-
+
@@ -250,7 +250,7 @@
baseSpikingCell
- extends baseCell |
+ extends baseCell
@@ -275,7 +275,7 @@
|
- Any spiking cell which has a membrane potential v with voltage units. |
+ Any spiking cell which has a membrane potential v with units of voltage (as opposed to a dimensionless membrane potential used in baseCellMembPotDL).
@@ -304,7 +304,7 @@
- Any spiking cell which has a dimensioness membrane potential, V. |
+ Any spiking cell which has a dimensioness membrane potential, V (as opposed to a membrane potential units of voltage, baseCellMembPot).
@@ -329,11 +329,11 @@
baseChannelPopulation
- extends baseVoltageDepPointCurrent |
+ extends baseVoltageDepPointCurrent
- Base type for any current produced by a population of channels, all of type ionChannel |
+ Base type for any current produced by a population of channels, all of which are of type ionChannel
@@ -356,7 +356,7 @@
Requirements
|
- v (from baseVoltageDepPointCurrent) |
+ v (from baseVoltageDepPointCurrent) |
voltage |
@@ -366,21 +366,21 @@
channelPopulation
- extends baseChannelPopulation |
+ extends baseChannelPopulation
- Population of number ohmic ion channels. These each produce a conductance channelg across a reversal potential erev, giving a total current i. |
+ Population of a number of ohmic ion channels. These each produce a conductance channelg across a reversal potential erev, giving a total current i. Note that active membrane currents are more frequently specified as a density over an area of the cell using channelDensity
Parameters
|
- erev |
+ erev The reversal potential of the current produced |
voltage |
-
number |
+
number The number of channels present. This will be multiplied by the time varying conductance of the individual ion channel (which extends _baseIonChannel_) to produce the total conductance |
Dimensionless |
@@ -411,7 +411,7 @@
Requirements
|
- v (from baseVoltageDepPointCurrent) |
+ v (from baseVoltageDepPointCurrent) |
voltage |
@@ -438,18 +438,18 @@
channelPopulationNernst
- extends baseChannelPopulation |
+ extends baseChannelPopulation
- Population of channels with a time varying reversal potential erev determined by Nernst equation. Hard coded for Ca only! |
+ Population of a number of channels with a time varying reversal potential erev determined by Nernst equation. Note: hard coded for Ca only!
Parameters
|
- number |
+ number The number of channels present. This will be multiplied by the time varying conductance of the individual ion channel (which extends _baseIonChannel_) to produce the total conductance |
Dimensionless |
@@ -481,7 +481,7 @@
Exposures
|
- erev |
+ erev The reversal potential of the current produced, calculated from _caConcExt and _caConc |
voltage |
i (from basePointCurrent) |
@@ -492,16 +492,16 @@
Requirements
|
-
caConc |
+
caConc The internal Ca2+ concentration, as calculated/exposed by the parent Component |
concentration |
-
caConcExt |
+
caConcExt The external Ca2+ concentration, as calculated/exposed by the parent Component |
concentration |
-
temperature |
+
temperature The temperature to use in the calculation of _erev. Note this is generally exposed by a _networkWithTemperature_. |
temperature |
-
v (from baseVoltageDepPointCurrent) |
+
v (from baseVoltageDepPointCurrent) |
voltage |
@@ -534,7 +534,7 @@
- Base type for current distributed on an area of a cell |
+ Base type for a current of density iDensity distributed on an area of a cell, flowing through the specified ionChannel. Instances of this (normally channelDensity) are specified in the membraneProperties of the cell.
@@ -567,7 +567,7 @@
baseChannelDensityCond
- extends baseChannelDensity |
+ extends baseChannelDensity
@@ -589,7 +589,7 @@
| gDensity |
conductanceDensity |
-
iDensity (from baseChannelDensity) |
+
iDensity (from baseChannelDensity) |
currentDensity |
@@ -597,7 +597,7 @@
Requirements
|
- v (from baseChannelDensity) |
+ v (from baseChannelDensity) |
voltage |
@@ -611,7 +611,7 @@
- Specifies a parameter which can vary its value across a segmentGroup |
+ Specifies a parameter (e.g. condDensity) which can vary its value across a segmentGroup. The value is calculated from value attribute of the inhomogeneousValue subelement. This element is normally a child of channelDensityNonUniform, channelDensityNonUniformNernst or channelDensityNonUniformGHK and is used to calculate the value of the conductance, etc. which will vary on different parts of the cell. The segmentGroup specified here needs to define an inhomogeneousParameter (referenced from inhomogeneousParameter in the inhomogeneousValue), which calculates a variable (e.g. p) varying across the cell (e.g. based on the path length from soma), which is then used in the value attribute of the inhomogeneousValue (so for example condDensity = f(p))
@@ -628,7 +628,7 @@
Child elements
inhomogeneousValue |
- inhomogeneousValue |
+ inhomogeneousValue |
@@ -641,7 +641,7 @@
- Specifies the value of a variableParameter |
+ Specifies the value of an inhomogeneousParameter. For usage see variableParameter
@@ -659,18 +659,18 @@
channelDensityNonUniform
- extends baseChannelDensity |
+ extends baseChannelDensity
- Specifies a time varying ohmic conductance density, which is distributed on a region of the cell. The conductance density of the channel is not uniform, but is set using the variableParameter. Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON |
