Viewing XML file: NeuroMLFiles/Examples/NetworkML/ExtendNetSpec.xml

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<neuroml xmlns="http://morphml.org/neuroml/schema"  
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:net="http://morphml.org/networkml/schema"
    xmlns:mml="http://morphml.org/morphml/schema"
    xmlns:meta="http://morphml.org/metadata/schema"
    xmlns:bio="http://morphml.org/biophysics/schema"  
    xmlns:cml="http://morphml.org/channelml/schema"  
    xsi:schemaLocation="http://morphml.org/neuroml/schema http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd"
    length_units="micrometer"
>

                        

    
<meta:notes>A network of cells connected in NeuroML Level 3. Extra tags are included to give an
      idea how the standard can be extended. Note most NeuroML compliant applications will ignore this extra
      data, but will still be able to extract the essential physiological information.
      
    
</meta:notes>

    
    
<cells>
        
<cell name="CellA">
            
            
<meta:notes>Simple test cell, just 2 segments</meta:notes>               <!-- Human readable comment -->
            
            
<meta:properties>
                
<meta:property tag="Abstraction level" value="Reduced cell model"/>  <!-- Property of the cell. Meaningful to some applications -->
            
</meta:properties>
        
            
<segments xmlns="http://morphml.org/morphml/schema">
                
                
<segment id ="0" name="Soma"  cable="0">
                    
<proximal x="0" y="0" z="0" diameter="10"/>
                    
<distal x="10" y="0" z="0" diameter="10"/>
                
</segment>
                
                
<segment id ="1" name="Dendrite" parent="0" cable="1">
                    
<proximal x="10" y="0" z="0" diameter="3"/>
                    
<distal x="100" y="0" z="0" diameter="3"/>
                    
<properties>
                        
<meta:property tag="display:transparency" value="50%"/>        <!-- Show this segment as 50% transparent -->
                    
</properties>
                
</segment>
                
            
</segments>

            
<cables xmlns="http://morphml.org/morphml/schema">
                
<cable id="0" name="SomaCable">
                    
<meta:properties>
                        
<meta:property tag="display:colour" value="red"/>          <!-- Colour for displaying the soma -->
                    
</meta:properties>
                    
<meta:group>soma_group</meta:group>
                
</cable>
                
<cable id="1" name="DendriteCable">
                    
<meta:properties>
                        
<meta:property tag="display:colour" value="green"/>        <!-- Colour for displaying the dendrite -->
                    
</meta:properties>
                    
<meta:group>dendrite_group</meta:group>
                
</cable>
            
</cables>
                    
            
<biophysics  units="Physiological Units" >

                
<bio:mechanism name="pas"  type="Channel Mechanism">
                    
<bio:parameter name="gmax" value="0.033">
                        
<bio:group>all</bio:group>
                    
</bio:parameter>
                    
                    
<!-- Only gmax is a standardised parameter name, but the extra values below could be used -->
                    
<!--  by an application which wishes to vary the properties of a cell between instances. -->

                    
<bio:parameter name="gmax_max" value="0.011">        
                        
<bio:group>all</bio:group>                              
                    
</bio:parameter>                                                              
                    
<bio:parameter name="gmax_min" value="0.055">
                        
<bio:group>all</bio:group>
                    
</bio:parameter>
                
</bio:mechanism>

                
<!-- The channel mechanism here is only available in a NEURON NMODL file -->

                
<bio:mechanism name="Na_Channel_NMODL" type="Channel Mechanism">
                    
<bio:parameter name="gmax" value="0.8">
                        
<bio:group>all</bio:group>
                    
</bio:parameter>
                
</bio:mechanism>

                
<bio:spec_capacitance>
                    
<bio:parameter value="1.0">
                        
<bio:group>all</bio:group>
                    
</bio:parameter>
                
</bio:spec_capacitance>
                
<bio:spec_axial_resistance>
                    
<bio:parameter value="0.1">
                        
<bio:group>all</bio:group>
                    
</bio:parameter>
                
</bio:spec_axial_resistance>
              
            
</biophysics>
        
</cell>
    
</cells>
                      
<!-- The biophysical mechanisms present in the network-->
    
    
<channels units="Physiological Units">

        
<channel_type name="pas" density="yes"   xmlns="http://morphml.org/channelml/schema">
            
