Merge pull request #4 from OpenSourceBrain/master

BK added

NEURON/analyse_mod_files.sh

@@ -12,5 +12,7 @@ pynml-modchananalysis Golgi_KA -stepV 5 -temperature [20,23]
 pynml-modchananalysis Golgi_Ca_HVA -stepV 5 -temperature [20,23] 
 pynml-modchananalysis Golgi_Ca_LVA -stepV 5 -temperature [20,23] 
 
+pynml-modchananalysis Golgi_BK -stepV 5 -temperature [20,23] -caConc 5e-4
+
 
 #pynml-modchananalysis Golgi_hcn1 -stepV 5 -temperature [20,23] 

NeuroML2/Golgi_BK.channel.nml

@@ -0,0 +1,67 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="Golgi_BK">
+
+    <notes>ChannelML file containing a single Channel description from Solinas et al 2007</notes>
+
+    <ionChannel id="Golgi_BK" conductance="10pS" type="ionChannelHH" species="k">
+
+        <notes>BK type voltage and [Ca2+] dependent K+ channel</notes>
+
+        <annotation>
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+                <rdf:Description rdf:about="Golgi_BK">
+
+                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>Solinas S, Forti L, Cesana E, Mapelli J, De Schutter E, D'Angelo E. (2007) Computational reconstruction of pacemaking and intrinsic electroresponsiveness in cerebellar Golgi cells.  Front Cell Neurosci. 2007;1:2.</rdf:li>
+                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/18946520"/>
+                        </rdf:Bag>
+                    </bqmodel:isDescribedBy>
+
+
+                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+                        <rdf:Bag>
+                            <rdf:li>K channels</rdf:li>
+                            <rdf:li rdf:resource="http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table3"/>
+                        </rdf:Bag>
+                    </bqbiol:isVersionOf>
+
+                </rdf:Description>
+            </rdf:RDF>
+        </annotation>
+
+        <gate id="c" type="gateHHrates" instances="1">
+            <q10Settings type="q10ExpTemp" q10Factor="3" experimentalTemp="30 degC"/>
+            <forwardRate type="Golgi_BK_c_alpha_rate"/>
+            <reverseRate type="Golgi_BK_c_beta_rate"/>
+        </gate>
+
+    </ionChannel>
+
+    <ComponentType name="Golgi_BK_c_alpha_rate" extends="baseVoltageConcDepRate">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="CONC_SCALE" dimension="concentration" value="1 mol_per_cm3"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <DerivedVariable name="ca_conc" dimension="none" value="caConc / CONC_SCALE"/>
+            <DerivedVariable name="r" exposure="r" dimension="per_time" value="(7/(1 + (0.0015 * (exp (V/-11.765))/(ca_conc * 1e6)))) / TIME_SCALE"/>
+        </Dynamics>
+
+    </ComponentType>
+
+    <ComponentType name="Golgi_BK_c_beta_rate" extends="baseVoltageConcDepRate">
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="CONC_SCALE" dimension="concentration" value="1 mol_per_cm3"/>
+
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <DerivedVariable name="ca_conc" dimension="none" value="caConc / CONC_SCALE"/>
+            <DerivedVariable name="r" exposure="r" dimension="per_time" value="(1/(1 + (ca_conc * 1e6)/(0.00015* (exp (V/-11.765)) ))) / TIME_SCALE"/>
+        </Dynamics>
+
+    </ComponentType>
+
+</neuroml>

NeuroML2/update.sh

@@ -26,6 +26,7 @@ copyNml2 'KV_CML' 'Golgi_KV'
 copyNml2 'CaHVA_CML' 'Golgi_Ca_HVA'
 copyNml2 'CaLVA_CML' 'Golgi_Ca_LVA'
 
+copyNml2 'KC_CML' 'Golgi_BK'
 
 
 copyNml2 'hcn1f_CML' 'Golgi_hcn1f'