+ Specifies a time varying ohmic conductance density, which is distributed on a region of the cell. The conductance density of the channel is not uniform, but is set using the variableParameter. Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON
Parameters
|
- erev |
+ erev The reversal potential of the current produced |
voltage |
@@ -688,7 +688,7 @@
Child elements
variableParameter |
- variableParameter |
+ variableParameter |
@@ -703,7 +703,7 @@
Exposures
|
- iDensity (from baseChannelDensity) |
+ iDensity (from baseChannelDensity) |
currentDensity |
@@ -711,7 +711,7 @@
Requirements
|
- v (from baseChannelDensity) |
+ v (from baseChannelDensity) |
voltage |
@@ -736,11 +736,11 @@
channelDensityNonUniformNernst
- extends baseChannelDensity |
+ extends baseChannelDensity
- Specifies a time varying conductance density, which is distributed on a region of the cell, and whose reversal potential is calculated from the Nernst equation. Hard coded for Ca only!. The conductance density of the channel is not uniform, but is set using the variableParameter. Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON |
+ Specifies a time varying conductance density, which is distributed on a region of the cell, and whose reversal potential is calculated from the Nernst equation. Hard coded for Ca only!. The conductance density of the channel is not uniform, but is set using the variableParameter. Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON
@@ -757,7 +757,7 @@
Child elements
variableParameter |
- variableParameter |
+ variableParameter |
@@ -772,7 +772,7 @@
Exposures
|
- iDensity (from baseChannelDensity) |
+ iDensity (from baseChannelDensity) |
currentDensity |
@@ -780,7 +780,7 @@
Requirements
|
- v (from baseChannelDensity) |
+ v (from baseChannelDensity) |
voltage |
@@ -805,11 +805,11 @@
channelDensityNonUniformGHK
- extends baseChannelDensity |
+ extends baseChannelDensity
- Specifies a time varying conductance density, which is distributed on a region of the cell, and whose current is calculated from the Goldman-Hodgkin-Katz equation. Hard coded for Ca only!. The conductance density of the channel is not uniform, but is set using the variableParameter. Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON |
+ Specifies a time varying conductance density, which is distributed on a region of the cell, and whose current is calculated from the Goldman-Hodgkin-Katz equation. Hard coded for Ca only!. The conductance density of the channel is not uniform, but is set using the variableParameter. Note, there is no dynamical description of this in LEMS yet, as this type only makes sense for multicompartmental cells. A ComponentType for this needs to be present to enable export of NeuroML 2 multicompartmental cells via LEMS/jNeuroML to NEURON
@@ -826,7 +826,7 @@
Child elements
variableParameter |
- variableParameter |
+ variableParameter |
@@ -841,7 +841,7 @@
Exposures
|
- iDensity (from baseChannelDensity) |
+ iDensity (from baseChannelDensity) |
currentDensity |
@@ -849,7 +849,7 @@
Requirements
|
- v (from baseChannelDensity) |
+ v (from baseChannelDensity) |
voltage |
@@ -878,7 +878,7 @@
- Specifies a time varying ohmic conductance density, gDensity, which is distributed on an area of the cell with fixed reversal potential erev producing a current density iDensity |
+ Specifies a time varying ohmic conductance density, gDensity, which is distributed on an area of the cell (specified in membraneProperties) with fixed reversal potential erev producing a current density iDensity
@@ -888,7 +888,7 @@
condDensity (from baseChannelDensityCond) |
conductanceDensity |
-
erev |
+
erev The reversal potential of the current produced |
voltage |
@@ -916,7 +916,7 @@
gDensity (from baseChannelDensityCond) |
conductanceDensity |
-
iDensity (from baseChannelDensity) |
+
iDensity (from baseChannelDensity) |
currentDensity |
@@ -924,7 +924,7 @@
Requirements
|
- v (from baseChannelDensity) |
+ v (from baseChannelDensity) |
voltage |
@@ -952,11 +952,11 @@
channelDensityVShift
- extends channelDensity |
+ extends channelDensity
- Same as channelDensity, but with a vShift parameter to change voltage activation of gates. The exact usage of vShift in expressions for rates is determined by the individual gates. |
+ Same as channelDensity, but with a vShift parameter to change voltage activation of gates. The exact usage of vShift in expressions for rates is determined by the individual gates.
@@ -966,7 +966,7 @@
condDensity (from baseChannelDensityCond) |
conductanceDensity |
-
erev (from channelDensity) |
+
erev (from channelDensity) |
voltage |
vShift |
@@ -989,7 +989,7 @@
gDensity (from baseChannelDensityCond) |
conductanceDensity |
-
iDensity (from baseChannelDensity) |
+
iDensity (from baseChannelDensity) |
currentDensity |
@@ -997,7 +997,7 @@
Requirements
|
- v (from baseChannelDensity) |
+ v (from baseChannelDensity) |
voltage |
@@ -1011,7 +1011,7 @@
- Specifies a time varying conductance density, gDensity, which is distributed on an area of the cell, producing a current density iDensity and whose reversal potential is calculated from the Nernst equation. Hard coded for Ca only! See https://github.com/OpenSourceBrain/ghk-nernst. |
+ Specifies a time varying conductance density, gDensity, which is distributed on an area of the cell, producing a current density iDensity and whose reversal potential is calculated from the Nernst equation. Hard coded for Ca only! See https://github.com/OpenSourceBrain/ghk-nernst.
