
2140 IF A%=5 OR A%=72 THEN I%=I%-1: IF I%<1 THEN I%=1: GOTO 2170 ELSE GOTO
2170 'ctrl-E or up arrow
2141 IF A%=73 THEN I%=1: GOTO 2170
2142 IF A%=24 OR A%=80 THEN I%=I%+1: IF I%>N%(DSPLYB%) THEN I%=N%(DSPLYB%): GOTO 2170 ELSE GOTO 2170 'ctrl-X or down arrow
2143 IF A%=81 THEN I%=N%(DSPLYB%): GOTO 2170
2144 IF A%=19 OR A%=75 THEN X%=X%-1: IF X%<0 THEN X%=0: GOTO 2170 'Ctl-S or Left arrow
2146 IF A%=4 OR A%=77 THEN X%=X%+1: IF X%>XSCALE/TINC THEN X%=XSCALE/TINC: GOTO 2170 'Ctl-D or Right arrow
2148 IF A%=1 OR A%=115 THEN X%=X%-XSCALE/TINC/SKIP%/FRCT%: IF X%<1 THEN X%=0: GOTO 2170 'Ctl-A or Ctl-left-arrow
2150 IF A%=6 OR A%=116 THEN X%=X%+XSCALE/TINC/SKIP%/FRCT%: IF X%>XSCALE/TINC/SKIP% THEN X%=XSCALE/TINC/SKIP%: GOTO 2170 'Ctl-F or Ctl-right-arrow
2152 IF A%=27 THEN X=0: X%=0: GOTO 2195 ' TO RETURN
2154 IF A%=71 THEN X%=0 'Ctl-Left arrow
2156 IF A%=79 THEN X%=XSCALE/TINC/SKIP% 'Ctl-Right arrow
2158 IF A%=22 OR A%=82 THEN SWAP X%,XF%: SWAP F%,M%: SWAP Y,YF: GOTO 2172 'Ctl-V or Ins
2160 IF A%=48 THEN FRCT%=FRCT%*10 '0
2161 IF A%=49 THEN FRCT%=2 '1
2162 IF A%=50 THEN FRCT%=5 '2
2163 IF A%=51 THEN FRCT%=10 '3
2164 IF A%=52 THEN FRCT%=20 '4
2165 IF A%=53 THEN FRCT%=50 '5
2166 IF A%=54 THEN FRCT%=100 '6
2167 IF A%=55 THEN FRCT%=200 '7
2168 IF A%=56 THEN FRCT%=500 '8
2169 IF A%=57 THEN FRCT%=1000 '9
2170 yscale = yscale(I%) 'restore stored YSCALE
2172 LINE (XXX, YYY-5*M%)-(XXX, YYY+5*M%),0: PSET (XXX,YYY),pcol% 'Erase old line (not pt)
2173 X=(X%-1)*TINC*SKIP%: Y=Y(I%,X%)+Y0
2175 XXX= X*SCX%/XSCALE: YYY= I%*(SCY%+1)/(N%+1) - Y*SCY%/YSCALE
2177 LINE (XXX, YYY-5*M%) - (XXX, YYY+5*M%)
2180 LOCATE M%,1: PRINT USING "T= ###.#### ";U-XSCALE+X;: PRINT T$;": ";D$(DSPLYV%);: PRINT USING " ####.## ";Y-Y0;
2182 LOCATE 1,40: PRINT USING "DELTA-T= ###.#### ";SKIP%*TINC*ABS(X%-XF%);: IF X%<>XF% THEN PRINT USING "1/DELTA-T= ####.## ";1/(TINC*ABS(X%-XF%)*SKIP%);
2184 LOCATE 2,40: PRINT USING "DELTA-Y= ####.## ";ABS(Y-YF);
2185 GOTO 2130
2195 RETURN
2198 '******* Display variable retrieval, file output, and plot-call *****
2200 IF SF% THEN PRINT #2, U; 'WRITE TIME VALUE ON DISK
if zpf% then 'plot zero line before..avoid
for k%=1 to n%(dsplyb%) 'overwriting important stuff
pset(XXX+1,(SCY%+1)*K%/(n%(dsplyb%)+1)),zcol% 'with a zero-line.
next k%
end if
2210 FOR K%=1 TO N%(DSPLYB%) 'DISPLAY FOR EACH OCCURRENCE OF VRBL
2220 GOSUB 1600 'GET DISPLAY VARIABLE VALUE
2230 Y(K%,X%)=Y 'PLACE IN DISPLAY BUFFER
2240 IF SF% THEN PRINT #2, Y; 'WRITE VARIABLE VALUE ON DISK
2250 GOSUB 2300 'PLOT
2260 NEXT K%
2270 X%=X%+1
2290 IF SF% THEN PRINT #2, ""
2295 RETURN
2298 '**************** Plot subroutines ***************************
2300 if pcol%=0 then pcol%=ncol% 'use default color if none is specified.
2305 XXX= X*SCX%/XSCALE: YYY= K%*(SCY%+1)/(N%+1) - (Y+Y0)*SCY%/YSCALE 'NORMAL PLOT
2310 PSET (XXX, YYY),pcol%
2330 RETURN
' 2400 not used.
2400 LINE (XXX, YYY)-(XXX, (SCY%+1)-I%*50 - (Y+Y0+SPKHT)*SCY%/YSCALE),scol% 'SPIKE PLOT
2410 RETURN
2991 '
2993 ' #######################
2995 '######################### NETWRK SUBROUTINE #####
2997 ' #######################
3000 TRGFLG% = 0
3009 '##################################
3010 '# PATCH: SUM ALL BRANCH CURRENTS #
3011 '##################################
3020 FOR I% = 1 TO N%: GOSUB 4010: NEXT I% 'CURRENT FROM PRINCIPAL CMPT
3030 FOR J% = LOWBR% TO HIBR% 'STEP THROUGH ALL BRANCH CODES (>lowbr)
3040 IF N%(J%)=0 OR TXFLG%(J%) THEN GOTO 3100 'SKIP VACANT & BLOCKED BRNCHS
3050 FOR K% = 1 TO N%(J%)
3060 I% = CP%(K%, J%): IF I% = 0 THEN GOTO 3100 'SET I% TO CMPT #
3070 II(I%) = II(I%) + I(K%, J%) 'SUM COMPARTMENT CURRENTS FROM EA BRNCH
3080 GI(I%) = GI(I%) + G(K%, J%) 'SUM CONDUCTANCES FROM EACH BRANCH
3090 NEXT K%
3100 NEXT J%
3110 FOR I% = 1 TO N% 'SUM I FROM OTHER CMPTS
3120 IM(I%) = IM0(I%)+INJ(I%) 'I FROM STIM + POOL-INJECTED
3125 IF TXFLG%(ELECTN%) THEN GOTO 3180
3130 FOR J% = 1 TO N%
3140 IF J% = I% THEN GOTO 3170
3150 IF GC(I%, J%) = 0 AND GC(J%, I%) = 0 THEN GOTO 3170
3160 IM(I%)=IM(I%) - (V(J%)>V(I%))*(V(J%)-V(I%))*GC(I%,J%) - (V(J%)<=V(I%))*(V(J%)-V(I%))*GC(J%,I%)
3170 NEXT J%
3180 NEXT I%
3190 FOR I%=1 TO N% 'CHARGE CAPACITANCE
3200 DV(I%)=(IM(I%)-II(I%))*TINC/C(I%)
3210 IF DBF% <> 0 THEN PRINT "3210: PATCH: I%="; I%; "II="; II(I%); " GI="; GI(I%); " DV="; DV(I%); "V="; V(I%)
3220 NEXT I%
3228 '########################
3230 '# TRIGR BRANCH UPDATES # TRIGGER ZONE KINETICS AND SPIKES
3232 '########################
3240 IF TXFLG%(TRIGR%) GOTO 3300
3250 FOR I%=1 TO N%(TRIGR%)
3260 VA(I%) = V(CP%(I%,TRIGR%))-VLK(CP%(I%,TRIGR%))
3270 GOSUB 4070 'TRIGR
3280 IF NOT SPKFLG%(I%) THEN GOTO 3295
3290 GOSUB 4590 'SPIKE
3295 NEXT I%
3296 '########################
3297 '# SPIKE BRANCH UPDATES #
3298 '########################
3300 IF TXFLG%(SPIKE%) THEN GOTO 3360
3310 FOR I%=1 TO N%(SPIKE%) 'SET SPKFLG% IF V JUST CROSSED ONTHR
3320 IF V(CP%(I%,SPIKE%))>ONTHR(I%) AND NOT REFR%(I%) THEN SPKFLG%(SPKF%(I%))=-1: REFR%(I%)=-1
3340 IF V(CP%(I%,SPIKE%))SUMTBL% THEN SUMTB0%= 1 'STROBE SUMTB
3950 RETURN 'END OF NETWRK SUBRTN
3992 '
3993 ' ########################################
3994 '################ SUBROUTINES FOR BRANCH-TYPE UPDATES #####
3995 ' ########################################
3996 ' Subroutines to compute branch conductances, G(K%,J%), and
3997 ' ionic currents, I(K%,J%), from state variables, then update
3998 ' the variables with their assigned kinetics.
