Biophysical Description

In the biophysical description layer, we specify synapses and cells' biophysical properties.

Synapses are identified by a name, type, and phase. Synapse's type is a function-defined dynamics, receiving a list of illuminated or not values and returning a transformed list containing synaptic activation times - the times of each synaptic activation.

In the following XML, we defined a synapse, which follows the dynamic of the light stimulus affecting SACs via Bipolar Cells (BCs). We named this synapse "light synapse". Synapse type was defined as "spatially dependent dynamic", which is defined in the SimSimulation.py file.

Each synapse is also defined with a weight and an SBML-defined density function, defining the probability of synapse existence as a function of its distance from the soma.

Each cell identified by its ID is set with biophysical characteristics. Here we defined the SAC's cytoplasmic resistivity and capacitance. We also set two passive properties: conductance (g_pas) [mV] and equilibrium potential and conductance (e_pas) [siemens/cm2].

<biophysics xmlns = "RSME.simulation_parameters">

  <biophysics_description> TEST </biophysics_description>

  <biophysics_models>

    <synapses>

        <synapse name='light_synapse' type='spatially_dependent_dynamic' phase = 'on'>

            <density_function>
                <math>
                    <apply>
                        <plus/>
                        <cn> 0 </cn>
                        <apply>
                            <times/>
                            <apply>
                                <lt/>
                                <ci> x </ci>
                                <cn> 125 </cn>
                            </apply> 
			                <cn> 0.2 </cn>
                         </apply>
                    </apply>
                </math>
            </density_function>
            
            <weight>
                <math>
                    <cn> 0.8 </cn>
                </math>
            </weight>
            
        </synapse>

    </synapses>

    <cells>

        <cell_id id = "0" >

            <cytoplasmic_resistivity> 75 </cytoplasmic_resistivity>
            <capicitance> 1 </capicitance>

            <channels_spatial_distribution>
                <pas>
                    <g_pas>
                        <math>
                            <cn> 0.00006 </cn>
                        </math>
                    </g_pas>

                    <e_pas>
                        <math>
                            <cn> -60 </cn>
                        </math>
                    </e_pas>

                </pas>
            </channels_spatial_distribution>

        </cell_id>

     </cells>
     
  </biophysics_models>

</biophysics>