@@ -1049,13 +1049,13 @@
Exposures
|
- erev |
+ erev The reversal potential of the current produced, calculated from caConcExt and caConc |
voltage |
gDensity (from baseChannelDensityCond) |
conductanceDensity |
-
iDensity (from baseChannelDensity) |
+
iDensity (from baseChannelDensity) |
currentDensity |
@@ -1072,7 +1072,7 @@
temperature |
temperature |
-
v (from baseChannelDensity) |
+
v (from baseChannelDensity) |
voltage |
@@ -1155,13 +1155,13 @@
Exposures
|
- erev |
+ erev The reversal potential of the current produced |
voltage |
gDensity (from baseChannelDensityCond) |
conductanceDensity |
-
iDensity (from baseChannelDensity) |
+
iDensity (from baseChannelDensity) |
currentDensity |
@@ -1178,7 +1178,7 @@
temperature |
temperature |
-
v (from baseChannelDensity) |
+
v (from baseChannelDensity) |
voltage |
@@ -1219,7 +1219,7 @@
channelDensityGHK
- extends baseChannelDensity |
+ extends baseChannelDensity
@@ -1261,7 +1261,7 @@
|
Exposures
|
- iDensity (from baseChannelDensity) |
+ iDensity (from baseChannelDensity) |
currentDensity |
@@ -1278,7 +1278,7 @@
temperature |
temperature |
-
v (from baseChannelDensity) |
+
v (from baseChannelDensity) |
voltage |
@@ -1356,7 +1356,7 @@
gDensity (from baseChannelDensityCond) |
conductanceDensity |
-
iDensity (from baseChannelDensity) |
+
iDensity (from baseChannelDensity) |
currentDensity |
@@ -1373,7 +1373,7 @@
temperature |
temperature |
-
v (from baseChannelDensity) |
+
v (from baseChannelDensity) |
voltage |
@@ -1418,7 +1418,7 @@
- Simple model of a conductance based cell, with no separate morphology element, just an absolute capacitance C, and a set of channel populations |
+ Simple model of a conductance based cell, with no separate morphology element, just an absolute capacitance C, and a set of channel populations. Note: use of cell is generally preferable (and more widely supported), even for a single compartment cell.
@@ -1428,10 +1428,10 @@
C (from baseCellMembPotCap) |
capacitance |
-
thresh |
+
thresh The voltage threshold above which the cell is considered to be _spiking |
voltage |
-
v0 |
+
v0 The initial membrane potential of the cell |
voltage |
@@ -1440,7 +1440,7 @@
Children elements
populations |
- baseChannelPopulation |
+ baseChannelPopulation |
@@ -1453,7 +1453,7 @@
iSyn (from baseCellMembPotCap) |
current |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
@@ -1518,7 +1518,7 @@
- TEMPORARY: Point cell with conductances and Ca concentration info. Not yet fully tested!!! |
+ TEMPORARY: Point cell with conductances and Ca concentration info. Not yet fully tested!!! TODO: Remove in favour of cell
@@ -1528,10 +1528,10 @@
C (from baseCellMembPotCap) |
capacitance |
-
thresh |
+
thresh The voltage threshold above which the cell is considered to be _spiking |
voltage |
-
v0 |
+
v0 The initial membrane potential of the cell |
voltage |
@@ -1540,7 +1540,7 @@
Children elements
populations |
- baseChannelPopulation |
+ baseChannelPopulation |
concentrationModels |
concentrationModel |
@@ -1562,7 +1562,7 @@
iSyn (from baseCellMembPotCap) |
current |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
@@ -1631,7 +1631,7 @@
- Point furthest from the soma in a segment |
+ Point on a segment furthest from the soma. Should always be present in the description of a segment, unlike proximal
@@ -1678,7 +1678,7 @@
- Point closest to the soma in a segment. Note, if the proximal point is equal to the distal point of the parent segment, proximal can be omitted. |
+ Point on a segment closest to the soma. Note, the proximal point can be omitted, and in this case is defined as being the point fractionAlong between the proximal and distal point of the parent, i.e. if fractionAlong = 1 (as it is by default) it will be the distal on the parent, or if fractionAlong = 0, it will be the proximal point. If between 0 and 1, it is the linear interpolation between the two points.
@@ -1725,7 +1725,7 @@
- Specifies the segment which is this segment's parent |
+ Specifies the segment which is this segment's parent. The fractionAlong specifies where it is connected, usually 1 (the default value), meaning the distal point of the parent, or 0, meaning the proximal point. If it is between these, a linear interpolation between the 2 points should be used.
@@ -1747,7 +1747,7 @@
- A segment defines the smallest unit within a possibly branching structure (morphology), such as a dendrite or axon. The shape is given by the proximal and distal points. If proximal is missing, the proximal point is assumed to be the distal point of the parent. parent specifies the parent segment. The first segment (no parent) usually represents the soma. NOTE: LEMS does not yet support multicompartmental modelling, so the Dynamics here is only appropriate for single compartment modelling. |
+ A segment defines the smallest unit within a possibly branching structure (morphology), such as a dendrite or axon. Its id should be a nonnegative integer (usually soma/root = 0). Its end points are given by the proximal and distal points. The proximal point can be omitted, usually because it is the same as a point on the parent segment, see proximal for details. parent specifies the parent segment. The first segment of a cell (with no parent) usually represents the soma. The shape is normally a cylinder (radii of the proximal and distal equal, but positions different) or a conical frustum (radii and positions different). If the x,y,x positions of the proximal and distal are equal, the segment can be interpreted as a sphere, and in this case the radii of these points must be equal. NOTE: LEMS does not yet support multicompartmental modelling, so the Dynamics here is only appropriate for single compartment modelling.
@@ -1762,13 +1762,13 @@
Child elements
parent |
- parent |
+ parent |
distal |
-
distal |
+
distal |
proximal |
-
proximal |
+
proximal |
@@ -1830,7 +1830,7 @@
- A method to describe a group of segments in a morphology |
+ A method to describe a group of segments in a morphology, e.g. soma_group, dendrite_group, axon_group. While a name is useful to describe the group, the neuroLexId attribute can be used to explicitly specify the meaning of the group, e.g. sao1044911821 for 'Neuronal Cell Body', sao1211023249 for 'Dendrite'. The segments in this group can be specified as: a list of individual member segments; a path, all of the segments along which should be included; a subTree of the cell to include; other segmentGroups to include (so all segments from those get included here). An inhomogeneousParameter can be defined on the region of the cell specified by this group (see variableParameter for usage).