3999 '
4000 '******************** CODE CMPT: PRINCIPAL CELL CMPT *****
4010 II(I%) = GL(I%)*(V(I%)-VLK(I%)): GI(I%) = GL(I%)
4020 IF DBF% <> 0 THEN PRINT "4020: CODE 1: I%="; I%
4030 RETURN
4040 '
4050 '******************** CODE TRIGR: TRIGGER ZONE BRANCH *******
4060 'DESTROYS V,PMTHR,GM,DPM,DPG,DPL,DPH,XX,YY
4070 IF TXFLG%(TRIGR%) THEN RETURN
4090 V = VM(I%): PMTHR = PMTHR(I%): PM = P(I%)
4100 IF DBF% <> 0 THEN PRINT "4100: I%="; I%; "VM="; VM(I%); "THR="; THR(I%)
4110 IF NOT TRGFLG% THEN GOTO 4130 'TRGFLG% TRUE CAUSES ANTIDROMIC RESETS
4120 IF SPKFLG%(I%) OR V>THR(I%) THEN GOSUB 4590: SPKFLG%(I%)=0
4130 XSS(I%) = THR(I%) - V
4140 GM = GE(I%) + GS(I%) + 1 'GS()=COND (Spike); GE()=CONDCT (Active)
4150 TAU = TAUM0(I%) / GM
4160 EX(I%) = E0(I%) + (VA(I%)+EI(I%)-A1(I%)-A2(I%)-AR(I%))/GM: EX=EX(I%)
4170 CHI=E0(I%) + (VA(I%)+EI(I%)+(NOT ADPFLG%)*(A1(I%)+A2(I%)+AR(I%)))/GM
4180 '
4190 '********* Perturbation calculation **********
4200 W(I%) = W(I%) - W(I%) * TINC / TAU
4210 '
4220 '********* Current Contrib Calculation *******
4230 'IF CURFLG% THEN DJ=(EI(I%)/GM-J(I%))*TINC/TAU: J(I%)=J(I%)+DJ: GOTO
4280 'V2.4 RELIC
4240 DJ = EI(I%) - J(I%): W(I%) = W(I%) - DJ
4250 J(I%) = EI(I%)
4260 '
4270 '********* PM Potential **********************
4280 DPM = (EX - PMTHR) * KPM(I%)
4290 IF DPM < 0 THEN DPM = 0
4300 DPM = DPM - PM
4310 IF DPM < 0 THEN TAUPM = TAU ELSE TAUPM = TAUPM(I%)
4320 DPM = DPM * TINC / TAUPM: DPL = -P(I%) * TINC / TAU
4330 '******* FINAL VOLTAGE & PM DET WITH COMP FOR MID-TINC PMTHR XING
4340 IF V <= PMTHR THEN DPG = DPM: DPH = DPL ELSE DPG = DPL: DPH = DPM
4350 P(I%) = P(I%) + DPG
4360 VM(I%) = EX(I%) + P(I%) + W(I%) + DJ
4370 IF TAUAR(I%) <> 0 THEN VM(I%) = VM(I%) - (KAR(I%) * CHI - AR(I%)) * TINC / TAUAR(I%)
4380 L = VM(I%) - PMTHR
4390 IF V = PMTHR THEN IF L <= 0 THEN GOTO 4470 ELSE GOTO 4410
4400 IF (PMTHR - V) * L < 0 THEN GOTO 4470 'IF CROSSING, FIX VM
4410 IF VM(I%) = V THEN GOTO 4470
4420 XX=DPG*DPL/(VM(I%)-V): YY=DPH*DPL/(VM(I%)-V) 'FRACTIONAL POST-XING TINC
4430 VM(I%) = VM(I%) - XX + YY
4440 P(I%) = PM - XX + YY
4450 '
4460 '********* Exponential Decays ****************
4470 IF TAUCOND(I%) <> 0 THEN GS(I%) = GS(I%) + (CHI * KCOND(I%) - GS(I%)) * TINC / TAUCOND(I%)
4480 IF GS(I%) <= -1 THEN GS(I%) = -1
4490 IF TAUAR(I%) <> 0 THEN AR(I%) = AR(I%) + (CHI * KAR(I%) - AR(I%)) * TINC / TAUAR(I%)
4500 IF TAUA1(I%) <> 0 THEN A1(I%) = A1(I%) + (CHI * KA1(I%) - A1(I%)) * TINC / TAUA1(I%)
4510 IF TAUA2(I%) <> 0 THEN A2(I%) = A2(I%) + (CHI * KA2(I%) - A2(I%)) * TINC / TAUA2(I%)
4520 IF TAUTHR(I%) <> 0 THEN THR(I%) = THR(I%) + (CHI * KTHR(I%) - THR(I%) + THRINF(I%)) * TINC / TAUTHR(I%)
4530 '
4540 '********* Test for Spike Conditions *********
4550 IF VM(I%)>THR(I%) THEN SPKFLG%(I%)=-1
4560 RETURN
4570 '
4580 '****************** SPIKE ********************
4590 'Requires I% set to cell #
4600 GOTO 4655 'PATCH AROUND QUANTIZATION CORRN
4605 G = THR(I%)-VM(I%): IF G>0 THEN GOTO 4630
4610 T = XSS(I%)-THR(I%)+VM(I%)
4615 T = XSS(I%)-G: IF T=0 THEN GOTO 4635
4620 T = G/T: IF T>=0 THEN GOTO 4630 'FRACTIONAL INTERVAL OVERSHOOT
4625 IF T >=-1 THEN GOTO 4635 'T MUST BE >=-1
4630 T = 0
4635 T = T*TINC: TINC0=TINC: TINC=T 'SPI.2
4640 TRGFLG% = 0 'DISARM SPIKE FIRING
4645 IF T = 0 THEN GOTO 4655
4650 GOSUB 4070 'TRIGR (Run backwards to thr xing)
4655 P(I%) = 0
4660 IF MAXG(I%)<>0 THEN GS(I%)=GS(I%)+DG0(I%)*(MAXG(I%)-GS(I%))/MAXG(I%) ELSE GS(I%) = GS(I%) * DG0(I%)'IF MAX=0, IS FLAG FOR % SCALING
