diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 220a0d4..60b99d1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -5,10 +5,9 @@ name: Test commits on: push: - branches: [ master, development, experimental ] + branches: [ master, development, experimental, documentation_update, osb* ] pull_request: - branches: [ master, development, experimental ] - + branches: [ master, development, experimental, documentation_update, osb* ] jobs: build: @@ -16,7 +15,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - java: [ 8, 11.0.x, 11.0.3, 12, 13 ] + java: [ 8, 11, 16, 17 ] steps: - uses: actions/checkout@v2 @@ -27,6 +26,38 @@ jobs: java-version: ${{ matrix.java }} java-package: jdk - - name: Test build + - name: Install NeuroML 2 with Maven run: | + java -version mvn install + + - name: Install jNeuroML + run: | + export main_repo_branch=${GITHUB_REF##*/} + if [[ ${main_repo_branch} != "master" && ${main_repo_branch} != "development" && ${main_repo_branch} != "experimental" && ${main_repo_branch} != *"osb"* ]]; then main_repo_branch=development ; fi + echo Using branch $main_repo_branch + git clone https://github.com/NeuroML/jNeuroML.git + cd jNeuroML + git checkout $main_repo_branch + python getNeuroML.py $main_repo_branch # will call mvn install on this & other repos + ls -alt + mvn dependency:tree + ./jnml -v + cd .. + + - name: Install OMV + run: | + pwd + echo $GITHUB_WORKSPACE + export PATH=$PATH:$GITHUB_WORKSPACE/jNeuroML + export JNML_HOME=$GITHUB_WORKSPACE/jNeuroML + pip install git+https://github.com/OpenSourceBrain/osb-model-validation + omv list -V + env + pip freeze + + - name: Test examples using OMV + run: | + cd $GITHUB_WORKSPACE/NeuroML2/LEMSexamples + omv all -V --engine=jNeuroML --ignore-non-py3 + omv list -V diff --git a/.gitignore b/.gitignore index 2d19ca8..024d011 100644 --- a/.gitignore +++ b/.gitignore @@ -11,7 +11,6 @@ target *~ *.pyc -results build *.log *.xml0 @@ -64,3 +63,4 @@ examples/*.pov /LEMSexamples/report.txt /LEMSexamples/test/x86_64 /LEMSexamples/report.ex*.txt +/LEMSexamples/results/*.spikes diff --git a/HISTORY.md b/HISTORY.md index a632f7e..ca37e28 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -8,6 +8,20 @@ and [LEMS](https://github.com/LEMS/LEMS), but also the Python ([libNeuroML](http **Only contributors who are not [NeuroML Editors](https://neuroml.org/editors) are specifically pointed out below.** +v2.2 / 2021-12-15 +-------------------- + +* **Renamed the main Schema from NeuroML_v2.1.xsd to [NeuroML_v2.2.xsd](https://github.com/NeuroML/NeuroML2/blob/master/Schemas/NeuroML2/NeuroML_v2.2).** + +* Significant updates to documentation in NeuroML LEMS XML definitions. Have been propagated to core documentation e.g. https://docs.neuroml.org/Userdocs/Schemas/Networks.html + +* Major changes to pyNeuroML & libNeuroML to aid usability. These updates have been reflected in the NeuroML user guides & other documentation, e.g.: https://docs.neuroml.org/Userdocs/GettingStarted.html + +* Updates to automated testing of Python & Java libraries: all moved to GitHub Actions (for overview see [here](https://github.com/NeuroML/.github/tree/main/testsheet)); updated to test on latest version of Python & Java and Windows/Mac. + +* Removed `ValueAcrossSegOrSegGroup` (https://github.com/NeuroML/NeuroML2/pull/165 that fixes https://github.com/NeuroML/NeuroML2/issues/162) and update any elements using it to directly include `Value` and `SegmentGroup` attributes. This allows their correct validation. + + v2.1 / 2021-03-22 -------------------- diff --git a/LEMSexamples/regression-tests/LEMS_NML2_Ex5_DetCell_unformatted.xml b/LEMSexamples/regression-tests/LEMS_NML2_Ex5_DetCell_unformatted.xml new file mode 100644 index 0000000..3c475ff --- /dev/null +++ b/LEMSexamples/regression-tests/LEMS_NML2_Ex5_DetCell_unformatted.xml @@ -0,0 +1 @@ + diff --git a/LEMSexamples/regression-tests/results/README b/LEMSexamples/regression-tests/results/README new file mode 100644 index 0000000..944c767 --- /dev/null +++ b/LEMSexamples/regression-tests/results/README @@ -0,0 +1 @@ +Temporary folder for the results of simulations run with LEMS diff --git a/NeuroML2CoreTypes/Cells.xml b/NeuroML2CoreTypes/Cells.xml index 41ae249..122164f 100644 --- a/NeuroML2CoreTypes/Cells.xml +++ b/NeuroML2CoreTypes/Cells.xml @@ -1,6 +1,6 @@ - @@ -12,7 +12,7 @@ @@ -29,7 +29,7 @@ + description="Any spiking cell which has a membrane potential _v with units of voltage (as opposed to a dimensionless membrane potential used in _baseCellMembPotDL_)."> @@ -38,7 +38,7 @@ + description="Any spiking cell which has a dimensioness membrane potential, _V (as opposed to a membrane potential units of voltage, _baseCellMembPot_)."> @@ -47,7 +47,7 @@ + description="Base type for any current produced by a population of channels, all of which are of type _ionChannel"> @@ -56,15 +56,14 @@ + description="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_"> - - + + - - + @@ -81,9 +80,9 @@ + description="Population of a _number of channels with a time varying reversal potential _erev determined by Nernst equation. Note: hard coded for Ca only!"> - + @@ -92,13 +91,13 @@ - + - - - + + + - + @@ -120,7 +119,7 @@ + description="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_."> @@ -143,7 +142,7 @@ + description="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))"> @@ -154,7 +153,7 @@ + description="Specifies the _value of an _inhomogeneousParameter. For usage see _variableParameter_"> @@ -165,9 +164,9 @@ + description="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"> - + @@ -175,8 +174,8 @@ - + + - + + - + + - - + + @@ -281,9 +279,9 @@ - - + + + @@ -294,22 +292,22 @@ + description="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."> - + - - + + + @@ -349,14 +347,15 @@ - + - - + + + @@ -401,10 +400,9 @@ - + + - @@ -437,10 +435,9 @@ - + + - @@ -474,10 +471,10 @@ + description="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."> - - + + @@ -515,10 +512,10 @@ + description="TEMPORARY: Point cell with conductances and Ca concentration info. Not yet fully tested!!! TODO: Remove in favour of _cell_"> - - + + @@ -563,26 +560,26 @@ + description="Point on a _segment_ furthest from the soma. Should always be present in the description of a _segment_, unlike _proximal_"> + description="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."> - - + description="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."