@@ -1845,17 +1845,17 @@
Child elements
notes |
- notes |
+ notes |
annotation |
-
annotation |
+
annotation |
Children elements
|
property |
-
property |
+
property |
members |
member |
@@ -1867,10 +1867,10 @@
subTree |
includes |
-
include |
+
include |
inhomogeneousParameter |
-
inhomogeneousParameter |
+
inhomogeneousParameter |
@@ -1883,7 +1883,7 @@
- A single identified segment which is part of the segmentGroup |
+ A single identified segment which is part of the segmentGroup
@@ -1903,7 +1903,7 @@
- Specifies which segment distal from which to calculate the segmentGroup |
+ In a path or subTree, specifies which segment (inclusive) from which to calculate the segmentGroup
@@ -1923,7 +1923,7 @@
- Specifies which segment up to which to calculate the segmentGroup |
+ In a path, specifies which segment (inclusive) up to which to calculate the segmentGroup
@@ -1943,7 +1943,7 @@
- Include all members of another segmentGroup in this |
+ Include all members of another segmentGroup in this group
@@ -1965,7 +1965,7 @@
- Include all the segments between those specified by from and to, inclusive |
+ Include all the segments between those specified by from and to, inclusive
@@ -1973,10 +1973,10 @@
Child elements
from |
- from |
+ from |
to |
-
to |
+
to |
@@ -1989,7 +1989,7 @@
- Include all the segments distal to that specified by from in the segmentGroup |
+ Include all the segments distal to that specified by from in the segmentGroup
@@ -1997,7 +1997,7 @@
Child elements
from |
- from |
+ from |
@@ -2010,7 +2010,7 @@
- An inhomogeneous parameter specified across the segmentGroup |
+ An inhomogeneous parameter specified across the segmentGroup (see variableParameter for usage).
@@ -2083,7 +2083,7 @@
- The collection of segments which specify the 3D structure of the cell, along with a number of segmentGroups |
+ The collection of segments which specify the 3D structure of the cell, along with a number of segmentGroups
@@ -2091,10 +2091,10 @@
Children elements
segments |
- segment |
+ segment |
segmentGroups |
-
segmentGroup |
+
segmentGroup |
@@ -2218,10 +2218,10 @@
specificCapacitance |
populations |
-
baseChannelPopulation |
+
baseChannelPopulation |
channelDensities |
-
baseChannelDensity |
+
baseChannelDensity |
@@ -2297,10 +2297,10 @@
specificCapacitance |
populations |
-
baseChannelPopulation |
+
baseChannelPopulation |
channelDensities |
-
baseChannelDensity |
+
baseChannelDensity |
@@ -3003,11 +3003,11 @@
cell
- extends baseCellMembPot |
+ extends baseCellMembPot
- Cell with segments 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. |
+ Cell with segments 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.
@@ -3056,7 +3056,7 @@
totSpecCap |
specificCapacitance |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
@@ -3134,7 +3134,7 @@
- Variant of cell with two independent Ca2+ pools. Cell with segments 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. |
+ Variant of cell with two independent Ca2+ pools. Cell with segments 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.
@@ -3189,7 +3189,7 @@
totSpecCap (from cell) |
specificCapacitance |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
@@ -3269,7 +3269,7 @@
baseCellMembPotCap
- extends baseCellMembPot |
+ extends baseCellMembPot
@@ -3280,7 +3280,7 @@
|
Parameters
|
- C |
+ C Total capacitance of the cell membrane |
capacitance |
@@ -3294,7 +3294,7 @@
iSyn Total current due to synaptic inputs |
current |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
@@ -3312,7 +3312,7 @@
baseIaf
- extends baseCellMembPot |
+ extends baseCellMembPot
@@ -3323,10 +3323,10 @@
|
Parameters
|
- reset |
+ reset The value the membrane potential is reset to on spiking |
voltage |
-
thresh |
+
thresh The membrane potential at which to emit a spiking event and reset voltage |
voltage |
@@ -3334,7 +3334,7 @@
Exposures
|
- v (from baseCellMembPot) |
+ v (from baseCellMembPot) |
voltage |
@@ -3380,7 +3380,7 @@
Exposures
|
- v (from baseCellMembPot) |
+ v (from baseCellMembPot) |
voltage |
@@ -3452,7 +3452,7 @@
Exposures
|
- v (from baseCellMembPot) |
+ v (from baseCellMembPot) |
voltage |
@@ -3536,7 +3536,7 @@
iSyn (from baseCellMembPotCap) |
current |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
@@ -3591,7 +3591,7 @@
iSyn (from baseCellMembPotCap) |
current |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
@@ -3686,7 +3686,7 @@
iSyn (from baseCellMembPotCap) |
current |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
@@ -3753,7 +3753,7 @@
izhikevichCell
- extends baseCellMembPot |
+ extends baseCellMembPot
@@ -3764,22 +3764,22 @@