4665 IF MAXAR(I%)<>0 THEN DAR=DAR(I%)*(MAXAR(I%)-AR(I%))/MAXAR(I%) ELSE DAR=(DAR(I%)-1)*AR(I%)
4670 AR(I%) = AR(I%)+DAR '(NEED DAR LATER TOO)
4675 IF MAXA1(I%)<>0 THEN A1(I%)=A1(I%)+DA1(I%)*(MAXA1(I%)-A1(I%))/MAXA1(I%) ELSE A1(I%)=A1(I%)*DA1(I%)
4680 IF MAXA2(I%)<>0 THEN A2(I%)=A2(I%)+DA2(I%)*(MAXA2(I%)-A2(I%))/MAXA2(I%) ELSE A2(I%) = A2(I%)*DA2(I%)
4685 IF MAXTHR(I%)<>0 THEN THR(I%)=THR(I%)+DTHR(I%)*(MAXTHR(I%)-THR(I%)+THRINF(I%))/MAXTHR(I%) ELSE THR(I%)=THRINF(I%)+(THR(I%)-THRINF(I%))*DTHR(I%)
4690 IF MAXV(I%)<>0 THEN VM(I%)=VM(I%)+DV0(I%)*(MAXV(I%)-VM(I%))/MAXV(I%)-DAR ELSE VM(I%)=VM(I%)*DV0(I%)-DAR
4695 W(I%)=VM(I%)-E0(I%)-(VA(I%)+EI(I%)-AR(I%)-A1(I%)-A2(I%))/GM
4696 RETURN
4698 '
4699 'COND: ************** CODE 7: FIXED CONDUCTANCE BRANCH *****
4700 I(K%, COND%) = G(K%, COND%)*(V(I%)-VCOND(K%))
4710 RETURN
4797 '
4798 'DRIVER: ************ CODE 8: DRIVER POTENTIAL BRANCH *****
4800 IF MUNA(K%)<>0 THEN GNA(K%)=GBARNA(K%)/(1+EXP((V0NA(K%)-V(I%))/MUNA(K%)))
4810 IF MUK(K%)<>0 THEN ACTK=1/(1+EXP((V0K(K%)-V(I%))/MUK(K%))) ELSE ACTK=0
4820 GK(K%)=GBARK(K%)*ACTK
4830 IF TAUK1(K%)<>0 THEN GK1(K%)=GK1(K%)+(GBARK1(K%)*ACTK-GK1(K%))*TINC/TAUK1(K%)
4840 IF TAUK2(K%)<>0 THEN GK2(K%)=GK2(K%)+(GBARK2(K%)*ACTK-GK2(K%))*TINC/TAUK2(K%)
4850 GKTOT(K%)=GK(K%)+GK1(K%)+GK2(K%)
4860 I(K%,DRIVER%)=GNA(K%)*(V(I%)-VNA(K%))+GKTOT(K%)*(V(I%)-VK(K%))
4870 G(K%,DRIVER%)=GNA(K%)+GKTOT(K%)
4880 IF DBF%<>0 THEN PRINT "4880: CODE 8: K%=";K%;" G=";G(K%, DRIVER%);" I="; I(K%, 8); " GK="; GK(K%); " GNA="; GNA(K%)
4890 RETURN
4898 '
4899 'ICALC: ************* CODE 9: FIXED TAU HH BRANCH *****
4900 IF QM(K%)=0 THEN M(K%)=1: GOTO 4930
4910 MINF = 1/(1+EXP((V0M(K%)-V(I%))/MUM(K%)))
4920 M(K%) = M(K%)+(MINF-M(K%))*TINC/TAUMA(K%)
4930 IF QH(K%)=0 THEN H(K%)=1: GOTO 4960
4940 HINF = 1/(1+EXP((V0H(K%)-V(I%))/MUH(K%)))
4950 H(K%) = H(K%)+(HINF-H(K%))*TINC/TAUH(K%)
4960 G(K%, HHFXD%) = GBAR(K%)*(M(K%)^QM(K%))*(H(K%)^QH(K%))
4970 I(K%, HHFXD%) = G(K%, HHFXD%)*(V(I%)-VEQ(K%))
4980 IF DBF%<>0 THEN PRINT "4980: CODE 9: K%="; K%; " G="; G(K%, HHFXD%); " I="; I(K%, 9); " M="; M(K%);" MINF=";MINF; "H="; H(K%);" HINF=";HINF
4990 RETURN
4998 '
4999 'HH: **************** CODE 10: FULL HH BRANCH *****
5000 IF QMHH(K%)=0 THEN MHH(K%)=1: GOTO 5040
5010 IF EAM(K%)=-1 AND V(I%)=-CAM(K%) THEN ALPHAM(K%)=BAM(K%)*DAM(K%) ELSE ALPHAM(K%)=(AAM(K%)+BAM(K%)*(V(I%)+CAM(K%)))/(EXP(-(V(I%)+CAM(K%))/DAM(K%))+EAM(K%))
5020 IF EBM(K%)=-1 AND V(I%)=-CBM(K%) THEN BETAM(K%)= BBM(K%)*DBM(K%) ELSE BETAM(K%) =(ABM(K%)+BBM(K%)*(V(I%)+CBM(K%)))/(EXP(-(V(I%)+CBM(K%))/DBM(K%))+EBM(K%))
5030 MHH(K%)=MHH(K%)+(ALPHAM(K%)*(1-MHH(K%))-BETAM(K%)*MHH(K%))*KTEMP(K%)*TINC
5040 IF QHHH(K%)=0 THEN HHH(K%)=1: GOTO 5080
5050 IF EAH(K%)=-1 AND V(I%)=-CAH(K%) THEN ALPHAH(K%)=AAH(K%)*DAH(K%) ELSE ALPHAH(K%)=(AAH(K%)+BAH(K%)*(V(I%)+CAH(K%)))/(EXP(-(V(I%)+CAH(K%))/DAH(K%))+EAH(K%))
5060 IF EBH(K%)=-1 AND V(I%)=-CBH(K%) THEN BETAH(K%)= BBH(K%)*DBH(K%) ELSE BETAH(K%) =(ABH(K%)+BBH(K%)*(V(I%)+CBH(K%)))/(EXP(-(V(I%)+CBH(K%))/DBH(K%))+EBH(K%))
5070 HHH(K%) = HHH(K%)+(ALPHAH(K%)*(1-HHH(K%))-BETAH(K%)*HHH(K%))*KTEMP(K%)*TINC
5080 G(K%,HH%) = GBARHH(K%)*(MHH(K%)^QMHH(K%))*(HHH(K%)^QHHH(K%))
5085 I(K%,HH%) = G(K%,HH%)*(V(I%)-VEQHH(K%))
5090 IF DBF% <> 0 THEN PRINT "5090: CODE 10: K%="; K%; " G="; G(K%, HH%); " I="; I(K%, 10); " AM="; ALPHAM(K%); " BM="; BETAM(K%); " AH="; ALPHAH(K%); " BH="; BETAH(K%)
5095 RETURN
5097 '
5098 'SYNAPSE: *********** CODE 11: SYNAPTIC INPUT BRANCH ********************
5189 '(destroys A; F; L%; LL%)
