Chapter 1: The Brain

This is the top level structure in the simulator. This will contain some values to define the simulation as a whole such as the amount of time being simulated and random seed.
During input, the Brain Section will also provide a preliminary outline of other structures to be used in the simulation. The overall structure of the input file is to describe different aspects within the brain as blocks of text. The NCS parser recognizes keywords and creates structures within the model as defined within the blocks. These keywords and their associated parameters are described in the user documentation located on brain.unr.edu/ncsDocs/ncsUser/TOC.html
The order of the blocks is not important as long as the blocks are complete.
Also, the input file can be split up into several files and included using the INCLUDE keyword. The only restriction is that the INCLUDE statement be located outside of any block structure.
The maximum number of characters allowed within a string value is currently 128 characters. Numbers are transformed into their appropriate type, float, double, etc.

Keyword

Value

Description

BRAIN

N/A

REQUIRED: Indicates the start of a Brain definition block.

TYPE

name

(string)

REQUIRED: The name of this Brain configuration. Currently used by the Server program (port-based IO) to create and manage the ports.

JOB

name

(string)

REQUIRED: Job Name Any files generated during the simulation will be given the JOB string as a prefix followed by a period or a dash (depending on the version of NCS used) then whatever the filename is to be called (ex. myJob.report1 or myJob-report1 )
By default JOB is the string "job".

DURATION

value

(real)

REQUIRED: Duration of the simulation in seconds.
The amount of time, in seconds, which will be simulated.
This value is multiplied by the FSV to determine the number of timesteps for the simulation.

FSV

value

(integer)

REQUIRED: FSV = Frequency of Sampling Value
Default value is 1
Typical Value is 10,000
This scales DURATION to set the number of DoThink loop timesteps the simulation will run.
(ex. DURATION = 1.8, FSV = 10000, timesteps = 1.8*10000 = 18000 )

INTERACTIVE

YES/NO

Currently not implemented

SEED

value

(integer)

Random Number Generator Seed Value
This value should be a negative integer. (ex. -999) This sets the seed to be used by the brain's random number generator. This seed is used for the connectivity wthin the brain block as well as the connections between layers and within layers
Note: This SEED value is not responsible for other areas that utilize their own seeds. (ex. COMPARTMENT, CHANNEL, SYNAPSE, SYN_FACIL_DEPRESS, LEARNING (hebbian)
SYN_DATA(deprecated),
STIMULUS)

DISTANCE

YES/NO

Distance Toggle
Flag to indicate that cells should be assigned specific coordinates so that synaptic delays can be calculated based on distance between the source and destination cells. Set to NO by default.
This value must be YES if you want to set OUTPUT_CELLS, OUTPUT_CONNECT_MAP to YES or use the Decay Step Value within a CONNECT statement

COLUMN_TYPE

name

(string)

Column Creation
Alerts the simulator to expect a column(s) to be defined with the name given. If a column is defined without being listed in the Brain section, that column will be ignored and not generated in the resulting brain model structure.
Can have multiple values listed.

STIMULUS_INJECT

name

(string)

Stimulus Injection Creation
Alerts the simulator to expect a stimulus to be defined with the name given. If a stimulus is defined without being listed in the Brain section, that stimulus will be ignored and not generated in the resulting brain model structure.
Can have multiple values listed.

REPORT

name

(string)

Report Creation
Alerts the simulator to expect a report to be defined with the name given. If a report is defined without being listed in the Brain section, that report will be ignored and not generated in the resulting brain model structure.
Can have multiple values listed.

EVENT

name

(string)

Change synapse's USE value
Alerts the simulator to expect a event to be difined with the name given. If a event is defined without being listed in the Brain section, that event will be ignored and not generated in the resulting brain model structure.
Can have multiple values listed.

CONNECT

Column	(string)
Layer	(string)
CellType	(string)
Compartment	(string)
Column	(string)
Layer	(string)
CellType	(string)
Compartment	(string)
SynpaseType	(string)
Probability	(real)
Speed	(real)

Intercolumn Connection Creation
Synapse connections between Columns. Signifies that synapse connections of the type specified should be made from the source (the first four parameters) to the destination (the next four params).
SynapseType is the Type value from the SYNAPSE block of the desired synapse to be used in this connection.
Probability determines how many connections are made randomly.
The speed indicates how quickly the destination cell will receive a signal from the source cell in millimeters per millisecond (mm/ms).
Can have multiple values listed.

CONNECT

Column	(string)
Layer	(string)
CellType	(string)
Compartment	(string)
Column	(string)
Layer	(string)
CellType	(string)
Compartment	(string)
SynpaseType	(string)
Probability	(real)
Decay_Step	(real)
Speed	(real)

Intercolumn Connection Creation with Decaying Distance Effects
Definitions are the same as above with the following exception:
If DISTANCE is set to YES, then connections are made based on a decaying probability based on distance.
The probability is at its maximum (the value given) if there is no distance between the source and destination cell. As the distance increases by the Decay Step, the probability exponentially decays.
If DISTANCE is set to NO, then probability is used as a constant for all connections and the Decay Step value is ignored.