|
Parameters
|
- a |
+ a Time scale of the recovery variable U |
Dimensionless |
-
b |
+
b Sensitivity of U to the subthreshold fluctuations of the membrane potential V |
Dimensionless |
-
c |
+
c After-spike reset value of V |
Dimensionless |
-
d |
+
d After-spike increase to U |
Dimensionless |
-
thresh |
+
thresh Spike threshold |
voltage |
-
v0 |
+
v0 Initial membrane potential |
voltage |
@@ -3801,7 +3801,7 @@
U |
Dimensionless |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
@@ -3818,7 +3818,7 @@
Attachments
synapses |
- basePointCurrentDL |
+ basePointCurrentDL |
@@ -3913,7 +3913,7 @@
u |
current |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
@@ -4028,7 +4028,7 @@
iSyn (from baseCellMembPotCap) |
current |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
w |
@@ -4106,7 +4106,7 @@
fitzHughNagumoCell
- extends baseCellMembPotDL |
+ extends baseCellMembPotDL
@@ -4133,7 +4133,7 @@
|
Exposures
|
- V (from baseCellMembPotDL) |
+ V (from baseCellMembPotDL) |
Dimensionless |
W |
@@ -4172,7 +4172,7 @@
pinskyRinzelCA3Cell
- extends baseCellMembPot |
+ extends baseCellMembPot
@@ -4307,7 +4307,7 @@
| sd |
Dimensionless |
-
v (from baseCellMembPot) |
+
v (from baseCellMembPot) |
voltage |
diff --git a/docs/Channels.html b/docs/Channels.html
index bd7fb5f..e421bac 100644
--- a/docs/Channels.html
+++ b/docs/Channels.html
@@ -15,7 +15,7 @@
- NeuroML v2.1 Component Types
+ NeuroML v2.2 Component Types
-
+
Channels |
- NeuroML2 ComponentType definitions from Channels.xml |
- Original LEMS ComponentType definitions: Channels.xml Schema against which NeuroML based on these should be valid: NeuroML_v2.1.xsd |
+ 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 |
@@ -1187,7 +1187,7 @@
Child elements
notes |
- notes |
+ notes |
@@ -1883,7 +1883,7 @@
Child elements
notes |
- notes |
+ notes |
timeCourse |
baseVoltageDepTime |
@@ -1977,10 +1977,10 @@
Child elements
notes |
- notes |
+ notes |
annotation |
- annotation |
+ annotation |
diff --git a/docs/Inputs.html b/docs/Inputs.html
index ffa96d3..20bbe52 100644
--- a/docs/Inputs.html
+++ b/docs/Inputs.html
@@ -15,7 +15,7 @@
- NeuroML v2.1 Component Types
+ NeuroML v2.2 Component Types
-
+
basePointCurrent
- extends baseStandalone |
+ extends baseStandalone
@@ -116,7 +116,7 @@
|
Exposures
|
- i The total (time varying) current produced by this ComponentType |
+ i The total (usually time varying) current produced by this ComponentType |
current |
@@ -130,7 +130,7 @@
- Base type for all ComponentTypes which produce a current i (with dimension current) and require a membrane potential v exposed on the parent Component |
+ Base type for all ComponentTypes which produce a current i (with dimension current) and require a voltage v exposed on the parent Component, which would often be the membrane potential of a Component extending baseCellMembPot
@@ -145,7 +145,7 @@
Requirements
|
- v |
+ v The current may vary with the voltage exposed by the ComponentType on which this is placed |
voltage |
@@ -155,7 +155,7 @@
baseVoltageDepPointCurrentSpiking
- extends baseVoltageDepPointCurrent |
+ extends baseVoltageDepPointCurrent
@@ -177,7 +177,7 @@
|
Requirements
|
- v (from baseVoltageDepPointCurrent) |
+ v (from baseVoltageDepPointCurrent) |
voltage |
@@ -199,7 +199,7 @@
- Base type for all ComponentTypes which produce a dimensionless current I. There will eventually be dimensionless equivalents of all the core current producing ComponentTypes such as pulseGenerator, sineGenerator and rampGenerator |
+ Base type for all ComponentTypes which produce a dimensionless current I. There are many dimensionless equivalents of all the core current producing ComponentTypes such as pulseGenerator / pulseGeneratorDL, sineGenerator / sineGeneratorDL and rampGenerator / rampGeneratorDL
@@ -216,7 +216,7 @@
baseVoltageDepPointCurrentDL
- extends basePointCurrentDL |
+ extends basePointCurrentDL
@@ -227,7 +227,7 @@
|
Exposures
|
- I (from basePointCurrentDL) |
+ I (from basePointCurrentDL) |
Dimensionless |
@@ -235,7 +235,7 @@
Requirements
|
- V |
+ V The current may vary with the dimensionless voltage exposed by the ComponentType on which this is placed |
Dimensionless |
@@ -249,7 +249,7 @@
- Base for any ComponentType whose main purpose is to emit spikes (on a port spike). The exposed variable tsince can be used for plotting the time since the Component has spiked last |
+ Base for any ComponentType whose main purpose is to emit spikes (on a port spike). The exposed variable tsince can be used for plotting the time since the Component has spiked last.
