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Update to latest nml2.3 schema
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@pgleeson
pgleeson committed Sep 20, 2023
1 parent 1bf6b3e commit 188b0f9
Showing 1 changed file with 93 additions and 28 deletions.
121 changes: 93 additions & 28 deletions public/schema/neuroml2/NeuroML_v2.3.xsd
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Original file line number Diff line number Diff line change
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<xs:pattern value="[a-zA-Z0-9_:]*"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2PopulationReferencePath">
<xs:annotation>
<xs:documentation>A path referring to another component.
</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:pattern value="(\.\./)?([a-zA-Z_][a-zA-Z0-9_]*)((\[[0-9]+\])|(/[0-9]+)+((/[a-zA-Z_][a-zA-Z0-9_]*)?)/?)"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="NonNegativeInteger">
<xs:annotation>
<xs:documentation>An attribute useful as id of segments, connections, etc: integer &gt;=0 only!</xs:documentation>
Expand Down Expand Up @@ -494,6 +503,7 @@
<xs:element name="fitzHughNagumoCell" type="FitzHughNagumoCell" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="fitzHughNagumo1969Cell" type="FitzHughNagumo1969Cell" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="pinskyRinzelCA3Cell" type="PinskyRinzelCA3Cell" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="hindmarshRose1984Cell" type="HindmarshRose1984Cell" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:group>
<xs:group name="PyNNCellTypes">
Expand Down Expand Up @@ -1586,23 +1596,23 @@
<xs:annotation>
<xs:documentation>Cell based on the modified Izhikevich model in Izhikevich 2007, Dynamical systems in neuroscience, MIT Press
\n
:param v0:
:param v0: Initial membrane potential
:type v0: voltage
:param k:
:type k: conductance_per_voltage
:param vr:
:param vr: Resting membrane potential
:type vr: voltage
:param vt:
:param vt: Spike threshold
:type vt: voltage
:param vpeak:
:param vpeak: Peak action potential value
:type vpeak: voltage
:param a:
:param a: Time scale of recovery variable u
:type a: per_time
:param b:
:param b: Sensitivity of recovery variable u to subthreshold fluctuations of membrane potential v
:type b: conductance
:param c:
:param c: After-spike reset value of v
:type c: voltage
:param d:
:param d: After-spike increase to u
:type d: current
:param C: Total capacitance of the cell membrane
:type C: capacitance
Expand All @@ -1627,25 +1637,25 @@
<xs:annotation>
<xs:documentation>Model based on Brette R and Gerstner W ( 2005 ) Adaptive Exponential Integrate-and-Fire Model as an Effective Description of Neuronal Activity. J Neurophysiol 94:3637-3642
\n
:param gL:
:param gL: Leak conductance
:type gL: conductance
:param EL:
:param EL: Leak reversal potential
:type EL: voltage
:param VT:
:param VT: Spike threshold
:type VT: voltage
:param thresh:
:param thresh: Spike detection threshold
:type thresh: voltage
:param reset:
:param reset: Reset potential
:type reset: voltage
:param delT:
:param delT: Slope factor
:type delT: voltage
:param tauw:
:param tauw: Adaptation time constant
:type tauw: time
:param refract:
:param refract: Refractory period
:type refract: time
:param a:
:param a: Sub-threshold adaptation variable
:type a: conductance
:param b:
:param b: Spike-triggered adaptation variable
:type b: current
:param C: Total capacitance of the cell membrane
:type C: capacitance
Expand Down Expand Up @@ -1714,7 +1724,7 @@
</xs:complexType>
<xs:complexType name="PinskyRinzelCA3Cell">
<xs:annotation>
<xs:documentation>Reduced CA3 cell model from Pinsky and Rinzel 1994. See https://github.com/OpenSourceBrain/PinskyRinzelModel
<xs:documentation>Reduced CA3 cell model from Pinsky, P. F. , Rinzel, J. Intrinsic and network rhythmogenesis in a reduced traub model for CA3 neurons. J Comput Neurosci 1, 39-60 ( 1994 ). See https://github.com/OpenSourceBrain/PinskyRinzelModel
\n
:param iSoma:
:type iSoma: currentDensity
Expand Down Expand Up @@ -1787,6 +1797,53 @@
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="HindmarshRose1984Cell">
<xs:annotation>
<xs:documentation>The Hindmarsh Rose model is a simplified point cell model which captures complex firing patterns of single neurons, such as periodic and chaotic bursting. It has a fast spiking subsystem, which is a generalization of the FitzHugh-Nagumo system, coupled to a slower subsystem which allows the model to fire bursts. The dynamical variables x, y, z correspond to the membrane potential, a recovery variable, and a slower adaptation current, respectively. See Hindmarsh J. L. , and Rose R. M. ( 1984 ) A model of neuronal bursting using three coupled first order differential equations. Proc. R. Soc. London, Ser. B 221:87–102.
