diff --git a/NeuroML2CoreTypes/Cells.xml b/NeuroML2CoreTypes/Cells.xml index a3a3126..49748c4 100644 --- a/NeuroML2CoreTypes/Cells.xml +++ b/NeuroML2CoreTypes/Cells.xml @@ -667,19 +667,19 @@ - - + + - + - + diff --git a/README.md b/README.md index b54669d..f3aee50 100644 --- a/README.md +++ b/README.md @@ -26,5 +26,5 @@ Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, For information on how to contribute to the NeuroML initiative, see [here](https://docs.neuroml.org/Devdocs/DevSOP.html). -This code is distributed under the terms of the GNU Lesser General Public License. +This code is distributed under the terms of the [GNU Lesser General Public License](https://github.com/NeuroML/NeuroML2/blob/master/LICENSE.lesser). diff --git a/docs/Cells.html b/docs/Cells.html index 1ff7e50..c9b02c2 100644 --- a/docs/Cells.html +++ b/docs/Cells.html @@ -15,7 +15,7 @@ - NeuroML v2.2 Component Types + NeuroML v2.3 Component Types
-

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.2 definitions, using the latest version of LEMS!
+

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.3 definitions, using the latest version of LEMS!
- +

Cells

Defines both abstract cell models (e.g. izhikevichCell, adaptive exponential integrate and fire cell, adExIaFCell), point conductance based cell models (pointCellCondBased, pointCellCondBasedCa) and cells models (cell) which specify the morphology (containing segments) and biophysicalProperties separately.
Original LEMS ComponentType definitions: Cells.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd
Original LEMS ComponentType definitions: Cells.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.3.xsd

  @@ -2027,18 +2027,18 @@ Child elements - + - +
proximalproximalPropertiesproximalDetails
distaldistalPropertiesdistalDetails
-  +  @@ -2054,11 +2054,11 @@
- proximalProperties + proximalDetails
-  +  @@ -3798,7 +3798,7 @@ - + @@ -3872,31 +3872,31 @@ - + - + - + - + - + - + - + - + @@ -3910,7 +3910,7 @@ - + @@ -3987,34 +3987,34 @@ - + - + - + - + - + - + - + - + - + - + @@ -4031,7 +4031,7 @@ - + @@ -4176,7 +4176,7 @@ + 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 @@ -4283,10 +4283,10 @@ - + - + diff --git a/docs/Channels.html b/docs/Channels.html index e421bac..348b419 100644 --- a/docs/Channels.html +++ b/docs/Channels.html @@ -15,7 +15,7 @@ - NeuroML v2.2 Component Types + NeuroML v2.3 Component Types
-

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.2 definitions, using the latest version of LEMS!
+

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.3 definitions, using the latest version of LEMS!
- distalProperties + distalDetails
Exposures UU
    Membrane recovery variable
Dimensionless
v    (from baseCellMembPot)C    (from baseCellMembPotCap) capacitance
aa
    Time scale of recovery variable u
per_time
bb
    Sensitivity of recovery variable u to subthreshold fluctuations of membrane potential v
conductance
cc
    After-spike reset value of v
voltage
dd
    After-spike increase to u
current
k conductance_per_voltage
v0v0
    Initial membrane potential
voltage
vpeakvpeak
    Peak action potential value
voltage
vrvr
    Resting membrane potential
voltage
vtvt
    Spike threshold
voltage
iSyn    (from baseCellMembPotCap) current
uu
    Membrane recovery variable
current
v    (from baseCellMembPot)C    (from baseCellMembPotCap) capacitance
ELEL
    Leak reversal potential
voltage
VTVT
    Spike threshold
voltage
aa
    Sub-threshold adaptation variable
conductance
bb
    Spike-triggered adaptation variable
current
delTdelT
    Slope factor
voltage
gLgL
    Leak conductance
conductance
refractrefract
    Refractory period
time
resetreset
    Reset potential
voltage
tauwtauw
    Adaptation time constant
time
threshthresh
    Spike detection threshold
voltage
v    (from baseCellMembPot) voltage
ww
    Adaptation current
current
- Reduced CA3 cell model from Pinsky and Rinzel 1994. See https://github.com/OpenSourceBrain/PinskyRinzelModel
Si Dimensionless
VdVd
    Dendritic membrane potential
voltage
VsVs
    Somatic membrane potential
voltage
Wi
- +

Channels

Defines voltage (and concentration) gated ion channel models. Ion channels will generally extend baseIonChannel. The most commonly used voltage dependent gate will extend baseGate.
Original LEMS ComponentType definitions: Channels.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd
Original LEMS ComponentType definitions: Channels.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.3.xsd

  diff --git a/docs/Inputs.html b/docs/Inputs.html index 20bbe52..1aa19ac 100644 --- a/docs/Inputs.html +++ b/docs/Inputs.html @@ -15,7 +15,7 @@ - NeuroML v2.2 Component Types + NeuroML v2.3 Component Types
-