@@ -274,18 +274,18 @@
spikeGenerator
- extends baseSpikeSource |
+ extends baseSpikeSource
- Simple generator of spikes at a regular interval set by period. |
+ Simple generator of spikes at a regular interval set by period
Parameters
|
- period |
+ period Time between spikes. The first spike will be emitted after this time. |
time |
@@ -304,7 +304,7 @@
tnext When the next spike should ideally be emitted (dt permitting) |
time |
-
tsince (from baseSpikeSource) |
+
tsince (from baseSpikeSource) |
time |
@@ -312,7 +312,7 @@
Event Ports
|
- spike (from baseSpikeSource) |
+ spike (from baseSpikeSource) |
Direction: out |
@@ -332,7 +332,7 @@
tnext = period
On Conditions
- IF tnext-t < SMALL_TIME THEN
+ IF tnext - t < SMALL_TIME THEN
tsince = 0
tnext = tnext+period
EVENT OUT on port spike
@@ -350,7 +350,7 @@
spikeGeneratorRandom
- extends baseSpikeSource |
+ extends baseSpikeSource
@@ -361,10 +361,10 @@
|
Parameters
|
- maxISI |
+ maxISI Maximum interspike interval |
time |
-
minISI |
+
minISI Minimum interspike interval |
time |
@@ -386,7 +386,7 @@
tnext When the next spike should ideally be emitted (dt permitting) |
time |
-
tsince (from baseSpikeSource) |
+
tsince (from baseSpikeSource) |
time |
@@ -394,7 +394,7 @@
Event Ports
|
- spike (from baseSpikeSource) |
+ spike (from baseSpikeSource) |
Direction: out |
@@ -436,18 +436,18 @@
spikeGeneratorPoisson
- extends baseSpikeSource |
+ extends baseSpikeSource
- Generator of spikes whose ISI is distributed according to an exponential pdf with scale 1/_averageRate |
+ Generator of spikes whose ISI is distributed according to an exponential PDF with scale: 1 / averageRate
Parameters
|
- averageRate |
+ averageRate The average rate at which spikes are emitted |
per_time |
@@ -463,16 +463,16 @@
Exposures
|
- isi |
+ isi The interval until the next spike |
time |
-
tnextIdeal |
+
tnextIdeal This is the ideal/perfect next spike time, based on a newly generated isi, but dt precision will mean that it's usually slightly later than this |
time |
-
tnextUsed |
+
tnextUsed This is the next spike time for practical purposes, ensuring that it's later than the current time |
time |
-
tsince (from baseSpikeSource) |
+
tsince (from baseSpikeSource) |
time |
@@ -480,7 +480,7 @@
Event Ports
|
- spike (from baseSpikeSource) |
+ spike (from baseSpikeSource) |
Direction: out |
@@ -527,21 +527,21 @@
spikeGeneratorRefPoisson
- extends spikeGeneratorPoisson |
+ extends spikeGeneratorPoisson
- Generator of spikes whose ISI distribution is the maximum entropy distribution over [_minimumISI, +infinity) with mean 1/_averageRate |
+ Generator of spikes whose ISI distribution is the maximum entropy distribution over [ minimumISI, +infinity ) with mean: 1 / averageRate
Parameters
|
- averageRate (from spikeGeneratorPoisson) |
+ averageRate (from spikeGeneratorPoisson) |
per_time |
-
minimumISI |
+
minimumISI The minimum interspike interval |
time |
@@ -557,16 +557,16 @@
Exposures
|
- isi (from spikeGeneratorPoisson) |
+ isi (from spikeGeneratorPoisson) |
time |
-
tnextIdeal (from spikeGeneratorPoisson) |
+
tnextIdeal (from spikeGeneratorPoisson) |
time |
-
tnextUsed (from spikeGeneratorPoisson) |
+
tnextUsed (from spikeGeneratorPoisson) |
time |
-
tsince (from baseSpikeSource) |
+
tsince (from baseSpikeSource) |
time |
@@ -574,7 +574,7 @@
Event Ports
|
- spike (from baseSpikeSource) |
+ spike (from baseSpikeSource) |
Direction: out |
@@ -625,14 +625,14 @@
- Poisson spike generator connected to single synapse providing an input current |
+ Poisson spike generator firing at averageRate, which is connected to single synapse that is triggered every time a spike is generated, producing an input current. See also transientPoissonFiringSynapse.
Parameters
|
- averageRate |
+ averageRate The average rate at which spikes are emitted |
per_time |
@@ -674,7 +674,7 @@
i (from basePointCurrent) |
current |
-
isi |
+
isi The interval until the next spike |
time |
tnextIdeal |
@@ -691,7 +691,7 @@
Requirements
|
-
v (from baseVoltageDepPointCurrent) |
+
v (from baseVoltageDepPointCurrent) |
voltage |
@@ -767,7 +767,7 @@
- Poisson spike generator with delay and duration connected to single synapse providing an input current. Similar to ComponentType poissonFiringSynapse. |
+ Poisson spike generator firing at averageRate after a delay and for a duration, connected to single synapse that is triggered every time a spike is generated, providing an input current. Similar to ComponentType poissonFiringSynapse.
@@ -842,7 +842,7 @@
Requirements
|
- v (from baseVoltageDepPointCurrent) |
+ v (from baseVoltageDepPointCurrent) |
voltage |
@@ -918,7 +918,7 @@
- Spike array connected to a single synapse, producing current triggered by each spike in the array |
+ Spike array connected to a single synapse, producing a current triggered by each spike in the array.