> + + + description="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. "> @@ -593,7 +590,7 @@ - + @@ -620,7 +617,7 @@ - + @@ -631,44 +628,45 @@ - + - + - + - + - - + + - + - + - + @@ -689,7 +687,6 @@ - @@ -1048,9 +1045,9 @@ extends="baseCellMembPot" description="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."> - + - + @@ -1377,12 +1374,12 @@ extends="baseCellMembPot" description="Cell based on the 2003 model of Izhikevich, see http://izhikevich.org/publications/spikes.htm"> - - - - - - + + + + + + @@ -1394,8 +1391,8 @@ - - + + diff --git a/NeuroML2CoreTypes/Channels.xml b/NeuroML2CoreTypes/Channels.xml index 7189ab4..3275b84 100644 --- a/NeuroML2CoreTypes/Channels.xml +++ b/NeuroML2CoreTypes/Channels.xml @@ -1,6 +1,6 @@ - diff --git a/NeuroML2CoreTypes/Inputs.xml b/NeuroML2CoreTypes/Inputs.xml index 127d40b..6eb5228 100644 --- a/NeuroML2CoreTypes/Inputs.xml +++ b/NeuroML2CoreTypes/Inputs.xml @@ -1,7 +1,7 @@ - + xsi:schemaLocation="http://www.neuroml.org/lems/0.7.6 ../../LEMS/Schemas/LEMS/LEMS_v0.7.6.xsd" + description="A number of ComponentTypes for providing spiking (e.g. _spikeGeneratorPoisson_, _spikeArray_) and current inputs (e.g. _pulseGenerator_, _voltageClamp_, _timedSynapticInput_, _poissonFiringSynapse_) to other ComponentTypes"> @@ -11,14 +11,14 @@ description="Base type for all ComponentTypes which produce a current _i (with dimension current)" extends="baseStandalone"> - + + description="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_"> @@ -41,7 +41,7 @@ + description="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_"> @@ -52,13 +52,13 @@ extends="basePointCurrentDL" description="Base type for all ComponentTypes which produce a dimensionless current _I and require a dimensionless membrane potential _V exposed on the parent Component"> - + + description="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."> + description="Simple generator of spikes at a regular interval set by _period"> - + - + @@ -98,7 +98,7 @@ - + @@ -117,7 +117,7 @@ - + @@ -152,15 +152,15 @@ + description="Generator of spikes whose ISI is distributed according to an exponential PDF with scale: 1 / _averageRate"> - + - - - + + + @@ -210,11 +210,11 @@ + description="Generator of spikes whose ISI distribution is the maximum entropy distribution over [ _minimumISI, +infinity ) with mean: 1 / _averageRate"> - + - + @@ -248,14 +248,14 @@ - + - + @@ -269,11 +269,11 @@ - + - + @@ -317,8 +317,8 @@ @@ -396,7 +396,7 @@ @@ -436,6 +436,63 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -448,7 +505,7 @@ - + @@ -476,7 +533,7 @@ + description="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"> @@ -500,7 +557,7 @@ + description="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"> @@ -525,7 +582,7 @@ + description="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"> @@ -561,15 +618,15 @@ + description="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"> - - - - - + + + + + @@ -596,15 +653,15 @@ + description="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"> - - - - - + + + + + @@ -632,15 +689,15 @@ + description="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"> - - - - - + + + + + @@ -673,15 +730,15 @@ + description="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"> - - - - - + + + + + @@ -717,7 +774,7 @@ - + @@ -799,61 +856,4 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/NeuroML2CoreTypes/Networks.xml b/NeuroML2CoreTypes/Networks.xml index c400f9e..ae60592 100644 --- a/NeuroML2CoreTypes/Networks.xml +++ b/NeuroML2CoreTypes/Networks.xml @@ -1,7 +1,7 @@ - + xsi:schemaLocation="http://www.neuroml.org/lems/0.7.6 ../../LEMS/Schemas/LEMS/LEMS_v0.7.6.xsd" + description="Network descriptions for NeuroML 2. Describes _network_ elements containing _population_s (potentially of type _populationList_, and so specifying a list of cell _location_s), _projection_s (i.e. lists of _connection_s) and _input_s."> @@ -10,10 +10,12 @@ + + @@ -28,7 +30,7 @@ - + @@ -36,7 +38,7 @@ @@ -47,7 +49,7 @@ - + @@ -55,14 +57,14 @@ - + - + - + @@ -71,13 +73,13 @@ - + - + @@ -394,7 +396,7 @@ - + @@ -403,12 +405,12 @@ - + - - + + diff --git a/NeuroML2CoreTypes/NeuroML2CoreTypes.xml b/NeuroML2CoreTypes/NeuroML2CoreTypes.xml index 36563d2..93ff52e 100644 --- a/NeuroML2CoreTypes/NeuroML2CoreTypes.xml +++ b/NeuroML2CoreTypes/NeuroML2CoreTypes.xml @@ -1,6 +1,6 @@ - diff --git a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml index ca400fd..5bac908 100644 --- a/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml +++ b/NeuroML2CoreTypes/NeuroMLCoreCompTypes.xml @@ -1,46 +1,46 @@ - + xsi:schemaLocation="http://www.neuroml.org/lems/0.7.6 ../../LEMS/Schemas/LEMS/LEMS_v0.7.6.xsd"> - + - + - + - - - + + + + description="Base type of any Component which can have _Notes_, _Annotation_, or a _property_ list."> - + - + @@ -63,7 +63,7 @@ - + @@ -106,13 +106,13 @@ - + - + @@ -120,15 +120,15 @@ - - - - - - - - - + + + + + + + + + diff --git a/NeuroML2CoreTypes/NeuroMLCoreDimensions.xml b/NeuroML2CoreTypes/NeuroMLCoreDimensions.xml index e1db27e..cf7ef80 100644 --- a/NeuroML2CoreTypes/NeuroMLCoreDimensions.xml +++ b/NeuroML2CoreTypes/NeuroMLCoreDimensions.xml @@ -1,6 +1,6 @@ - + xsi:schemaLocation="http://www.neuroml.org/lems/0.7.6 ../../LEMS/Schemas/LEMS/LEMS_v0.7.6.xsd"> diff --git a/NeuroML2CoreTypes/PyNN.xml b/NeuroML2CoreTypes/PyNN.xml index e71ac0e..cd0e2b8 100644 --- a/NeuroML2CoreTypes/PyNN.xml +++ b/NeuroML2CoreTypes/PyNN.xml @@ -1,6 +1,6 @@ - diff --git a/NeuroML2CoreTypes/Simulation.xml b/NeuroML2CoreTypes/Simulation.xml index 43552f7..7737bff 100644 --- a/NeuroML2CoreTypes/Simulation.xml +++ b/NeuroML2CoreTypes/Simulation.xml @@ -1,6 +1,7 @@ - + xsi:schemaLocation="http://www.neuroml.org/lems/0.7.6 ../../LEMS/Schemas/LEMS/LEMS_v0.7.6.xsd" + description="Specification of the LEMS Simulation element which is normally used to define simulations of NeuroML2 files. Note: not actually part of NeuroML v2, but this is required by much of the NeuroML toolchain for defining Simulations (which NeuroML model to use and how long to run for), as well as what to _Display_ and what to save in _OutputFile_s."