<meta:notes>Simple example of a leak/passive conductance.</meta:notes>
        
            
<current_voltage_relation cond_law="ohmic" ion="non_specific" default_erev="-54.3" default_gmax="0.3"/>
        
</channel_type>
        
        
<synapse_type name="DoubExpSynA"  xmlns="http://morphml.org/channelml/schema">

            
<meta:properties>
                
<meta:property tag="Impl requirement" value="dt less than 0.02 ms"/> <!-- Suggestions for implementation of model -->
            
</meta:properties>
            
<meta:annotation></meta:annotation>

            
<doub_exp_syn max_conductance="1.0E-5" rise_time=".1" decay_time="2" reversal_potential="0"/>
        
</synapse_type>

        
<synapse_type name="VoltDepGapJunc"  xmlns="http://morphml.org/channelml/schema">

            
<electrical_syn  conductance="1.0E-9">

                
<!--
                 Note: this is a CUSTOM EXTENSION. The parsing application which generates the NMODL
                 file for NEURON should replace the standard Ohmic current at a gap junction:

                   i = weight * g * (v - vgap)

                 with the voltage dependent one below. The file remains valid NeuroML. Only
                 simulators which support this custom extension will model the synpase correctly.
                 Note: not a physiological voltage dependence.
               -->


                
<meta:properties>
                    
<meta:property tag="NMODL current expression" value="i = weight * g * (v - vgap) * (v - vgap)"/>
                
</meta:properties>

            
</electrical_syn>

        
</synapse_type>

    
</channels>
    
    
                      
<!-- The cell populations present in the network-->

    
<populations  xmlns="http://morphml.org/networkml/schema">
        
<population name="CellGroupA" cell_type="CellA">
            
<instances size="3">
                
<instance id="0">
                    
<meta:properties>
                        
<meta:property tag="display:transparency" value="0.9"/>    <!-- Transparency of the the cell -->
                    
</meta:properties>
                    
<location x="0" y="0" z="0"/>
                
</instance>
                
<instance id="1">
                    
<meta:properties>
                        
<meta:property tag="colour" value="red"/>
                    
</meta:properties>
                    
<location x="0" y="10" z="0"/>
                
</instance>
                
<instance id="2">
                    
<meta:properties>
                        
<meta:property tag="colour" value="green"/>
                    
</meta:properties>
                    
<location x="0" y="20" z="0"/>
                
</instance>
            
</instances>
        
</population>
        
<population name="CellGroupB" cell_type="CellA">
            
<instances size="2">
                
<instance id="0"><location x="0" y="100" z="0"/></instance>
                
<instance id="1"><location x="20" y="100" z="0"/></instance>
            
</instances>
        
</population>
    
</populations>
    
    
                      
<!-- The projections between populations in the network-->
    
    
<projections units="Physiological Units" xmlns="http://morphml.org/networkml/schema">
        
<projection name="NetworkConnection" source="CellGroupA" target="CellGroupB">
            
            
<synapse_props synapse_type="VoltDepGapJunc"/>
            
            
<connections>
                
<connection id="0" pre_cell_id="0" pre_segment_id = "0" post_cell_id="1" post_segment_id = "1">
                    
                    
<meta:properties>
                        
<meta:property tag="display:weight" value="bold"/>   <!-- A flag to highlight this connection -->
                    
</meta:properties>
                    
                
</connection>
                
<connection id="1" pre_cell_id="2" pre_segment_id = "0" post_cell_id="1" post_segment_id = "0"/>
                
<connection id="2" pre_cell_id="3" pre_segment_id = "0" post_cell_id="1" post_segment_id = "1"/>
            
</connections>
        
</projection>
    
</projections>
    
                  


</neuroml>