@@ -959,7 +959,7 @@
Requirements
|
- v (from baseVoltageDepPointCurrent) |
+ v (from baseVoltageDepPointCurrent) |
voltage |
@@ -1006,6 +1006,140 @@
+
+
+
+
+ spikeArray
+ extends baseSpikeSource |
+
+
+
+ Set of spike ComponentTypes, each emitting one spike at a certain time. Can be used to feed a predetermined spike train into a cell |
+
+
+
+
+ Children elements
+ |
+ spikes |
+ spike |
+
+
+
+
+ Exposures
+ |
+ tsince (from baseSpikeSource) |
+ time |
+
+
+
+
+ Event Ports
+ |
+ in This will receive events from the children |
+ Direction: in |
+
+ spike (from baseSpikeSource) |
+ Direction: out |
+
+
+
+
+ Dynamics
+ |
+
+State Variables
+ tsince time (exposed as tsince)
+
+
+On Start
+ tsince = 0
+
+On Events
+ EVENT IN on port: in
+ tsince = 0
+ EVENT OUT on port spike
+
+Time Derivatives
+ d tsince /dt = 1
+
+ |
+
+
+
+
+
+
+
+ spike
+ extends baseSpikeSource |
+
+
+
+ Emits a single spike at the specified time |
+
+
+
+
+ Parameters
+ |
+ time Time at which to emit one spike event |
+ time |
+
+
+
+
+ Exposures
+ |
+ spiked 0 signals not yet spiked, 1 signals has spiked |
+ Dimensionless |
+
+ tsince (from baseSpikeSource) |
+ time |
+
+
+
+
+ Event Ports
+ |
+ spike (from baseSpikeSource) |
+ Direction: out |
+
+
+
+
+ Dynamics
+ |
+
+Structure
+ WITH this AS a
+ WITH parent AS b
+ EVENT CONNECTION from a TO b, RECEIVER: , TARGET PORT:
+
+State Variables
+ tsince time (exposed as tsince)
+
+ spiked Dimensionless (exposed as spiked)
+
+
+On Start
+ tsince = 0
+
+On Conditions
+ IF (t >= time) AND (spiked = 0) THEN
+ spiked = 1
+ tsince = 0
+ EVENT OUT on port spike
+
+Time Derivatives
+ d tsince /dt = 1
+
+ |
+
+
+
@@ -1022,13 +1156,13 @@
Parameters
|
- amplitude |
+ amplitude Amplitude of current pulse |
current |
- delay |
+ delay Delay before change in current. Current is zero prior to this. |
time |
- duration |
+ duration Duration for holding current at amplitude. Current is zero after delay + duration. |
time |
@@ -1044,7 +1178,7 @@
Event Ports
|
- in Note this is not used here. Will be removed in future |
+ in Note: this is not used here. Will be removed in future |
Direction: in |
@@ -1083,7 +1217,7 @@
- Generates a current which is the sum of all its child basePointCurrent elements |
+ Generates a current which is the sum of all its child basePointCurrent element, e.g. can be a combination of pulseGenerator, sineGenerator elements producing a single i. Scaled by weight, if set
@@ -1132,11 +1266,11 @@
compoundInputDL
- extends basePointCurrentDL |
+ extends basePointCurrentDL
- Generates a current which is the sum of all its child basePointCurrentDL elements |
+ Generates a current which is the sum of all its child basePointCurrentDL elements, e.g. can be a combination of pulseGeneratorDL, sineGeneratorDL elements producing a single i. Scaled by weight, if set
@@ -1144,14 +1278,14 @@
Children elements
currents |
- basePointCurrentDL |
+ basePointCurrentDL |
Exposures
|
- I (from basePointCurrentDL) |
+ I (from basePointCurrentDL) |
Dimensionless |
@@ -1185,24 +1319,24 @@
pulseGeneratorDL
- extends basePointCurrentDL |
+ extends basePointCurrentDL
- Dimensionless equivalent of pulseGenerator. Generates a constant current pulse of a certain amplitude for a specified duration after a delay |
+ Dimensionless equivalent of pulseGenerator. Generates a constant current pulse of a certain amplitude for a specified duration after a delay. Scaled by weight, if set
Parameters
|
- amplitude |
+ amplitude Amplitude of current pulse |
Dimensionless |
- delay |
+ delay Delay before change in current. Current is zero prior to this. |
time |
- duration |
+ duration Duration for holding current at amplitude. Current is zero after delay + duration. |
time |
@@ -1210,7 +1344,7 @@
Exposures
|
- I (from basePointCurrentDL) |
+ I (from basePointCurrentDL) |
Dimensionless |
@@ -1257,26 +1391,26 @@
- Generates a sinusoidally varying current after a time delay, for a fixed duration. The period and maximum amplitude of the current can be set as well as the phase at which to start. |
+ Generates a sinusoidally varying current after a time delay, for a fixed duration. The period and maximum amplitude of the current can be set as well as the phase at which to start. Scaled by weight, if set
Parameters
|
- amplitude |
+ amplitude Maximum amplitude of current |
current |
- delay |
+ delay Delay before change in current. Current is zero prior to this. |
time |
- duration |
+ duration Duration for holding current at amplitude. Current is zero after delay + duration. |
time |
- period |
+ period Time period of oscillation |
time |
- phase |
+ phase Phase (between 0 and 2*pi) at which to start the varying current (i.e. at time given by delay) |
Dimensionless |
@@ -1327,30 +1461,30 @@
sineGeneratorDL
- extends basePointCurrentDL |
+ extends basePointCurrentDL
- Generates a sinusoidally varying current after a time delay, for a fixed duration. The period and maximum amplitude of the current can be set as well as the phase at which to start. |
+ Dimensionless equivalent of sineGenerator. Generates a sinusoidally varying current after a time delay, for a fixed duration. The period and maximum amplitude of the current can be set as well as the phase at which to start. Scaled by weight, if set
Parameters
|
- amplitude |
+ amplitude Maximum amplitude of current |
Dimensionless |
- delay |
+ delay Delay before change in current. Current is zero prior to this. |
time |
- duration |
+ duration Duration for holding current at amplitude. Current is zero after delay + duration. |
time |
- period |
+ period Time period of oscillation |
time |
- phase |