> @@ -8,63 +9,62 @@ + + + - - - - - - - - + + + - + - - - - + + + + - - - - - - + - - - + + + + + + - - - + - + - + + + + - - - + + + + + - + - + - - + + @@ -72,21 +72,21 @@ - - + + - + - - - + + + @@ -94,9 +94,9 @@ - - - + + + diff --git a/NeuroML2CoreTypes/Synapses.xml b/NeuroML2CoreTypes/Synapses.xml index e23082e..7e76884 100644 --- a/NeuroML2CoreTypes/Synapses.xml +++ b/NeuroML2CoreTypes/Synapses.xml @@ -1,8 +1,8 @@ - - + xsi:schemaLocation="http://www.neuroml.org/lems/0.7.6 ../../LEMS/Schemas/LEMS/LEMS_v0.7.6.xsd" + description="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_."> + + + + + + An id attribute for elements which need to be identified uniquely (normally just within their parent element). + + + + + + + + A value for a physical quantity in NeuroML 2, e.g. 20, -60.0mV or 5nA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An id string for pointing to an entry in an annotation element related to a MIRIAM resource. Based on metaid of SBML + + + + + + + + An id string for pointing to an entry in the NeuroLex ontology. Use of this attribute is a shorthand for a full + RDF based reference to the MIRIAM Resource urn:miriam:neurolex, with an bqbiol:is qualifier + + + + + + + + + An attribute useful as id of segments, connections, etc: integer >=0 only! + + + + + + + + + + + Integer >=1 only! + + + + + + + + + + + Double >0 only + + + + + + + + Value which is either 0 or 1 + + + + + + + + + + + + + Textual human readable notes related to the element in question. It's useful to put these into + the NeuroML files instead of XML comments, as the notes can be extracted and repeated in the files to which the NeuroML is mapped. + + + + + + + A property ( a **tag** and **value** pair ), which can be on any **baseStandalone** either as a direct child, or within an **Annotation** . Generally something which helps the visual display or facilitates simulation of a Component, but is not a core physiological property. Common examples include: **numberInternalDivisions,** equivalent of nseg in NEURON; **radius,** for a radius to use in graphical displays for abstract cells ( i. e. without defined morphologies ); **color,** the color to use for a **Population** or **populationList** of cells; **recommended_dt_ms,** the recommended timestep to use for simulating a **Network** , **recommended_duration_ms** the recommended duration to use when running a **Network** + + + + + + + + A structured annotation containing metadata, specifically RDF or **property** elements + + + + + + + + + + Contains an extension to NeuroML by creating custom LEMS ComponentType. + + + + + + + + + + + + + + + + + LEMS ComponentType for Constant. + + + + + + + + + LEMS Exposure (ComponentType property) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + LEMS ComponentType for Dynamics + + + + + + + + + + + LEMS ComponentType for DerivedVariable + + + + + + + + + + + + + + + + + + + LEMS ComponentType for ConditionalDerivedVariable + + + + + + + + + + + + + + + + + + Float value restricted to between 1 and 0 + + + + + + + + + + + + The root NeuroML element. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Various types of cells which are defined in NeuroML 2. This list will be expanded... + + + + + + + + + + + + + + + + + + + + Various types of cells which are defined in NeuroML 2 based on PyNN standard cell models. + + + + + + + + + + + + + + Various types of synapse which are defined in NeuroML 2. This list will be expanded... + + + + + + + + + + + + + + + + + + Various types of synapse which are defined in NeuroML 2 based on PyNN standard cell/synapse models. + + + + + + + + + + + Various types of inputs which are defined in NeuroML2. This list will be expanded... + + + + + + + + + + + + + + + + + + + + + + + + + Various types of input which are defined in NeuroML 2 based on PyNN standard cell/synapse models. + + + + + + + + Various types of concentration model which are defined in NeuroML 2. This list will be expanded... + + + + + + + + + + + + + + + + + + + + + A kinetic scheme based ion channel with multiple **gateKS** s, each of which consists of multiple **KSState** s and **KSTransition** s giving the rates of transition between them +\n +:param conductance: +:type conductance: conductance + + + + + + + + + + + + + + + + Note **ionChannel** and **ionChannelHH** are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH. NeuroML v2beta4 should remove one of these, probably ionChannelHH. +\n +:param conductance: +:type conductance: conductance + + + + + + + + + + + + + + + + + + + + + + + + Note **ionChannel** and **ionChannelHH** are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH. NeuroML v2beta4 should remove one of these, probably ionChannelHH. +\n +:param conductance: +:type conductance: conductance + + + + + + + + + + Same as **ionChannel** , 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. +\n +:param vShift: +:type vShift: voltage +:param conductance: +:type conductance: conductance + + + + + + + + + + + + + + + + + + + A value for the conductance scaling which varies as a standard function of the difference between the current temperature, **temperature,** and the temperature at which the conductance was originally determined, **experimentalTemp** +\n +:param q10Factor: +:type q10Factor: none +:param experimentalTemp: +:type experimentalTemp: temperature + + + + + + + + + + + + + + + + + + + + + A **KSState** with **relativeConductance** of 0 +\n +:param relativeConductance: +:type relativeConductance: none + + + + + + + + + + + + A **KSState** with **relativeConductance** of 1 +\n +:param relativeConductance: +:type relativeConductance: none + + + + + + + + + + + + A forward only **KSTransition** for a **gateKS** which specifies a **rate** ( type **baseHHRate** ) which follows one of the standard Hodgkin Huxley forms ( e. g. **HHExpRate** , **HHSigmoidRate** , **HHExpLinearRate** + + + + + + + + + + + + + + + + A reverse only **KSTransition** for a **gateKS** which specifies a **rate** ( type **baseHHRate** ) which follows one of the standard Hodgkin Huxley forms ( e. g. **HHExpRate** , **HHSigmoidRate** , **HHExpLinearRate** + + + + + + + + + + + + + + + + + + + + + + KS Transition specified in terms of time constant **tau** and steady state **inf** + + + + + + + + + + + + + + + + A gate which consists of multiple **KSState** s and **KSTransition** s giving the rates of transition between them +\n +:param instances: +:type instances: none + + + + + + + + + + + + + + + + + + + + + + Note all sub elements for gateHHrates, gateHHratesTau, gateFractional etc. allowed here. Which are valid should be constrained by what type is set + + + + + + + + + + + + + + + + + + + + + Gate which follows the general Hodgkin Huxley formalism +\n +:param instances: +:type instances: none + + + + + + + + + + + + + + + + + + + Gate which follows the general Hodgkin Huxley formalism +\n +:param instances: +:type instances: none + + + + + + + + + + + + + + + + + + + Gate which follows the general Hodgkin Huxley formalism +\n +:param instances: +:type instances: none + + + + + + + + + + + + + + + + + + + + + Gate which follows the general Hodgkin Huxley formalism +\n +:param instances: +:type instances: none + + + + + + + + + + + + + + + + + + + + Gate which follows the general Hodgkin Huxley formalism +\n +:param instances: +:type instances: none + + + + + + + + + + + + + + + + + + + + Gate which follows the general Hodgkin Huxley formalism but is instantaneous, so tau = 0 and gate follows exactly inf value +\n +:param instances: +:type instances: none + + + + + + + + + + + + + + + + + Gate composed of subgates contributing with fractional conductance +\n +:param instances: +:type instances: none + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Model of an intracellular buffering mechanism for **ion** ( currently hard Coded to be calcium, due to requirement for **iCa** ) which has a baseline level **restingConc** and tends to this value with time course **decayConstant.** The ion is assumed to occupy a shell inside the membrane of thickness **shellThickness.** +\n +:param restingConc: +:type restingConc: concentration +:param decayConstant: +:type decayConstant: time +:param shellThickness: +:type shellThickness: length + + + + + + + + + + + + + + + + + + Model of buffering of concentration of an ion ( currently hard coded to be calcium, due to requirement for **iCa** ) which has a baseline level **restingConc** and tends to this value with time course **decayConstant.** A fixed factor **rho** is used to scale the incoming current *independently of the size of the compartment* to produce a concentration change. +\n +:param restingConc: +:type restingConc: concentration +:param decayConstant: +:type decayConstant: time +:param rho: +:type rho: rho_factor + + + + + + + + + + + + + + + + + + + + + Base type for all synapses, i. e. ComponentTypes which produce a current ( dimension current ) and change Dynamics in response to an incoming event. cno_0000009 + + + + + + + + + + + Base type for synapses with a dependence on membrane potential + + + + + + + + + + + Synapse model which produces a synaptic current. + + + + + + + + + + + Synapse model which exposes a conductance **g** in addition to producing a current. Not necessarily ohmic!! cno_0000027 +\n +:param gbase: Baseline conductance, generally the maximum conductance following a single spike +:type gbase: conductance +:param erev: Reversal potential of the synapse +:type erev: voltage + + + + + + + + + + + + + Synapse model suited for a sum of two expTwoSynapses which exposes a conductance **g** in addition to producing a current. Not necessarily ohmic!! cno_0000027 +\n +:param gbase1: Baseline conductance 1 +:type gbase1: conductance +:param gbase2: Baseline conductance 2 +:type gbase2: conductance +:param erev: Reversal potential of the synapse +:type erev: voltage + + + + + + + + + + + + + + Gap junction/single electrical connection +\n +:param conductance: +:type conductance: conductance + + + + + + + + + + + + Dummy synapse which emits no current. Used as presynaptic endpoint for analog synaptic connection. + + + + + + + + + + + Behaves just like a one way gap junction. +\n +:param conductance: +:type conductance: conductance + + + + + + + + + + + + Graded/analog synapse. Based on synapse in Methods of http://www. nature.com/neuro/journal/v7/n12/abs/nn1352.html +\n +:param conductance: +:type conductance: conductance +:param delta: Slope of the activation curve +:type delta: voltage +:param k: Rate constant for transmitter-receptor dissociation rate +:type k: per_time +:param Vth: The half-activation voltage of the synapse +:type Vth: voltage +:param erev: The reversal potential of the synapse +:type erev: voltage + + + + + + + + + + + + + + + + Alpha current synapse: rise time and decay time are both **tau.** +\n +:param tau: Time course for rise and decay +:type tau: time +:param ibase: Baseline current increase after receiving a spike +:type ibase: current + + + + + + + + + + + + + Ohmic synapse model where rise time and decay time are both **tau.** Max conductance reached during this time ( assuming zero conductance before ) is **gbase** * **weight.** +\n +:param tau: Time course of rise/decay +:type tau: time +:param gbase: Baseline conductance, generally the maximum conductance following a single spike +:type gbase: conductance +:param erev: Reversal potential of the synapse +:type erev: voltage + + + + + + + + + + + + Ohmic synapse model whose conductance rises instantaneously by ( **gbase** * **weight** ) on receiving an event, and which decays exponentially to zero with time course **tauDecay** +\n +:param tauDecay: Time course of decay +:type tauDecay: time +:param gbase: Baseline conductance, generally the maximum conductance following a single spike +:type gbase: conductance +:param erev: Reversal potential of the synapse +:type erev: voltage + + + + + + + + + + + + Ohmic synapse model whose conductance waveform on receiving an event has a rise time of **tauRise** and a decay time of **tauDecay.** Max conductance reached during this time ( assuming zero conductance before ) is **gbase** * **weight.