5100 XMTR=SUMTB(K%,SUMTB0%): G(K%,SYNAPSE%)=GBARS(K%)*XMTR/(KDS(K%)+XMTR)'G FROM BINDING EQ
5105 I(K%,SYNAPSE%)=G(K%,SYNAPSE%)*(V(CP%(K%,SYNAPSE%))-VREVS(K%))
5110 IF DBF%<>0 THEN PRINT "5110: CODE 11: K%=";K%;" G=";G(K%,SYNAPSE%);"I=";I(K%,SYNAPSE%)
5115 IF NOT SPKFLG%(CPS%(K%)) THEN RETURN
5120 F=0 'CLEAR FACILITATION
5122 IF NF%(K%)=0 THEN GOTO 5135 'IF NO FACIL, GOTO PSP
5124 FOR L%=FLOC%(K%) TO FLOC%(K%)+NF%(K%)-1
5126 XF(L%) = 1+(XF(L%)-1)*EXP((TPREV(K%)-T)/TAUF(L%))
5128 F = F+XF(L%)^NF(L%)-1
5130 XF(L%) = XF(L%)+C1F(L%)-C2F(L%)*XF(L%)
5132 NEXT L%
5135 TPREV(K%)=U: T%=0
5140 A = A0S(K%)*(1+F) 'TRANSMITTER RELEASE SCALED UP BY FACIL
5145 LL% = SUMTB0%+INT(DLY(K%)/TINC)'START PSP SUMMATION AT POINTER + DELAY
5150 IF LL%>=SUMTBL% THEN LL% = LL%-SUMTBL%
5155 FOR L%=LL% TO SUMTBL% 'CARRY SUM TO END OF SUMTB ...
5160 SUMTB(K%,L%) = SUMTB(K%,L%)+A*VPSP(PSPSHP%(K%),T%)
5165 T% = T%+1: IF T%>PSPL% THEN GOTO 5195
5170 NEXT L%
5175 IF LL% = 0 THEN GOTO 5195
5180 FOR L% = 0 TO LL%-1 '... THEN WRAP AROUND TO BEGINNING
5185 SUMTB(K%, L%) = SUMTB(K%,L%)+A*VPSP(PSPSHP%(K%),T%)
5187 T% = T%+1: IF T%>PSPL% THEN GOTO 5195
5190 NEXT L%
5193 IF DBF%<>0 THEN PRINT "5193: SPIKE IN UNIT";CPS%(K%);" AMPL=";A
5195 RETURN
5198 '
5199 'CHEMOX: ************ CODE 12: EXPONENTIAL CHEMOTONIC INPUT BRANCH
5200 IF KS(K%)=0 THEN S(K%)=S0(K%)*EXP(V(CPC%(K%))/MUC(K%)): GOTO 5250
5210 S(K%)=S(K%) + S0(K%)*EXP(V(CPC%(K%))/MUC(K%))*TINC - KS(K%)*S(K%)*TINC
5250 G(K%,CHEMOX%) = GBARC(K%)*S(K%)/(KDC(K%)+S(K%))
5260 I(K%,CHEMOX%) = G(K%,CHEMOX%)*(V(I%)-VREVC(K%))
5270 IF DBF%<>0 THEN PRINT "5230: CODE CHEMOX: K%="; K%; " G="; G(K%,CHEMOX%); " I="; I(K%, CHEMOX%); " CPC%="; CPC%(K%); " V(PRE)=";V(CPC%(K%)); " XMTR="; XMTR
5280 RETURN
5290 ' ************************************************
5291 ' * LINES 5300 - 5900 RESERVED FOR CODES 13 - 19 *
5292 ' ************************************************
5300 L%=5300: GOTO 5990 'Code 13
5399 'CONNOR: ****** CODE 14: MODIFIED HH KINETICS (Connor et al 1977)
5400 IF QMC(K%)=0 THEN MC(K%)=1: GOTO 5430
5410 MCINF = (MCA(K%)*EXP((V(I%)+MCB(K%))/MCC(K%))/(1+EXP((V(I%)-V0MC(K%))/MUMC(K%))))^(1/QMC(K%))
5415 TAUMC(K%)= TMC0(K%)+TMCA(K%)/(1+EXP((V(I%)-V0TM(K%))/MUTM(K%)))
5420 MC(K%) = MC(K%)+(MCINF-MC(K%))*KTEMPC(K%)*TINC/TAUMC(K%)
5430 IF QHC(K%)=0 THEN HC(K%)=1: GOTO 5460
5440 HCINF = 1/(1+EXP((V(I%)-V0HC(K%))/MUHC(K%)))^QHC(K%)
5445 TAUHC(K%)=THC0(K%)+THCA(K%)/(1+EXP((V(I%)-V0TH(K%))/MUTH(K%)))
5450 HC(K%) = HC(K%)+(HCINF-HC(K%))*KTEMPC(K%)*TINC/TAUHC(K%)
5460 G(K%, CONNOR%) = GBARCON(K%)*(MC(K%)^QMC(K%))*HC(K%)
5470 I(K%, CONNOR%) = G(K%, CONNOR%)*(V(I%)-VEQC(K%))
5490 RETURN
5500 L%=5500: GOTO 5990 'Code 15
5600 L%=5600: GOTO 5990 'Code 16
5700 L%=5700: GOTO 5990 'Code 17
5800 L%=5800: GOTO 5990 'Code 18
5900 L%=5900: GOTO 5990 'Code 19
5990 PRINT L%;": ILLEGAL BRANCH CODE CALL IN KINETICS"
5991 RETURN
5992 '
5993 ' ###########################################
5994 '############### SUBROUTINES FOR BRANCH PARAMETER INPUT #####
5995 ' ###########################################
5996 ' Subroutines to read branch parameters from the Parameter File, PFILE$
5997 ' Entries at 6000 + 10x where x=Code#
5998 '******************* CODE CMPT (1): INPUT OF PRINCIPAL CMPT PARAMS
5999 '8 file entries per branch; g (in umho) = gdens (mmho/uf) * C (uf) * 1000
6010 INPUT #1, CELL%(K%), CELL$(K%), C(K%), VLK(K%), GL(K%), GAMMA
6011 IF GL(K%)=0 THEN GL(K%)=GAMMA*C(K%)*1000
6012 RETURN
6018 '******************* CODE TRIGR (2): INPUT OF TRIGR PARAMETERS *****
6019 '31 file entries per branch
6020 INPUT #1, CP%(K%, TRIGR%), E0(K%), TAUM0(K%), PMTHR(K%), KPM(K%), TAUPM(K%), KCOND(K%)
6021 INPUT #1, TAUCOND(K%), KAR(K%), TAUAR(K%), KA1(K%), TAUA1(K%)
6022 INPUT #1, KA2(K%), TAUA2(K%), THRINF(K%), KTHR(K%), TAUTHR(K%), DV0(K%)
6023 INPUT #1, MAXV(K%), DG0(K%), MAXG(K%), GAMMA, DAR0(K%), MAXAR(K%)
6024 INPUT #1, DA10(K%), MAXA1(K%), DA20(K%), MAXA2(K%), DTHR0(K%), MAXTHR(K%)
6025 THR(K%) = THRINF(K%): IF K%>NSPF% THEN NSPF%=K% 'UPDATE # SPK FLGS
6026 IF MAXG(K%)=0 THEN MAXG(K%)=GAMMA*C(CP%(K%,TRIGR%))*1000: DG0(K%)=DG0(K%)*C(CP%(K%,TRIGR%))*1000
6028 RETURN
6029 '***************** CODE ELECTN (3): COMPARTMENT COUPLING CONDUCTANCES
6030 INPUT #1, I%, GC(K%,I%): IF K%=I% THEN PRINT "ILLEGAL COUPLING"
6031 GC(I%,K%) = GC(K%,I%)
6032 RETURN
6039 '***************** CODE DIODE (4): COMPARTMENT COUPLING CONDUCTANCES
6040 INPUT #1, I%, GC(K%,I%): IF K%=I% THEN PRINT "ILLEGAL COUPLING"
6042 RETURN
6049 '***************** CODE SPIKE (5): VOLTAGE-TRIGGERED SPIKE ***
6050 INPUT #1, CP%(K%,SPIKE%), SPKF%(K%), ONTHR(K%), OFFTHR%(K%)
6051 IF SPKF%(K%)>NSPF% THEN NSPF%=SPKF%(K%)
6052 RETURN
6059 '***************** CODE UNDEFINED (6) **********
6060 GOTO 6190 'Code 6