+ phase Phase (between 0 and 2*pi) at which to start the varying current (i.e. at time given by delay) |
Dimensionless |
@@ -1358,7 +1492,7 @@
Exposures
|
- I (from basePointCurrentDL) |
+ I (from basePointCurrentDL) |
Dimensionless |
@@ -1405,26 +1539,26 @@
- Generates a ramping current after a time delay, for a fixed duration. During this time the current steadily changes from startAmplitude to finishAmplitude. |
+ Generates a ramping current after a time delay, for a fixed duration. During this time the current steadily changes from startAmplitude to finishAmplitude. Scaled by weight, if set
Parameters
|
- baselineAmplitude |
+ baselineAmplitude Amplitude of current before time delay, and after time delay + duration |
current |
- delay |
+ delay Delay before change in current. Current is baselineAmplitude prior to this. |
time |
- duration |
+ duration Duration for holding current at amplitude. Current is baselineAmplitude after delay + duration. |
time |
- finishAmplitude |
+ finishAmplitude Amplitude of linearly varying current at time delay + duration |
current |
- startAmplitude |
+ startAmplitude Amplitude of linearly varying current at time delay |
current |
@@ -1478,30 +1612,30 @@
rampGeneratorDL
- extends basePointCurrentDL |
+ extends basePointCurrentDL
- Generates a ramping current after a time delay, for a fixed duration. During this time the dimensionless current steadily changes from startAmplitude to finishAmplitude. |
+ Dimensionless equivalent of rampGenerator. Generates a ramping current after a time delay, for a fixed duration. During this time the dimensionless current steadily changes from startAmplitude to finishAmplitude. Scaled by weight, if set
Parameters
|
- baselineAmplitude |
+ baselineAmplitude Amplitude of current before time delay, and after time delay + duration |
Dimensionless |
- delay |
+ delay Delay before change in current. Current is baselineAmplitude prior to this. |
time |
- duration |
+ duration Duration for holding current at amplitude. Current is baselineAmplitude after delay + duration. |
time |
- finishAmplitude |
+ finishAmplitude Amplitude of linearly varying current at time delay + duration |
Dimensionless |
- startAmplitude |
+ startAmplitude Amplitude of linearly varying current at time delay |
Dimensionless |
@@ -1509,7 +1643,7 @@
Exposures
|
- I (from basePointCurrentDL) |
+ I (from basePointCurrentDL) |
Dimensionless |
@@ -1555,7 +1689,7 @@
voltageClamp
- extends baseVoltageDepPointCurrent |
+ extends baseVoltageDepPointCurrent
@@ -1566,16 +1700,16 @@
|
Parameters
|
- delay |
+ delay Delay before change in current. Current is zero prior to this. |
time |
- duration |
+ duration Duration for attempting to keep parent at targetVoltage. Current is zero after delay + duration. |
time |
- simpleSeriesResistance |
+ simpleSeriesResistance Current will be calculated by the difference in voltage between the target and parent, divided by this value |
resistance |
- targetVoltage |
+ targetVoltage Current will be applied to try to get parent to this target voltage |
voltage |
@@ -1591,7 +1725,7 @@
Requirements
|
- v (from baseVoltageDepPointCurrent) |
+ v (from baseVoltageDepPointCurrent) |
voltage |
@@ -1634,7 +1768,7 @@
voltageClampTriple
- extends baseVoltageDepPointCurrent |
+ extends baseVoltageDepPointCurrent
@@ -1645,25 +1779,25 @@
|
Parameters
|
- active |
+ active Whether the voltage clamp is active (1) or inactive (0). |
Dimensionless |
- conditioningVoltage |
+ conditioningVoltage Target voltage before time delay |
voltage |
- delay |
+ delay Delay before switching from conditioningVoltage to testingVoltage. |
time |
- duration |
+ duration Duration to hold at testingVoltage. |
time |
- returnVoltage |
+ returnVoltage Target voltage after time duration |
voltage |
- simpleSeriesResistance |
+ simpleSeriesResistance Current will be calculated by the difference in voltage between the target and parent, divided by this value |
resistance |
- testingVoltage |
+ testingVoltage Target voltage between times delay and delay + duration |
voltage |
@@ -1679,7 +1813,7 @@
Requirements
|
- v (from baseVoltageDepPointCurrent) |
+ v (from baseVoltageDepPointCurrent) |
voltage |
@@ -1717,140 +1851,6 @@
-
-
-
-
- spikeArray
- extends baseSpikeSource |
-
-
-
- Set of spike ComponentTypes, each emitting one spike at a certain time. Can be used to feed a predetermined spike train into a cell |
-
-
-
-
- Children elements
- |
- spikes |
- spike |
-
-
-
-
- Exposures
- |
- tsince (from baseSpikeSource) |
- time |
-
-
-
-
- Event Ports
- |
- in This will receive events from the children |
- Direction: in |
-
- spike (from baseSpikeSource) |
- Direction: out |
-
-
-
-
- Dynamics
- |
-
-State Variables
- tsince time (exposed as tsince)
-
-
-On Start
- tsince = 0
-
-On Events
- EVENT IN on port: in
- tsince = 0
- EVENT OUT on port spike
-
-Time Derivatives
- d tsince /dt = 1
-
- |
-
-
-
-
-
-
-
- spike
- extends baseSpikeSource |
-
-
-
- Emits a single spike at the specified time |
-
-
-
-
- Parameters
- |
- time |
- time |
-
-
-
-
- Exposures
- |
- spiked 0 signals not yet spiked, 1 signals has spiked |
- Dimensionless |
-
- tsince (from baseSpikeSource) |
- time |
-
-
-
-
- Event Ports
- |
- spike (from baseSpikeSource) |
- Direction: out |
-
-
-
-
- Dynamics
- |
-
-Structure
- WITH this AS a
- WITH parent AS b
- EVENT CONNECTION from a TO b, RECEIVER: , TARGET PORT:
-
-State Variables
- tsince time (exposed as tsince)
-
- spiked Dimensionless (exposed as spiked)
-
-
-On Start
- tsince = 0
-
-On Conditions
- IF (t >= time) AND (spiked = 0) THEN
- spiked = 1
- tsince = 0
- EVENT OUT on port spike
-
-Time Derivatives
- d tsince /dt = 1
-
- |
-
-
-