** +\n +:param tauRise: +:type tauRise: time +:param tauDecay: +:type tauDecay: time +:param gbase: Baseline conductance, generally the maximum conductance following a single spike +:type gbase: conductance +:param erev: Reversal potential of the synapse +:type erev: voltage + + + + + + + + + + + + + Ohmic synapse similar to expTwoSynapse but consisting of two components that can differ in decay times and max conductances but share the same rise time. +\n +:param tauRise: +:type tauRise: time +:param tauDecay1: +:type tauDecay1: time +:param tauDecay2: +:type tauDecay2: time +:param gbase1: Baseline conductance 1 +:type gbase1: conductance +:param gbase2: Baseline conductance 2 +:type gbase2: conductance +:param erev: Reversal potential of the synapse +:type erev: voltage + + + + + + + + + + + + + + Synapse consisting of two independent synaptic mechanisms ( e. g. AMPA-R and NMDA-R ), which can be easily colocated in connections + + + + + + + + + + + + + + Biexponential synapse that allows for optional block and plasticity mechanisms, which can be expressed as child elements. +\n +:param tauRise: +:type tauRise: time +:param tauDecay: +:type tauDecay: time +:param gbase: Baseline conductance, generally the maximum conductance following a single spike +:type gbase: conductance +:param erev: Reversal potential of the synapse +:type erev: voltage + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Base type of any cell ( e. g. point neuron like **izhikevich2007Cell** , or a morphologically detailed **Cell** with **segment** s ) which can be used in a **population** + + + + + + + + + + Integrate and fire cell which returns to its leak reversal potential of **leakReversal** with a time constant **tau** +\n +:param leakReversal: +:type leakReversal: voltage +:param tau: +:type tau: time +:param thresh: The membrane potential at which to emit a spiking event and reset voltage +:type thresh: voltage +:param reset: The value the membrane potential is reset to on spiking +:type reset: voltage + + + + + + + + + + + + + + + Integrate and fire cell which returns to its leak reversal potential of **leakReversal** with a time course **tau.** It has a refractory period of **refract** after spiking +\n +:param refract: +:type refract: time +:param leakReversal: +:type leakReversal: voltage +:param tau: +:type tau: time +:param thresh: The membrane potential at which to emit a spiking event and reset voltage +:type thresh: voltage +:param reset: The value the membrane potential is reset to on spiking +:type reset: voltage + + + + + + + + + + + + Integrate and fire cell with capacitance **C,** **leakConductance** and **leakReversal** +\n +:param leakConductance: +:type leakConductance: conductance +:param leakReversal: +:type leakReversal: voltage +:param thresh: +:type thresh: voltage +:param reset: +:type reset: voltage +:param C: Total capacitance of the cell membrane +:type C: capacitance + + + + + + + + + + + + + + + + Integrate and fire cell with capacitance **C,** **leakConductance,** **leakReversal** and refractory period **refract** +\n +:param refract: +:type refract: time +:param leakConductance: +:type leakConductance: conductance +:param leakReversal: +:type leakReversal: voltage +:param thresh: +:type thresh: voltage +:param reset: +:type reset: voltage +:param C: Total capacitance of the cell membrane +:type C: capacitance + + + + + + + + + + + + Cell based on the 2003 model of Izhikevich, see http://izhikevich.org/publications/spikes.htm +\n +:param v0: Initial membrane potential +:type v0: voltage +:param a: Time scale of the recovery variable U +:type a: none +:param b: Sensitivity of U to the subthreshold fluctuations of the membrane potential V +:type b: none +:param c: After-spike reset value of V +:type c: none +:param d: After-spike increase to U +:type d: none +:param thresh: Spike threshold +:type thresh: voltage + + + + + + + + + + + + + + + + + Any cell with a membrane potential **v** with voltage units and a membrane capacitance **C.** Also defines exposed value **iSyn** for current due to external synapses and **iMemb** for total transmembrane current ( usually channel currents plus **iSyn** ) +\n +:param C: Total capacitance of the cell membrane +:type C: capacitance + + + + + + + + + + + + + + + + + + Cell based on the modified Izhikevich model in Izhikevich 2007, Dynamical systems in neuroscience, MIT Press +\n +:param v0: +:type v0: voltage +:param k: +:type k: conductance_per_voltage +:param vr: +:type vr: voltage +:param vt: +:type vt: voltage +:param vpeak: +:type vpeak: voltage +:param a: +:type a: per_time +:param b: +:type b: conductance +:param c: +:type c: voltage +:param d: +:type d: current +:param C: Total capacitance of the cell membrane +:type C: capacitance + + + + + + + + + + + + + + + + + + + + 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: +:type gL: conductance +:param EL: +:type EL: voltage +:param VT: +:type VT: voltage +:param thresh: +:type thresh: voltage +:param reset: +:type reset: voltage +:param delT: +:type delT: voltage +:param tauw: +:type tauw: time +:param refract: +:type refract: time +:param a: +:type a: conductance +:param b: +:type b: current +:param C: Total capacitance of the cell membrane +:type C: capacitance + + + + + + + + + + + + + + + + + + + + + Simple dimensionless model of spiking cell from FitzHugh and Nagumo. Superseded by **fitzHughNagumo1969Cell** ( See https://github.com/NeuroML/NeuroML2/issues/42 ) +\n +:param I: +:type I: none + + + + + + + + + + + + The Fitzhugh Nagumo model is a two-dimensional simplification of the Hodgkin-Huxley model of spike generation in squid giant axons. This system was suggested by FitzHugh ( FitzHugh R. [1961]: Impulses and physiological states in theoretical models of nerve membrane. Biophysical J. 1:445-466 ), who called it " Bonhoeffer-van der Pol model ", and the equivalent circuit by Nagumo et al. ( Nagumo J. , Arimoto S. , and Yoshizawa S. [1962] An active pulse transmission line simulating nerve axon. Proc IRE. 50:2061-2070. 1962 ). This version corresponds to the one described in FitzHugh R. [1969]: Mathematical models of excitation and propagation in nerve. Chapter 1 ( pp. 1-85 in H. P. Schwan, ed. Biological Engineering, McGraw-Hill Book Co. , N. Y. ) +\n +:param a: +:type a: none +:param b: +:type b: none +:param I: plays the role of an external injected current +:type I: none +:param phi: +:type phi: none +:param V0: +:type V0: none +:param W0: +:type W0: none + + + + + + + + + + + + + + + + + Reduced CA3 cell model from Pinsky and Rinzel 1994. See https://github.com/OpenSourceBrain/PinskyRinzelModel +\n +:param iSoma: +:type iSoma: currentDensity +:param iDend: +:type iDend: currentDensity +:param gLs: +:type gLs: conductanceDensity +:param gLd: +:type gLd: conductanceDensity +:param gNa: +:type gNa: conductanceDensity +:param gKdr: +:type gKdr: conductanceDensity +:param gCa: +:type gCa: conductanceDensity +:param gKahp: +:type gKahp: conductanceDensity +:param gKC: +:type gKC: conductanceDensity +:param gc: +:type gc: conductanceDensity +:param eNa: +:type eNa: voltage +:param eCa: +:type eCa: voltage +:param eK: +:type eK: voltage +:param eL: +:type eL: voltage +:param pp: +:type pp: none +:param cm: +:type cm: specificCapacitance +:param alphac: +:type alphac: none +:param betac: +:type betac: none +:param gNmda: +:type gNmda: conductanceDensity +:param gAmpa: +:type gAmpa: conductanceDensity +:param qd0: +:type qd0: none + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + + + + + + + + + + + + + + + + + + + + + + Variant of cell with two independent Ca2+ pools. 