\n
:param a: cubic term in x nullcline
:type a: none
:param b: quadratic term in x nullcline
:type b: none
:param c: constant term in y nullcline
:type c: none
:param d: quadratic term in y nullcline
:type d: none
:param r: timescale separation between slow and fast subsystem ( r greater than 0; r much less than 1 )
:type r: none
:param s: related to adaptation
:type s: none
:param x1: related to the system's resting potential
:type x1: none
:param v_scaling: scaling of x for physiological membrane potential
:type v_scaling: voltage
:param x0:
:type x0: none
:param y0:
:type y0: none
:param z0:
:type z0: none
:param C: Total capacitance of the cell membrane
:type C: capacitance

</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="BaseCellMembPotCap">
<xs:attribute name="a" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="b" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="c" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="d" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="s" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="x1" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="r" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="x0" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="y0" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="z0" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="v_scaling" type="Nml2Quantity_voltage" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="Cell">
<xs:annotation>
<xs:documentation>Cell with **segment** s specified in a **morphology** element along with details on its **biophysicalProperties** . NOTE: this can only be correctly simulated using jLEMS when there is a single segment in the cell, and **v** of this cell represents the membrane potential in that isopotential segment.
Expand Down Expand Up @@ -1932,13 +1989,21 @@
</xs:restriction>
</xs:simpleType>
<xs:complexType name="ProximalDetails">
<xs:annotation>
<xs:documentation>What to do at the proximal point when creating an inhomogeneous parameter
</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="BaseWithoutId">
<xs:attribute name="translationStart" type="xs:double" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="DistalDetails">
<xs:annotation>
<xs:documentation>What to do at the distal point when creating an inhomogeneous parameter
</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="BaseWithoutId">
<xs:attribute name="normalizationEnd" type="xs:double" use="required"/>
Expand Down Expand Up @@ -3097,9 +3162,9 @@
<xs:complexContent>
<xs:extension base="BaseWithoutId">
<xs:attribute name="neuroLexId" type="NeuroLexId" use="optional"/>
<xs:attribute name="from" type="xs:string" use="required"/>
<xs:attribute name="to" type="xs:string" use="required"/>
<xs:attribute name="synapse" type="xs:string" use="required"/>
<xs:attribute name="from" type="Nml2PopulationReferencePath" use="required"/>
<xs:attribute name="to" type="Nml2PopulationReferencePath" use="required"/>
<xs:attribute name="synapse" type="NmlId" use="required"/>
<xs:attribute name="destination" type="NmlId" use="optional"/>
</xs:extension>
</xs:complexContent>
Expand Down Expand Up @@ -3148,10 +3213,10 @@
</xs:annotation>
<xs:complexContent>
<xs:extension base="BaseConnection">
<xs:attribute name="preCellId" type="xs:string" use="required"/>
<xs:attribute name="preCellId" type="Nml2PopulationReferencePath" use="required"/>
<xs:attribute name="preSegmentId" type="NonNegativeInteger" default="0"/>
<xs:attribute name="preFractionAlong" type="ZeroToOne" default="0.5"/>
<xs:attribute name="postCellId" type="xs:string" use="required"/>
<xs:attribute name="postCellId" type="Nml2PopulationReferencePath" use="required"/>
<xs:attribute name="postSegmentId" type="NonNegativeInteger" default="0"/>
<xs:attribute name="postFractionAlong" type="ZeroToOne" default="0.5"/>
</xs:extension>
Expand Down Expand Up @@ -3309,9 +3374,9 @@
</xs:annotation>
<xs:complexContent>
<xs:extension base="BaseWithoutId">
<xs:attribute name="target" type="xs:string" use="required"/>
<xs:attribute name="input" type="xs:string" use="required"/>
<xs:attribute name="destination" type="xs:string"/>
<xs:attribute name="target" type="Nml2PopulationReferencePath" use="required"/>
<xs:attribute name="input" type="NmlId" use="required"/>
<xs:attribute name="destination" type="NmlId"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
Expand All @@ -3338,7 +3403,7 @@
</xs:annotation>
<xs:complexContent>
<xs:extension base="BaseNonNegativeIntegerId">
<xs:attribute name="target" type="xs:string" use="required"/>
<xs:attribute name="target" type="Nml2PopulationReferencePath" use="required"/>
<xs:attribute name="destination" type="NmlId" use="required"/>
<xs:attribute name="segmentId" type="NonNegativeInteger"/>
<xs:attribute name="fractionAlong" type="ZeroToOne"/>
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