6069 '***************** CODE COND (7): FIXED CONDUCTANCE AND BATTERY *****
6070 INPUT #1, CP%(K%,COND%), VCOND(K%), G(K%, COND%), GAMMA
6071 IF G(K%,COND%)=0 THEN G(K%,COND%)=GAMMA*C(CP%(K%,COND%))*1000
6072 RETURN
6079 '***************** CODE DRIVER (8): INPUT DRIVER POTENTIAL PARAMETERS
6080 INPUT #1, CP%(K%, DRIVER%), VNA(K%), GBARNA(K%), GAMMA, V0NA(K%), MUNA(K%)
6081 INPUT #1, VK(K%), GBARK(K%), GAMMAK, V0K(K%), MUK(K%)
6082 INPUT #1, GBARK1(K%), GAMMAK1, TAUK1(K%), GBARK2(K%), GAMMAK2, TAUK2(K%)
6083 IF GBARNA(K%)=0 THEN GBARNA(K%) = GAMMA*C(CP%(K%,DRIVER%))*1000
6084 IF GBARK(K%)=0 THEN GBARK(K%) = GAMMAK*C(CP%(K%,DRIVER%))*1000
6085 IF GBARK1(K%)=0 THEN GBARK1(K%) = GAMMAK1*C(CP%(K%,DRIVER%))*1000
6086 IF GBARK2(K%)=0 THEN GBARK2(K%) = GAMMAK2*C(CP%(K%,DRIVER%))*1000
6087 RETURN
6089 '***************** CODE HHFXD (9): INPUT OF FIXED TAU HH PARAMETERS
6090 INPUT #1, CP%(K%, HHFXD%), VEQ(K%), GBAR(K%), GAMMA
6091 INPUT #1, QM(K%), V0M(K%), MUM(K%), TAUMA(K%)
6092 INPUT #1, QH(K%), V0H(K%), MUH(K%), TAUH(K%)
6093 IF GBAR(K%)=0 THEN GBAR(K%)=GAMMA*C(CP%(K%,HHFXD%))*1000
6094 RETURN
6099 '***************** CODE HH(10): INPUT OF FULL HH BRANCH PARAMETERS
6100 INPUT #1, CP%(K%, HH%), VEQHH(K%), GBARHH(K%), GAMMA
6101 INPUT #1, KTEMP(K%), QMHH(K%), QHHH(K%)
6102 INPUT #1, AAM(K%), BAM(K%), CAM(K%), DAM(K%), EAM(K%)
6103 INPUT #1, ABM(K%), BBM(K%), CBM(K%), DBM(K%), EBM(K%)
6105 INPUT #1, AAH(K%), BAH(K%), CAH(K%), DAH(K%), EAH(K%)
6106 INPUT #1, ABH(K%), BBH(K%), CBH(K%), DBH(K%), EBH(K%)
6107 IF GBARHH(K%)=0 THEN GBARHH(K%)=GAMMA*C(CP%(K%,HH%))*1000
6108 RETURN
6109 '************ CODE SYNAPSE (11): INPUT OF CONVENTIONAL PSP PARAMETERS
6110 INPUT #1, CP%(K%,SYNAPSE%),VREVS(K%),GBARS(K%), GAMMA, KDS(K%),CPS%(K%)
6111 INPUT #1, PSPSHP%(K%),DLY(K%),A0S(K%)
6112 INPUT #1, TAUF(FLOC%): IF TAUF(FLOC%) = 0 THEN GOTO 6116 'CHK FOR FACIL
6113 FLOC%(K%) = FLOC%
6114 INPUT #1, NF(FLOC%), C2F(FLOC%), C1F(FLOC%)
6115 FLOC% = FLOC%+1: GOTO 6111
6116 IF CPS%(K%)>NSPF% THEN NSPF%=CPS%(K%) 'KEEP TRACK OF HIGHEST SPIKE FLAG
6117 IF GBARS(K%)=0 THEN GBARS(K%)=GAMMA*C(CP%(K%,SYNAPSE%))*1000
6118 RETURN
6119 '***************** CODE CHEMOX (12): INPUT OF CHEMOTONIC (EXP) PARAMS
6120 INPUT #1, CP%(K%,CHEMOX%),VREVC(K%),GBARC(K%),GAMMA,KDC(K%)
6121 INPUT #1, CPC%(K%),S0(K%),MUC(K%),KS(K%)
6122 IF GBARC(K%)=0 THEN GBARC(K%)=GAMMA*C(CP%(K%,CHEMOX%))*1000
6123 RETURN
6130 GOTO 6192 'Code 13 = dynamic chemotonic conn
6139 '***************** CODE CONNOR (14): CONNOR-MODIFIED HH PARAMS
6140 INPUT #1, CP%(K%, CONNOR%), VEQC(K%), GBARCON(K%), GAMMA, KTEMPC(K%)
6141 INPUT #1, QMC(K%), MCA(K%), MCB(K%), MCC(K%), V0MC(K%), MUMC(K%)
6142 INPUT #1, TMC0(K%), TMCA(K%), V0TM(K%), MUTM(K%)
6143 INPUT #1, QHC(K%), V0HC(K%), MUHC(K%)
6144 INPUT #1, THC0(K%), THCA(K%), V0TH(K%), MUTH(K%)
6145 IF GBARCON(K%)=0 THEN GBARCON(K%)=GAMMA*C(CP%(K%,CONNOR%))*1000
6146 RETURN
6149 '***************** CODES not implemented: 15-19 *************************
6150 GOTO 6192
6160 GOTO 6192
6170 GOTO 6192 'Code 17: Reserved for user additions
6180 GOTO 6192 'Code 18: Reserved for user additions
6190 GOTO 6192 'Code 19: Reserved for user additions
6192 PRINT "6192: INPUT OF CODE "; J%; " NOT IMPLEMENTED": RETURN
6193 '
6194 '****************** CODE POOL (20): INPUT OF POOL PARAMETERS ****
6195 'Pool types:
6196 ' 1=bound transmitter-eqivalent: dpool0=sumtb(pprm1,sumtb0)*pprm3/(pprm2+sumtb(pprm1,sumtb0) - pool
6197 ' 2=transmitter-dependent: dpool0=sumtb(pprm1,sumtb0)*tinc*pprm3/(pprm2+sumtb(pprm1,sumtb0)
6198 ' 3=current-dependent: dpool0=I(pprm1,pprm2)*tinc*pprm3
6199 ' 4=general 1st-order; 5=bound CHEMOX transmitter dependent
6200 INPUT #1, CP%(K%, POOL%), XTYPE%(K%), XNAME$(K%), XVOL(K%), XPOOL0(K%)
6201 INPUT #1, PPRM1(K%), PPRM2(K%), PPRM3(K%), PPRM4(K%)
6202 RETURN
6204 '***************** CODE POOLK (21): INPUT DIFFUSION RATE CONSTANTS
6205 INPUT #1, L%, K(K%, L%)
6206 RETURN
6207 '***************** CODE POOLX (22): INPUT POOL INTERACTIONS ****
6208 'Interactions (XINTYP%): XPOOL(XSRC%) on XPOOL(XTARG%) or Branch(XTARG%)
6209 ' 1=Constant multiplier: Xtarg=Xtarg0+Xprm1*(Xsrc+Xsrc0)
6210 GOTO 6205
6211 ' 2=Equilibrium receptor-binding:Xtarg=Xtarg0+Xprm1*Xsrc/(Xprm2+dXsrc)
6212 ' 3=Pseudo first order kinetic: dXtarg=(Xprm1*Xsrc*(Xprm3-Xtarg)-Xprm2*Xtarg)*tinc
6213 ' 4=Vrev ion dependence: Xtarg=26*ln(Xsrc/Xprm1)
6214 ' 5=Synthesis rate modulation: dXtarg=Xprm1*Xsrc*tinc
6215 ' 6=Coupling-conductance modulation: GC(Xtarg%,Xprm2)=Xprm1*Xsrc + Xtarg0
6216 ' 7=Diffusion-constant modulation: K(Xtarg%,Xprm2)=Xprm1*Xsrc + Xtarg0
6217 '
6220 INPUT #1, XTARG%(K%), XSRC%(K%), XINTYP%(K%)
6221 INPUT #1, XPRM1(K%), XPRM2(K%), XPRM3(K%), XPRM4(K%)
6222 INPUT #1, XBRN%(K%), XPRM%(K%) 'BRANCH INDX, VRBL PRM#
6223 RETURN