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. + + + + + + + + + + + + + The collection of **segment** s which specify the 3D structure of the cell, along with a number of **segmentGroup** s + + + + + + + + + + + + + + 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. + + + + + + + + + + + + + + + + + + + + + Base type for ComponentTypes which specify an ( **x,** **y,** **z** ) coordinate along with a **diameter.** Note: no dimension used in the attributes for these coordinates! These are assumed to have dimension micrometer ( 10^-6 m ). This is due to micrometers being the default option for the majority of neuronal morphology formats, and dimensions are omitted here to facilitate reading and writing of morphologies in NeuroML. +\n +:param x: x coordinate of the point. Note: no dimension used, see description of **point3DWithDiam** for details. +:type x: none +:param y: y coordinate of the ppoint. Note: no dimension used, see description of **point3DWithDiam** for details. +:type y: none +:param z: z coordinate of the ppoint. Note: no dimension used, see description of **point3DWithDiam** for details. +:type z: none +:param diameter: Diameter of the ppoint. Note: no dimension used, see description of **point3DWithDiam** for details. +:type diameter: none + + + + + + + + + + + A method to describe a group of **segment** s 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 **segment** s 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 ). + + + + + + + + + + + + + + + + + + + + An inhomogeneous parameter specified across the **segmentGroup** ( see **variableParameter** for usage ). + + + + + + + + + + + + + + + + Allowed metrics for InhomogeneousParam + + + + + + + + + + + + + + A single identified **segment** which is part of the **segmentGroup** + + + + + + + Include all members of another **segmentGroup** in this group + + + + + + + Include all the **segment** s between those specified by **from** and **to** , inclusive + + + + + + + + + + Include all the **segment** s distal to that specified by **from** in the **segmentGroup** + + + + + + + + + + + + + + + + The biophysical properties of the **cell** , including the **membraneProperties** and the **intracellularProperties** + + + + + + + + + + + + + + + The biophysical properties of the **cell** , including the **membraneProperties2CaPools** and the **intracellularProperties2CaPools** for a cell with two Ca pools + + + + + + + + + + + + + + + Properties specific to the membrane, such as the **populations** of channels, **channelDensities,** **specificCapacitance,** etc. + + + + + + + + + + + + + + + + + + + + + Variant of membraneProperties with 2 independent Ca pools + + + + + + + + + + + + + + Membrane potential at which to emit a spiking event. Note, usually the spiking event will not be emitted again until the membrane potential has fallen below this value and rises again to cross it in a positive direction +\n +:param value: +:type value: voltage + + + + + + + + + Capacitance per unit area +\n +:param value: +:type value: specificCapacitance + + + + + + + + + Explicitly set initial membrane potential for the cell +\n +:param value: +:type value: voltage + + + + + + + + + The resistivity, or specific axial resistance, of the cytoplasm +\n +:param value: +:type value: resistivity + + + + + + + + + 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** +\n +:param 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 +:type number: none +:param erev: The reversal potential of the current produced +:type erev: voltage + + + + + + + + + + + + + + + + + + + + + + + + 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 +\n +:param erev: The reversal potential of the current produced +:type erev: voltage + + + + + + + + + + + + + + + + + + + + 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 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 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** +\n +:param erev: The reversal potential of the current produced +:type erev: voltage +:param condDensity: +:type condDensity: conductanceDensity + + + + + + + + + + + + + + + + + + + + + + + + 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. +\n +:param vShift: +:type vShift: voltage +:param erev: The reversal potential of the current produced +:type erev: voltage +:param condDensity: +:type condDensity: conductanceDensity + + + + + + + + + + + + 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. +\n +:param condDensity: +:type condDensity: conductanceDensity + + + + + + + + + + + + + + + + + + + + + + + This component is similar to the original component type **channelDensityNernst** but it is changed in order to have a reversal potential that depends on a second independent Ca++ pool ( ca2 ). See https://github.com/OpenSourceBrain/ghk-nernst. +\n +:param condDensity: +:type condDensity: conductanceDensity + + + + + + + + + + + + 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 Goldman Hodgkin Katz equation. Hard coded for Ca only! See https://github.com/OpenSourceBrain/ghk-nernst. +\n +:param permeability: +:type permeability: permeability + + + + + + + + + + + + + + + + + + + + Time varying conductance density, **gDensity,** which is distributed on an area of the cell, producing a current density **iDensity.** Modified version of Jaffe et al. 1994 ( used also in Lawrence et al. 2006 ). See https://github.com/OpenSourceBrain/ghk-nernst. +\n +:param condDensity: +:type condDensity: conductanceDensity + + + + + + + + + + + + + + + + + + + + + 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 ) ) + + + + + + + + + + + Specifies the **value** of an **inhomogeneousParameter.