RECURRENT_CONNECT

ColumnA	(string)
LayerA	(string)
CellTypeA	(string)
CompartmentA	(string)
ColumnB	(string)
LayerB	(string)
CellTypeB	(string)
CompartmentB	(string)
SynpaseType	(string)
ProbabilityAtoB	(real)
ProbabilityBtoA	(real)

Establishes that two previous CONNECT statments are recurrent with each other. This means that as the two cell groups are connected, a minimum percentage of cells have both forward connections and reverse connections. The first group listed (Column, Layer, Cell, Cmp) is designated group A while the second group (Column, Layer, Cell, Cmp) is designated group B. The previous CONNECT statements need to use these two groups with A connecting to B in one, and B connecting to A in another (order of appearance does not matter). Both these CONNECT statements must use the specified synapse. The Probability values indicate that a minimum percentage of connections made must be recurrent. For example, if ProbabilityAtoB is 0.5, then 50% of the cells with connections from A to B will also have a returning connection from the same cells in B to A.

SAVE

filename	(string)
value	(real)

Brain State Save
Specifies that the brain simulation should save the entire current state to the file name specified at the time (seconds) given. The file will save by default to your current working directory unless a full path is specified.

LOAD

filename

(string)

Brain State Load File
A brain saved in the file specified will be restored to run with new stimulus and reports. The file will load by default from your current working directory unless a full path is specified.

OPTION

WARNINGS_OFF

Disables simple warning messages. Warnings are on by default

OUTPUT_CELLS

YES/NO

Output Cell Locations
Flag to indicate that cell positions should be output to the file job.cells.dat in the current working directory.
See NCS Cell Coordinate Output for more details.
Set to NO by default.

OUTPUT_CONNECT_MAP

YES/NO

Output Synapse Locations
Flag to indicate that synaptic connections should be output to the file job.synapse.dat in the current working directory.
See NCS Connect Map Output for more details.
Set to NO by default.

END_BRAIN

N/A

REQUIRED: Indicates the end of a Brain definition section.

Example

The following BRAIN block would create a 3-column brain with two different stimulii.  There are two intercolumn connections. 
It would output two different reports. Distance and output is off for this run.
BRAIN
    TYPE               Brain1Col
    JOB                BinRep
    DURATION           1.8
    FSV                10000
    INTERACTIVE        NO
    SEED               -999
    DISTANCE           NO

    COLUMN_TYPE        AI1
    COLUMN_TYPE        AI2
    COLUMN_TYPE        ASSC1

    STIMULUS_INJECT    StimInject_AI3
    STIMULUS_INJECT    StimInject_AI1Clear

    REPORT             AI1_Lay3_Exc-cNAC_1
    REPORT             AI1_Lay4_Exc-cNAC_1

    CONNECT            AI1    Lay3    Exc-cNAC    s1
                       AI2    Lay3    Inh-cNAC    s1
                       ExcF2Hebb0	    0.05        3
    CONNECT            AI2    Lay3    Exc-cNAC    s1
                       AI1    Lay3    Inh-cNAC    s1
                       ExcF2Hebb0     0.05        3
        
    SAVE               Brain1Col.sav  1.0
    OUTPUT_CELLS       NO
    OUTPUT_CONNECT_MAP NO
END_BRAIN

RECURRENT_CONNECT Examples

1. Recurrent connects between a single cell group E1, declared in a BRAIN section.
	CONNECT
				R2A_AI_1	layer_R2	E1	sE1
				R2A_AI_1	layer_R2	E1	sE1
				ExcitSyn1_Intra_E1	0.12	0
	RECURRENT_CONNECT
				R2A_AI_1	layer_R2	E1	sE1
				R2A_AI_1	layer_R2	E1	sE1
				ExcitSyn1_Intra_E1	1.0	0

This can also be declared in COLUMN and LAYER sections. The difference would be the way we specify source and destination cell groups.
In COULMN section, specify Layer, CellType and Compartment. In case of LAYER section, just specify CellType and Compartment.

2. Recurrent connects between two cell groups E1 and E2, declared in a BRAIN section.
	CONNECT
				R2A_AI_1	layer_R2	E1	sE1
				R2A_AI_1	layer_R2	E2	sE2
				ExcitSyn1_Inter	0.04	0
	CONNECT
				R2A_AI_1	layer_R2	E2	sE2
				R2A_AI_1	layer_R2	E1	sE1
				ExcitSyn1_Inter	0.04	0
	RECURRENT_CONNECT
				R2A_AI_1	layer_R2	E1	sE1
				R2A_AI_1	layer_R2	E2	sE2
				ExcitSyn1_Inter	1.0	1.0

As in previous example, this can also be declared in COLUMN and LAYER sections with same difference.

Contents Next: Columns

Last updated Wednesday 1/23/2008