6993 '
6994 ' *******************************************
6995 '******************* SUBROUTINES TO SAVE STATE VARIABLES ******************
6996 ' * (lines 7000+NAME%*10; called from 1450) *
9097 ' *******************************************
7010 PRINT #1, V(K%);: RETURN 'PRINCIPAL BRANCH
7020 PRINT #1, VM(K%), W(K%), P(K%), EI(K%), GS(K%) 'TRIGR
7022 PRINT #1, AR(K%), A1(K%), A2(K%), THR(K%), XSS(K%);
7024 RETURN
7030 RETURN
7040 RETURN
7050 RETURN
7060 RETURN
7070 RETURN
7080 PRINT #1, GK1(K%), GK2(K%);: RETURN 'TYPE DRIVER
7090 PRINT #1, M(K%), H(K%);: RETURN 'TYPE HHFXD
7100 PRINT #1, MHH(K%), HHH(K%);: RETURN 'TYPE HH
7110 PRINT #1, NF%(K%), FLOC%, TPREV(K%); 'TYPE SYNAPSE
7112 FOR L% = FLOC% TO NF%(K%) + FLOC%: PRINT #1, XF(L%),: NEXT L%
7120 RETURN
7130 RETURN
7140 PRINT #1, MC(K%), HC(K%);: RETURN 'TYPE CONNOR
7150 RETURN
7160 RETURN
7170 RETURN
7180 RETURN
7190 RETURN
7200 PRINT #1, XPOOL(K%);: RETURN
7210 RETURN
7220 RETURN
7493 '
7494 ' ******************************************
7495 '******************* SUBROUTINES TO PRELOAD STATE VARIABLES *******************
7496 ' * (lines 7500+NAME%*10; called from ) *
7497 ' ******************************************
7510 INPUT #1, V(K%): RETURN 'PRINCIPAL BRANCH
7520 INPUT #1, VM(K%), W(K%), P(K%), EI(K%), GS(K%) 'TRIGR
7522 INPUT #1, AR(K%), A1(K%), A2(K%), THR(K%), XSS(K%)
7524 RETURN
7530 RETURN 'Code 3
7540 RETURN 'Code 4
7550 RETURN 'Code 5
7560 RETURN 'Code 6
7570 RETURN 'Code 7
7580 INPUT #1, GK1(K%), GK2(K%): RETURN 'TYPE DRIVER
7590 INPUT #1, M(K%), H(K%): RETURN 'TYPE HHFXD
7600 INPUT #1, MHH(K%), HHH(K%): RETURN 'TYPE HH
7610 INPUT #1, NF%(K%), FLOC%, TPREV(K%) 'TYPE SYNAPSE
7612 FOR L% = FLOC% TO NF%(K%) + FLOC%: INPUT #1, XF(L%): NEXT L%
7614 RETURN
7620 RETURN
7630 RETURN
7640 INPUT #1, MC(K%), HC(K%): RETURN 'TYPE CONNOR
7650 RETURN
7660 RETURN
7670 RETURN
7680 RETURN
7690 RETURN
7700 INPUT #1, XPOOL(K%): RETURN 'TYPE POOL
7710 RETURN
7720 RETURN
10991 '
10992 ' ###############################
10993 '#################### POOLS ##########################
10994 ' ###############################
10995 '
10996 ' Routines handling filling, diffusion, and modulation in pools
10997 '
10998 '**************** INTER-POOL DIFFUSION *******
11000 FOR K% = 1 TO N%(POOL%)
11140 IF CP%(K%, POOL%) = 0 THEN GOTO 11270 'SKIP EMPTY SLOTS
11150 ON XTYPE%(K%) GOSUB 11310, 11320, 11330, 11340, 11350'INPUT SPRING INPUT OF DPOOL
11160 IF TXFLG%(POOLK%) THEN K = K(0, K%): GOTO 11260 'FLG BLOCKS DIFFUSION
11170 FOR L% = 0 TO N%(POOL%) 'INFLOW FROM OTHER POOLS
11180 IF L% = K% OR CP%(L%,POOL%) = 0 THEN GOTO 11200
11190 DPOOL = DPOOL + K(K%,L%)*XPOOL(L%)*TINC/XVOL(L%)
11200 NEXT L%
11210 K = 0
11220 FOR L% = 0 TO N%(POOL%) 'OUTFLOW TO OTHER POOLS & DESTROYED
11230 IF L% = K% OR CP%(L%,POOL%) = 0 THEN GOTO 11250
11240 K = K + K(L%,K%) '[K(0,K%) IS BASE DECAY RATE]
11250 NEXT L%
11260 DPOOL(K%) = DPOOL - K * XPOOL(K%) * TINC / XVOL(K%)'NET POOL CHANGE
11265 IF DBF%<>0 THEN PRINT "11265: CODE POOL: POOL#";K%;"SPRING=";DPOOL;"DIFFUSED=";DPOOL-DPOOL(K%)
11270 NEXT K%
11290 RETURN
11299 '**************** CODE POOL: POOL SPRING SUBROUTINES ******
11310 DPOOL = SUMTB(PPRM1(K%), SUMTB0%) * PPRM3(K%) / (PPRM2(K%) + SUMTB(PPRM1(K%), SUMTB0%)) - XPOOL(K%): RETURN
11320 DPOOL = (SUMTB(PPRM1(K%), SUMTB0%) * PPRM3(K%) / (PPRM2(K%) + SUMTB(PPRM1(K%), SUMTB0%)) - PPRM4(K%)*XPOOL(K%)) * TINC: RETURN
11330 DPOOL = (I(PPRM1(K%), PPRM2(K%)) * PPRM3(K%) - PPRM4(K%)*XPOOL(K%)) *TINC: RETURN
11340 DPOOL = (PPRM1(K%) - PPRM2(K%) * XPOOL(K%)) * TINC: RETURN
11350 DPOOL = S(PPRM1%) * PPRM3(K%) / (PPRM2(K%) + S(PPRM1%) - XPOOL(K%)):RETURN
11991 '
11992 '**************** CODE POOLX: GENERATION OF POOL INTERACTIONS *****
12000 FOR K% = 1 TO N%(POOLX%)
12050 L% = XSRC%(K%) 'SOURCE POOL
12055 XTARG% = XTARG%(K%) 'TARGET POOL
12060 IF XTARG%<0 THEN I%=-XTARG%: XBRN% = XBRN%(K%): XPRM% = XPRM%(K%):GOSUB 13000: GOTO 12080 'FETCH K (Current value of target parameter)
12070 K = XPOOL(XTARG%) 'FETCH TARGET POOL VALUE
12080 ON XINTYP%(K%) GOSUB 12150, 12200, 12300, 12400, 12500,12600,12700
12085 TARG(K%)=K
12090 IF XTARG% < 0 THEN GOSUB 16000: GOTO 12105 'IF BRANCH, SAVE RESULT
12095 IF XINTYP%(K%)=6 OR XINTYP%(K%)=7 THEN GOTO 12105 'Types 6 & 7 different
12100 XPOOL(XTARG%) = K
12105 IF DBF%<>0 THEN PRINT "12105: CODE 22: K%=";K%;" SRC POOL=";L%; "XINTYP=";XINTYP%(K%);" XTARG=";XTARG%;"K=";K;: IF XTARG%<0 THEN PRINT" XBRN=";XBRN%;" XPRM=";XPRM%: ELSE PRINT
12110 NEXT K%
12120 RETURN
12148 '
12149 ' Type 1: Constant multiplier
12150 K = XPRM1(K%) * (XPOOL(L%) + XPOOL0(L%)) + XTARG0(K%)
12160 RETURN
12198 '
12199 ' Type 2: Equilibrium binding
12200 K = XPRM1(K%) * (XPOOL(L%)+XPOOL0(L%)) / (XPRM2(K%) + XPOOL(L%) + XPOOL0(L%)) + XTARG0(K%)