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.2 definitions, using the latest version of LEMS!
+

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.3 definitions, using the latest version of LEMS!
- +

Inputs

A number of ComponentTypes for providing spiking (e.g. spikeGeneratorPoisson, spikeArray) and current inputs (e.g. pulseGenerator, voltageClamp, timedSynapticInput, poissonFiringSynapse) to other ComponentTypes
Original LEMS ComponentType definitions: Inputs.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd
Original LEMS ComponentType definitions: Inputs.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.3.xsd

  diff --git a/docs/Networks.html b/docs/Networks.html index 7265723..55491e5 100644 --- a/docs/Networks.html +++ b/docs/Networks.html @@ -15,7 +15,7 @@ - NeuroML v2.2 Component Types + NeuroML v2.3 Component Types
-

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.2 definitions, using the latest version of LEMS!
+

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.3 definitions, using the latest version of LEMS!
- +

Networks

Network descriptions for NeuroML 2. Describes network elements containing populations (potentially of type populationList, and so specifying a list of cell locations), projections (i.e. lists of connections) and inputs.
Original LEMS ComponentType definitions: Networks.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd
Original LEMS ComponentType definitions: Networks.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.3.xsd

  diff --git a/docs/NeuroMLCoreCompTypes.html b/docs/NeuroMLCoreCompTypes.html index f539209..b99106e 100644 --- a/docs/NeuroMLCoreCompTypes.html +++ b/docs/NeuroMLCoreCompTypes.html @@ -15,7 +15,7 @@ - NeuroML v2.2 Component Types + NeuroML v2.3 Component Types
-

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.2 definitions, using the latest version of LEMS!
+

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.3 definitions, using the latest version of LEMS!
- +

NeuroMLCoreCompTypes

NeuroML2 ComponentType definitions from NeuroMLCoreCompTypes.xml
Original LEMS ComponentType definitions: NeuroMLCoreCompTypes.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd
Original LEMS ComponentType definitions: NeuroMLCoreCompTypes.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.3.xsd

  diff --git a/docs/NeuroMLCoreDimensions.html b/docs/NeuroMLCoreDimensions.html index a596e83..96c110e 100644 --- a/docs/NeuroMLCoreDimensions.html +++ b/docs/NeuroMLCoreDimensions.html @@ -15,7 +15,7 @@ - NeuroML v2.2 Component Types + NeuroML v2.3 Component Types
-

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.2 definitions, using the latest version of LEMS!
+

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.3 definitions, using the latest version of LEMS!
- +

NeuroMLCoreDimensions

NeuroML2 ComponentType definitions from NeuroMLCoreDimensions.xml
Original LEMS ComponentType definitions: NeuroMLCoreDimensions.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd
Original LEMS ComponentType definitions: NeuroMLCoreDimensions.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.3.xsd

  diff --git a/docs/PyNN.html b/docs/PyNN.html index a7c10d9..9986211 100644 --- a/docs/PyNN.html +++ b/docs/PyNN.html @@ -15,7 +15,7 @@ - NeuroML v2.2 Component Types + NeuroML v2.3 Component Types
-

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.2 definitions, using the latest version of LEMS!
+

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.3 definitions, using the latest version of LEMS!
- +

PyNN

A number of ComponentType description of PyNN standard cells. All of the cells extend basePyNNCell, and the synapses extend basePynnSynapse.
Original LEMS ComponentType definitions: PyNN.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd
Original LEMS ComponentType definitions: PyNN.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.3.xsd

  diff --git a/docs/Synapses.html b/docs/Synapses.html index 752913d..a16407b 100644 --- a/docs/Synapses.html +++ b/docs/Synapses.html @@ -15,7 +15,7 @@ - NeuroML v2.2 Component Types + NeuroML v2.3 Component Types
-

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.2 definitions, using the latest version of LEMS!
+

NOTE: the latest version of this documentation can be found on docs.neuroml.org!


For more information on NeuroML 2 and LEMS see here.
Note: these descriptions have been updated to the latest NeuroML v2.3 definitions, using the latest version of LEMS!
- +

Synapses

A number of synaptic ComponentTypes for use in NeuroML 2 documents, e.g. expOneSynapse, expTwoSynapse, blockingPlasticSynapse. These extend the baseSynapse ComponentType. Also defined continuously transmitting synapses, e.g. gapJunction and gradedSynapse.
Original LEMS ComponentType definitions: Synapses.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd
Original LEMS ComponentType definitions: Synapses.xml
Schema against which NeuroML based on these should be valid: NeuroML_v2.3.xsd