** For usage see **variableParameter** + + + + + + + + + Description of a chemical species identified by **ion,** which has internal, **concentration,** and external, **extConcentration** values for its concentration +\n +:param initialConcentration: +:type initialConcentration: concentration +:param initialExtConcentration: +:type initialExtConcentration: concentration + + + + + + + + + + + + + + + + + + + + + + + + Biophysical properties related to the intracellular space within the **cell** , such as the **resistivity** and the list of ionic **species** present. **caConc** and **caConcExt** are explicitly exposed here to facilitate accessing these values from other Components, even though **caConcExt** is clearly not an intracellular property + + + + + + + + + + Variant of intracellularProperties with 2 independent Ca pools + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Generates a constant current pulse of a certain **amplitude** for a specified **duration** after a **delay.** Scaled by **weight,** if set +\n +:param delay: Delay before change in current. Current is zero prior to this. +:type delay: time +:param duration: Duration for holding current at amplitude. Current is zero after delay + duration. +:type duration: time +:param amplitude: Amplitude of current pulse +:type amplitude: current + + + + + + + + + + + + + + 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 +\n +:param delay: Delay before change in current. Current is zero prior to this. +:type delay: time +:param duration: Duration for holding current at amplitude. Current is zero after delay + duration. +:type duration: time +:param amplitude: Amplitude of current pulse +:type amplitude: none + + + + + + + + + + + + + + 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 +\n +:param phase: Phase ( between 0 and 2*pi ) at which to start the varying current ( i. e. at time given by delay ) +:type phase: none +:param delay: Delay before change in current. Current is zero prior to this. +:type delay: time +:param duration: Duration for holding current at amplitude. Current is zero after delay + duration. +:type duration: time +:param amplitude: Maximum amplitude of current +:type amplitude: current +:param period: Time period of oscillation +:type period: time + + + + + + + + + + + + + + + + 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 +\n +:param phase: Phase ( between 0 and 2*pi ) at which to start the varying current ( i. e. at time given by delay ) +:type phase: none +:param delay: Delay before change in current. Current is zero prior to this. +:type delay: time +:param duration: Duration for holding current at amplitude. Current is zero after delay + duration. +:type duration: time +:param amplitude: Maximum amplitude of current +:type amplitude: none +:param period: Time period of oscillation +:type period: time + + + + + + + + + + + + + + + + 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 +\n +:param delay: Delay before change in current. Current is baselineAmplitude prior to this. +:type delay: time +:param duration: Duration for holding current at amplitude. Current is baselineAmplitude after delay + duration. +:type duration: time +:param startAmplitude: Amplitude of linearly varying current at time delay +:type startAmplitude: current +:param finishAmplitude: Amplitude of linearly varying current at time delay + duration +:type finishAmplitude: current +:param baselineAmplitude: Amplitude of current before time delay, and after time delay + duration +:type baselineAmplitude: current + + + + + + + + + + + + + + + + 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 +\n +:param delay: Delay before change in current. Current is baselineAmplitude prior to this. +:type delay: time +:param duration: Duration for holding current at amplitude. Current is baselineAmplitude after delay + duration. +:type duration: time +:param startAmplitude: Amplitude of linearly varying current at time delay +:type startAmplitude: none +:param finishAmplitude: Amplitude of linearly varying current at time delay + duration +:type finishAmplitude: none +:param baselineAmplitude: Amplitude of current before time delay, and after time delay + duration +:type baselineAmplitude: none + + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + Voltage clamp. Applies a variable current **i** to try to keep parent at **targetVoltage.** Not yet fully tested!!! Consider using voltageClampTriple!! +\n +:param delay: Delay before change in current. Current is zero prior to this. +:type delay: time +:param duration: Duration for attempting to keep parent at targetVoltage. Current is zero after delay + duration. +:type duration: time +:param targetVoltage: Current will be applied to try to get parent to this target voltage +:type targetVoltage: voltage +:param simpleSeriesResistance: Current will be calculated by the difference in voltage between the target and parent, divided by this value +:type simpleSeriesResistance: resistance + + + + + + + + + + + + + + + Voltage clamp with 3 clamp levels. Applies a variable current **i** ( through **simpleSeriesResistance** ) to try to keep parent cell at **conditioningVoltage** until time **delay,** **testingVoltage** until **delay** + **duration,** and **returnVoltage** afterwards. Only enabled if **active** = 1. +\n +:param active: Whether the voltage clamp is active ( 1 ) or inactive ( 0 ). +:type active: none +:param delay: Delay before switching from conditioningVoltage to testingVoltage. +:type delay: time +:param duration: Duration to hold at testingVoltage. +:type duration: time +:param conditioningVoltage: Target voltage before time delay +:type conditioningVoltage: voltage +:param testingVoltage: Target voltage between times delay and delay + duration +:type testingVoltage: voltage +:param returnVoltage: Target voltage after time duration +:type returnVoltage: voltage +:param simpleSeriesResistance: Current will be calculated by the difference in voltage between the target and parent, divided by this value +:type simpleSeriesResistance: resistance + + + + + + + + + + + + + + + + + + Emits a single spike at the specified **time** +\n +:param time: Time at which to emit one spike event +:type time: time + + + + + + + + + + + + Set of spike ComponentTypes, each emitting one spike at a certain time. Can be used to feed a predetermined spike train into a cell + + + + + + + + + + + + + Spike array connected to a single **synapse,** producing a current triggered by each **spike** in the array. + + + + + + + + + + + + + + + Simple generator of spikes at a regular interval set by **period** +\n +:param period: Time between spikes. The first spike will be emitted after this time. +:type period: time + + + + + + + + + + + + Generator of spikes with a random interspike