12210 RETURN
12298 '
12299 ' Type 3: Pseudo first-order kinetics
12300 DXTARG = (XPRM1(K%)*(XPOOL(L%)+XPOOL0(L%))*(XPRM3(K%) - K) - XPRM2(K%)*K )*TINC
12310 K = K + DXTARG '(IMPROPERLY DONE INCREMENT)
12320 RETURN
12398 '
12399 ' Type 4: Vrev ion dependence
12400 K = 26 * LOG((XPOOL(L%)+XPOOL0(L%)) / XPRM1(K%))
12410 RETURN
12498 '
12499 ' Type 5: Synthesis rate modulation
12500 K = K + XPRM1(K%) * (XPOOL(L%)+XPOOL0(L%)) * TINC
12510 RETURN
12598 '
12599 ' Type 6: Coupling-conductance modulation
12600 K = XPRM1(K%)*(XPOOL(L%)+XPOOL0(L%)) + XTARG0(K%)
12610 GC(XTARG%,XPRM2(K%)) = K
12620 RETURN
12698 '
12699 ' Type 7: Diffusion/Reaction constant modulation
12700 K = XPRM1(K%)*(XPOOL(L%)+XPOOL0(L%)) + XTARG0(K%)
12710 K(XTARG%,XPRM2(K%)) = K
12720 RETURN
12995 '
12996 '**************** FETCH BRANCH PARAMETER VIA K *******************
13000 ON I% GOTO 13100, 13200, 13300, 13400, 13500, 13600, 13700, 13800,
13900, 14000, 14100, 14200, 14300, 14400, 14500, 14600, 14700, 14800,
14900, 15000, 15100, 15200
13099 '----> CODE 1:
13100 ON XPRM% GOTO 13110, 13120, 13130, 13140
13105 GOTO 19100
13110 K = C(XBRN%): RETURN '1
13120 K = VLK(XBRN%): RETURN '2
13130 K = GL(XBRN%): RETURN '3
13140 K = INJ(XBRN%): RETURN '4 (= code for pool-injection current)
13190 '----> CODE 2
13200 ON XPRM% GOTO 13210, 13215,13220,13225,13230,13235
13205 GOTO 19100
13210 K = E0(XBRN%): RETURN '1
13215 K = TAUM0(XBRN%): RETURN '2
13220 K = PMTHR(XBRN%): RETURN '3
13225 K = KPM(XBRN%): RETURN '4
13230 K = TAUPM(XBRN%): RETURN '5
13235 K = KCOND(XBRN%): RETURN '6
13287 'TAUCOND(K%),KAR(K%),TAUAR(K%),KA1(K%),TAUA1(K%) 'For future exp
13288 'KA2(K%),TAUA2(K%),THRINF(K%),KTHR(K%),TAUTHR(K%)
13289 'DV0(K%),MAXV(K%),DG0(K%),MAXG(K%),DAR0(K%),MAXAR(K%)
13290 'DA10(K%),MAXA1(K%),DA20(K%),MAXA2(K%),DTHR0(K%),MAXTHR(K%)
13299 '---> (Code 3 modulation by Type 6 interaction needs special treat)
13300 GOTO 19000 'CODE 3
13400 GOTO 19000 'CODE 4
13500 GOTO 19000 'CODE 5
13600 GOTO 19000 'CODE 6
13699 '----> CODE 7
13700 ON XPRM% GOTO 13710, 13720
13705 GOTO 19100
13710 K=VCOND(XBRN%): RETURN
13720 K=G(XBRN%, COND%): RETURN
13790 '----> CODE 8
13800 ON XPRM% GOTO 13805, 13810, 13815, 13820, 13825, 13830, 13835, 13840,
13845, 13850, 13855, 13860
13803 GOTO 19100
13805 K = VNA(XBRN%): RETURN '1
13810 K = GBARNA(XBRN%): RETURN '2
13815 K = V0NA(XBRN%): RETURN '3
13820 K = MUNA(XBRN%): RETURN '4
13825 K = VK(XBRN%): RETURN '5
13830 K = GBARK(XBRN%): RETURN '6
13835 K = V0K(XBRN%): RETURN '7
13840 K = MUK(XBRN%): RETURN '8
13845 K = GBARK1(XBRN%): RETURN '9
13850 K = TAUK1(XBRN%): RETURN '10
13855 K = GBARK2(XBRN%): RETURN '11
13860 K = TAUK2(XBRN%): RETURN '12
13899 '----> CODE 9
13900 ON XPRM% GOTO 13910, 13920, 13930, 13940, 13950, 13960, 13970, 13980,
13990, 13995
13905 GOTO 19100
13910 K = VEQ(XBRN%): RETURN '1
13920 K = GBAR(XBRN%): RETURN '2
13930 K = QM(XBRN%): RETURN '3
13940 K = V0M(XBRN%): RETURN '4
13950 K = MUM(XBRN%): RETURN '5
13960 K = TAUMA(XBRN%):RETURN '6
13970 K = QH(XBRN%): RETURN '7
13980 K = V0H(XBRN%): RETURN '8
13990 K = MUH(XBRN%): RETURN '9
13995 K = TAUH(XBRN%): RETURN '10
13999 '----> CODE 10
14000 ON XPRM% GOTO 14010,14020
14005 GOTO 19100
14010 K = VEQHH(XBRN%): RETURN '1
14020 K = GBARHH(XBRN%): RETURN '2
14090 'KTEMP(XBRN%),QMHH(XBRN%),QHHH(XBRN%)
14091 'AAM(XBRN%),BAM(XBRN%),CAM(XBRN%),DAM(XBRN%),EAM(XBRN%)
14092 'ABM(XBRN%),BBM(XBRN%),CBM(XBRN%),DBM(XBRN%),EBM(XBRN%)
14093 'AAH(XBRN%),BAH(XBRN%),CAH(XBRN%),DAH(XBRN%),EAH(XBRN%)
14094 'ABH(XBRN%),BBH(XBRN%),CBH(XBRN%),DBH(XBRN%),EBH(XBRN%)
14099 '----> CODE 11
14100 ON XPRM% GOTO 14110, 14120, 14130, 14140
14105 GOTO 19100
14110 K = VREVS(XBRN%): RETURN '1
14120 K = GBARS(XBRN%): RETURN '2
14125 K = KDS(XBRN%): RETURN '3
14130 K = DLY(XBRN%): RETURN '4
14140 K = A0S(XBRN%): RETURN '5
14199 '----> CODE 12
14200 ON XPRM% GOTO 14210, 14220, 14230, 14240, 14250, 14260
14205 GOTO 19100
14210 K = VREVC(XBRN%): RETURN '1
14220 K = GBARC(XBRN%): RETURN '2
14230 K = KDC(XBRN%): RETURN '3
14240 K = S0(XBRN%): RETURN '4
14250 K = MUC(XBRN%): RETURN '5
14260 K = KS(XBRN%): RETURN '6
14299 '----> CODES 13-19 FOR FUTURE EXPANSION
14300 GOTO 19000 'TO IMPLEMENT, FOLLOW ABOVE FORMAT
14399 '----> CODE 14 (Connor HH)
14400 ON XPRM% GOTO 14410, 14420
14405 GOTO 19100
14410 K = VEQC(XBRN%) : RETURN
14420 K = GBARCON(XBRN%) : RETURN
14500 GOTO 19000
14600 GOTO 19000
14700 GOTO 19000
14800 GOTO 19000
14900 GOTO 19000
14999 '---> CODE 20
15000 ON XPRM% GOTO 15010,15020,15030,15040,15050,15060
15005 GOTO 19100
15010 K=XVOL(XBRN%) : RETURN '1
15020 K=XPOOL0(XBRN%): RETURN '2
15030 K=PPRM1(XBRN%) : RETURN '3
15040 K=PPRM2(XBRN%) : RETURN '4
15050 K=PPRM3(XBRN%) : RETURN '5
15060 K=PPRM4(XBRN%) : RETURN '6
15099 '---> CODE 21 (Diffusion modulation is via Type 7)
