Physiological Configuration File¶

The format of the physiological configuration file is different from that of the network and model configuration file in a sense that the parameters in the configuration file are placed vertically. Typically there are four types of columns in a physiological configuration file:

  • Variables: is the first column and contains the name of the variable. Some values are in form of key:value pairs and others are just a regular variable with a value.

    calcium_concentration   1

This line defines a variable called calcium_concentration and sets its value to 1. Note that the key is empty.

  • Keys: The keys for the former type of variables, i.e. those that contain key:value pairs, are defined in this column. In case the variable does not have a key, this cell in front of the variable could be left empty.
  • Values: Value will be set for either a variable with no keys, or for keys of a variable where the variable itself does not have a value, i.e. is in form of a key:value pairs.
BC C 100 * pF
  gL 10 * nS
  Vr -67.66 * mV
  EL -67.66 * mV
  VT -38.8 * mV
  DeltaT 2 * mV
  Ee 0 * mV
  Ei -75 * mV
  tau_e 3 * ms
  tau_i 8.3 * ms
  taum_soma C/gL
  V_res VT- 4 * mV
  Vcut VT+ 5*DeltaT

This example defines the different parameters and corresponding values for a BC neuron. The variable in this example is BC, where keys are its parameters and values are corresponding values.

Note the following line in the above example:

taum_soma C/gL

The key defines the Tau_m of the soma in the BC neuron. The value however, is a formula that uses the other keys of the BC neuron, i.e. C and gL.

  • comments: any cell starting with # will be considered as a comment. We recommend to dedicate the fourth column to write a short description of the parameters, or key/value pairs.

Note: Unlike network and model configuration file, the variable and key names in physiological configuration files could be set to any desired value that is used in the backend of the CxSystem. Attempts have been made to make the name of the current variable/keys descriptive so to make them understandable. All of the implemented variable/keys can be found in physiological configuration files in the Github page.