GENESIS: Documentation

Related Documentation:

Add the PulseGen{} Object to SSP

Reading Parameters

To integrate a solver object (here, we use the example PulseGen{}) with SSP, SSP must first be made aware of the parameters of the object. PulseGen{} takes parameters for Level1, Width1, Delay1, Level2, Width2, Delay2, BaseLevel{}, and TriggerMode{}, so SSP must be able to read in a value for each as an argument.

First, variables are declared for the optional arguments near the top of the bin/ssp file:

   my $option_pulsegen_level1;  
   my $option_pulsegen_width1;  
   my $option_pulsegen_delay1;  
   my $option_pulsegen_level2;  
   my $option_pulsegen_width2;  
   my $option_pulsegen_delay2;  
   my $option_pulsegen_baselvel;  
   my $option_pulsegen_triggermode;

Then in the Perl subroutine read_cmd_line we add the options to be read in to the call to GetOptions():

   "pulsegen-level1=s" => \$option_pulsegen_level1,  
   "pulsegen-width1=s" => \$option_pulsegen_width1,  
   "pulsegen-delay1=s" => \$option_pulsegen_delay1,  
   "pulsegen-level2=s" => \$option_pulsegen_level2,  
   "pulsegen-width2=s" => \$option_pulsegen_width2,  
   "pulsegen-delay2=s" => \$option_pulsegen_delay2,

This allows the values to be read from the command line and placed into memory. They must then be passed on to PulseGen{}.

Passing data to PulseGen{}

Now that PulseGen{} can read in values, each parameter must be checked and passed on to the PulseGen{} object. We do this by using a simple if statement that checks whether a variable has been defined and then passes on a value to SSP. A block similar to the following must be made for each parameter to be accepted byPulseGen{}. Here is an example for setting width1 in PulseGen{}:

   if (defined $option_pulsegen_width1)  
      my $pulsegen_inputclassname = "pulsegen";  
      my $inputclass  
         = {  
               module_name => "Experiment",  
               options => {  
                  command => $option_pulsegen_width1,  
                  name => "pulsegen set to $option_pulsegen_width1",  
               package => "Experiment::Pulsegen",  
      my $inputs  
         = [  
               component_name => "$model_root/segments/soma",  
               field => "WIDTH1",  
               inputclass => $pulsegen_inputclassname,  
      $scheduler->{inputclasses}->{$pulsegen_inputclassname} = $inputclass;  
         if (!defined $scheduler->{inputs})  
            $scheduler->{inputs} = [];  
         push @{$scheduler->{inputs}}, @$inputs;  

Creating a SSP specification

For testing purposes, a SSP specification is created to check the functionality of the PulseGen{} object. A test will load a model, create a PulseGen{} solver object, then clamp the PulseGen{} output to the model’s membrane potential (V m) at the soma. Although not biologically correct, this provides a good base case for a test.

First, a file pulsegen_freerun.yml is created as a large YAML hash. The simulation runs for 200 steps, similar to the examples in Create a Heccer Test and the associated GENESIS 2 script :

--- !!perl/hash:SSP  
    - arguments:  
        - commands:  
            - perl -e ’my $result = [ ‘cat /tmp/output‘, ]’  
      method: shell  
    - arguments:  
        - 200  
      method: steps

Here, the PulseGen{} object is created as an input class and all of the parameters previously used in the Create a Heccer Test and GENESIS 2 scripts are assigned to it.

    module_name: Experiment  
      level1: 50.0  
      width1: 3.0  
      delay1: 5.0  
      level2: -20.0  
      width2: 5.0  
      delay2: 8.0  
      baselevel: 10.0  
      triggermode: 0  
    package: Experiment::PulseGen

The PulseGen{} object is then ”clamped” to the model’s soma.

  - component_name: /Purkinje/segments/soma  
    field: Vm  
    inputclass: pulsegen  
  - modelname: /Purkinje  
    solverclass: heccer  
name: purkinje cell pulsegen

An output object double_2_ascii is then created that writes V m to the file /tmp/output.

    module_name: Experiment  
      filename: /tmp/output  
    package: Experiment::Output  
  - component_name: /Purkinje/segments/soma  
    field: Vm  
    outputclass: double_2_ascii

Here, the Model Container is invoked to load the desired model. Parameters for the Model Container can also be set in this block:

      - arguments:  
          - filename: cells/purkinje/edsjb1994.ndf  
            no-use-library: 1  
            - ssp configuration for edsjb1994 using pulsegen  
            - -R  
            - -A  
        method: load  
    module_name: Neurospaces

Finally, Heccer is invoked. The output granularity is set to 1 and the step size to 0.5 seconds. Again, in line with the previous examples:

          granularity: 1  
          tested_things: 6225920  
      dStep: 0.5  
        iOptions: 4  
    module_name: Heccer  
    service_name: model_container

After saving the specification, the simulation is started with the command:

   ssp pulsegen_freerun.yml

The expected output is then written to the file /tmp/output as declared in the specification.