15100 GOTO 19000
15199 '---> CODE 22
15200 ON XPRM% GOTO 15210,15220,15230,15240
15205 GOTO 19100
15210 K=XPRM1(XBRN%) : RETURN '1
15220 K=XPRM2(XBRN%) : RETURN '2
15230 K=XPRM3(XBRN%) : RETURN '3
15240 K=XPRM4(XBRN%) : RETURN '4
15998 '
15999 '********** SET BRANCH PARAMETER FROM K **********
16000 ON I% GOTO 16100, 16200, 16300, 16400, 16500, 16600, 16700, 16800,
16900, 17000, 17100, 17200, 17300, 17400, 17500, 17600, 17700, 17800,
17900, 18000, 18100, 18200
16009 '----> CODE 1
16100 ON XPRM% GOTO 16110, 16120, 16130, 16140
16105 GOTO 19300
16110 C(XBRN%) = K: RETURN
16120 VLK(XBRN%)= K: RETURN
16130 GL(XBRN%) = K: RETURN
16140 INJ(XBRN%)= K: RETURN
16190 '----> CODE 2
16200 ON XPRM% GOTO 16210, 16215,16220,16225,16230,16235
16205 GOTO 19300
16210 E0(XBRN%) = K: RETURN
16215 TAUM0(XBRN%) = K: RETURN
16220 PMTHR(XBRN%) = K: RETURN
16225 KPM(XBRN%) = K: RETURN
16230 TAUPM(XBRN%) = K: RETURN
16235 KCOND(XBRN%) = K: RETURN
16287 'TAUCOND(K%),KAR(K%),TAUAR(K%),KA1(K%),TAUA1(K%) 'For future exp
16288 'KA2(K%),TAUA2(K%),THRINF(K%),KTHR(K%),TAUTHR(K%)
16289 'DV0(K%),MAXV(K%),DG0(K%),MAXG(K%),DAR0(K%),MAXAR(K%)
16290 'DA10(K%),MAXA1(K%),DA20(K%),MAXA2(K%),DTHR0(K%),MAXTHR(K%),ESF(K%)
16299 '----> CODE 3 ILLEGAL; CODES 4-7 FOR FUTURE EXP
16300 GOTO 19200 'CODE 3
16400 GOTO 19200 'CODE 4
16500 GOTO 19200 'CODE 5
16600 GOTO 19200 'CODE 6
16699 '----> CODE 7
16700 ON XPRM% GOTO 16710, 16720
16705 GOTO 19300
16710 VCOND(XBRN%)=K: RETURN
16720 G(XBRN%, COND%)=K: RETURN
16790 '----> CODE 8
16800 ON XPRM% GOTO 16805, 16810, 16815, 16820, 16825, 16830, 16835, 16840,
16845, 16850, 16855, 16860
16803 GOTO 19300
16805 VNA(XBRN%) = K: RETURN
16810 GBARNA(XBRN%) = K: RETURN
16815 V0NA(XBRN%) = K: RETURN
16820 MUNA(XBRN%) = K: RETURN
16825 VK(XBRN%) = K: RETURN
16830 GBARK(XBRN%) = K: RETURN
16835 V0K(XBRN%) = K: RETURN
16840 MUK(XBRN%) = K: RETURN
16845 GBARK1(XBRN%) = K: RETURN
16850 TAUK1(XBRN%) = K: RETURN
16855 GBARK2(XBRN%) = K: RETURN
16860 TAUK2(XBRN%) = K: RETURN
16899 '----> CODE 9
16900 ON XPRM% GOTO 16910, 16920, 16930, 16940, 16950, 16960, 16970, 16980,
16990, 16995
16905 GOTO 19300
16910 VEQ(XBRN%) = K: RETURN
16920 GBAR(XBRN%) = K: RETURN
16930 QM(XBRN%) = K: RETURN
16940 V0M(XBRN%) = K: RETURN
16950 MUM(XBRN%) = K: RETURN
16960 TAUMA(XBRN%) = K: RETURN
16970 QH(XBRN%) = K: RETURN
16980 V0H(XBRN%) = K: RETURN
16990 MUH(XBRN%) = K: RETURN
16995 TAUH(XBRN%) = K: RETURN
16999 '----> CODE 10
17000 ON XPRM% GOTO 17010, 17015
17005 GOTO 19300
17010 VEQHH(XBRN%) = K: RETURN
17015 GBARHH(XBRN%)= K: RETURN
17090 'KTEMP(XBRN%)=K,QMHH(XBRN%)=K,QHHH(XBRN%)=K
17091 'AAM(XBRN%)=K,BAM(XBRN%)=K,CAM(XBRN%)=K,DAM(XBRN%)=K,EAM(XBRN%)=K
17092 'ABM(XBRN%)=K,BBM(XBRN%)=K,CBM(XBRN%)=K,DBM(XBRN%)=K,EBM(XBRN%)=K
17093 'AAH(XBRN%)=K,BAH(XBRN%)=K,CAH(XBRN%)=K,DAH(XBRN%)=K,EAH(XBRN%)=K
17094 'ABH(XBRN%)=K,BBH(XBRN%)=K,CBH(XBRN%)=K,DBH(XBRN%)=K,EBH(XBRN%)=K
17099 '----> CODE 11
17100 ON XPRM% GOTO 17110, 17120, 17130, 17140
17105 GOTO 19300
17110 VREVS(XBRN%) = K: RETURN
17120 GBARS(XBRN%) = K: RETURN
17125 KDS(XBRN%) = K: RETURN
17130 DLY(XBRN%) = K: RETURN
17140 A0S(XBRN%) = K: RETURN
17199 '----> CODE 12
17200 ON XPRM% GOTO 17210, 17220, 17230, 17240, 17250, 17260
17205 GOTO 19300
17210 VREVC(XBRN%) = K: RETURN
17220 GBARC(XBRN%) = K: RETURN
17230 KDC(XBRN%) = K: RETURN
17240 S0(XBRN%) = K: RETURN
17250 MUC(XBRN%) = K: RETURN
17260 KS(XBRN%) = K: RETURN
17299 '----> CODES 13-19 FOR FUTURE EXPANSION
17300 GOTO 19200 'CODE 13
17400 ON XPRM% GOTO 17410, 17420
17405 GOTO 19300
17410 VEQC(XBRN%) = K: RETURN
17420 GBARCON(XBRN%)=K: RETURN
17500 GOTO 19200 'CODE 15
17600 GOTO 19200 'CODE 16
17700 GOTO 19200 'CODE 17
17800 GOTO 19200 'CODE 18
17900 GOTO 19200 'CODE 19
17999 '---> CODE 20
18000 ON XPRM% GOTO 18010,18020,18030,18040,18050,18060
18005 GOTO 19300
18010 XVOL(XBRN%) = K: RETURN
18020 XPOOL0(XBRN%)=K: RETURN
18030 PPRM1(XBRN%) =K: RETURN
18040 PPRM2(XBRN%) =K: RETURN
18050 PPRM3(XBRN%) =K: RETURN
18060 PPRM4(XBRN%) =K: RETURN
18099 '---> CODE 21
18100 GOTO 19200 '(Modulation achieved by Type 7 interaction)
18199 '---> CODE 22
18200 ON XPRM% GOTO 18210,18220,18230,18240
18205 GOTO 19300
18210 XPRM1(XBRN%)=K: RETURN
18220 XPRM2(XBRN%)=K: RETURN
18230 XPRM3(XBRN%)=K: RETURN
18240 XPRM4(XBRN%)=K: RETURN
19000 PRINT "19000: TARGET-FETCH ";
19050 PRINT "CALLED ILLEGAL BRANCH CODE ";I%: ER%=-1: RETURN
19100 PRINT "19100: TARGET-FETCH ";
19150 PRINT "INVALID TARGET PARAMETER ";XPRM%(K%);"OF BRANCH ";I%;"FOR INTERACTION ";K%: ER%=-1: RETURN
19200 PRINT "19200: TARGET-SAVE ";: GOTO 19050
19300 PRINT "19300: TARGET-SAVE ";: GOTO 19150
For another excellent modeling program, see Michael Hines' NEURON
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