From 282a6b255d66307008aa42d0a362566fdc7d83bb Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 7 Aug 2023 13:49:15 +0100 Subject: [PATCH 1/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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). From bfa81f11031f1406e27f8256c54deecb1149862e Mon Sep 17 00:00:00 2001 From: pgleeson Date: Wed, 9 Aug 2023 15:31:24 +0100 Subject: [PATCH 2/4] Regenerated html versions of lems docs, not that they're used much --- docs/Cells.html | 56 ++++++++++++++++----------------- docs/Channels.html | 6 ++-- docs/Inputs.html | 6 ++-- docs/Networks.html | 6 ++-- docs/NeuroMLCoreCompTypes.html | 6 ++-- docs/NeuroMLCoreDimensions.html | 6 ++-- docs/PyNN.html | 6 ++-- docs/Synapses.html | 6 ++-- 8 files changed, 49 insertions(+), 49 deletions(-) diff --git a/docs/Cells.html b/docs/Cells.html index 1ff7e50..53b531e 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

  @@ -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
  • Cells
    • @@ -243,10 +243,10 @@
-

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!
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
  • Cells
    • @@ -95,10 +95,10 @@
-

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
  • Cells
    • @@ -137,10 +137,10 @@
-

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
  • Cells
    • @@ -91,10 +91,10 @@
-

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
  • Cells
    • @@ -134,10 +134,10 @@
-

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
  • Cells
    • @@ -71,10 +71,10 @@
-

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
  • Cells
    • @@ -87,10 +87,10 @@
-

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

  From 47c4ad1b4acb4f29dd31955df70e8310e8d789db Mon Sep 17 00:00:00 2001 From: "Ankur Sinha (Ankur Sinha Gmail)" Date: Wed, 9 Aug 2023 17:43:46 +0100 Subject: [PATCH 3/4] fix(cells.xml): match proximal/distal properties to schema fixes #211 --- NeuroML2CoreTypes/Cells.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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 @@ - - + + - + - + From f8f10687acbb95b4d76e11531cedf78eb2dea9da Mon Sep 17 00:00:00 2001 From: "Ankur Sinha (Ankur Sinha Gmail)" Date: Wed, 9 Aug 2023 17:45:55 +0100 Subject: [PATCH 4/4] chore: regenerate cells.html --- docs/Cells.html | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/Cells.html b/docs/Cells.html index 53b531e..c9b02c2 100644 --- a/docs/Cells.html +++ b/docs/Cells.html @@ -162,9 +162,9 @@                   ++ inhomogeneousParameter
-                     + proximal proximalProperties
+                     + proximal proximalDetails
-                     + distal distalProperties
+                     + distal distalDetails
            + biophysicalProperties
@@ -2027,18 +2027,18 @@ Child elements - + - +
proximalproximalPropertiesproximalDetails
distaldistalPropertiesdistalDetails
-  +  @@ -2054,11 +2054,11 @@
- proximalProperties + proximalDetails
-  + 
- distalProperties + distalDetails