interval of at least **minISI** and at most **maxISI** +\n +:param maxISI: Maximum interspike interval +:type maxISI: time +:param minISI: Minimum interspike interval +:type minISI: time + + + + + + + + + + + + + Generator of spikes whose ISI is distributed according to an exponential PDF with scale: 1 / **averageRate** +\n +:param averageRate: The average rate at which spikes are emitted +:type averageRate: per_time + + + + + + + + + + + + Generator of spikes whose ISI distribution is the maximum entropy distribution over [ **minimumISI,** +infinity ) with mean: 1 / **averageRate** +\n +:param minimumISI: The minimum interspike interval +:type minimumISI: time +:param averageRate: The average rate at which spikes are emitted +:type averageRate: per_time + + + + + + + + + + + + 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** . +\n +:param averageRate: The average rate at which spikes are emitted +:type averageRate: per_time + + + + + + + + + + + + + + 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** . +\n +:param averageRate: +:type averageRate: per_time +:param delay: +:type delay: time +:param duration: +:type duration: time + + + + + + + + + + + + + + + + + + + Network containing: **population** s ( potentially of type **populationList** , and so specifying a list of cell **location** s ); **projection** s ( with lists of **connection** s ) and/or **explicitConnection** s; and **inputList** s ( with lists of **input** s ) and/or **explicitInput** s. Note: often in NeuroML this will be of type **networkWithTemperature** if there are temperature dependent elements ( e. g. ion channels ). + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Initial attempt to specify 3D region for placing cells. Work in progress. . . + + + + + + + + + + + + + + + A population of components, with just one parameter for the **size,** i. e. number of components to create. Note: quite often this is used with type= **populationList** which means the size is determined by the number of **instance** s ( with **location** s ) in the list. The **size** attribute is still set, and there will be a validation error if this does not match the number in the list. +\n +:param size: Number of instances of this Component to create when the population is instantiated +:type size: none + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Specifies a single instance of a component in a **population** ( placed at **location** ). + + + + + + + + + + + + + + + + Specifies the ( x, y, z ) location of a single **instance** of a component in a **population** +\n +:param x: +:type x: none +:param y: +:type y: none +:param z: +:type z: none + + + + + + + + + + + + + + + + + + + + + Explicit event connection between named components, which gets processed via a new instance of a **synapse** component which is created on the target component + + + + + + + + + + Base for projection (set of synaptic connections) between two populations + + + + + + + + + + + Projection from one population, **presynapticPopulation** to another, **postsynapticPopulation,** through **synapse.** Contains lists of **connection** or **connectionWD** elements. + + + + + + + + + + + + + + + Base of all synaptic connections (chemical/electrical/analog, etc.) inside projections + + + + + + + + + + Base of all synaptic connections with preCellId, postSegmentId, etc. + Note: this is not the best name for these attributes, since Id is superfluous, hence BaseConnectionNewFormat + + + + + + + + + + + + + + + Base of all synaptic connections with preCell, postSegment, etc. + See BaseConnectionOldFormat + + + + + + + + + + + + + + + Event connection directly between named components, which gets processed via a new instance of a **synapse** component which is created on the target component. Normally contained inside a **projection** element. + + + + + + + + + + Event connection between named components, which gets processed via a new instance of a synapse component which is created on the target component, includes setting of **weight** and **delay** for the synaptic connection +\n +:param weight: +:type weight: none +:param delay: +:type delay: time + + + + + + + + + + + + + A projection between **presynapticPopulation** to another **postsynapticPopulation** through gap junctions. + + + + + + + + + + + + + + + To enable connections between populations through gap junctions. + + + + + + + + + + + To enable connections between populations through gap junctions. Populations need to be of type **populationList** and contain **instance** and **location** elements. + + + + + + + + + To enable connections between populations through gap junctions. Populations need to be of type **populationList** and contain **instance** and **location** elements. Includes setting of **weight** for the connection +\n +:param weight: +:type weight: none + + + + + + + + + + + + A projection between **presynapticPopulation** and **postsynapticPopulation** through components **preComponent** at the start and **postComponent** at the end of a **continuousConnection** or **continuousConnectionInstance** . Can be used for analog synapses. + + + + + + + + + + + + + + + An instance of a connection in a **continuousProjection** between **presynapticPopulation** to another **postsynapticPopulation** through a **preComponent** at the start and **postComponent** at the end. Can be used for analog synapses. + + + + + + + + + + + + An instance of a connection in a **continuousProjection** between **presynapticPopulation** to another **postsynapticPopulation** through a **preComponent** at the start and **postComponent** at the end. Populations need to be of type **populationList** and contain **instance** and **location** elements. Can be used for analog synapses. + + + + + + + + + An instance of a connection in a **continuousProjection** between **presynapticPopulation** to another **postsynapticPopulation** through a **preComponent** at the start and **postComponent** at the end. Populations need to be of type **populationList** and contain **instance** and **location** elements. Can be used for analog synapses. Includes setting of **weight** for the connection +\n +:param weight: +:type weight: none + + + + + + + + + + + + An explicit input ( anything which extends **basePointCurrent** ) to a target cell in a population + + + + + + + + + An explicit list of **input** s to a **population.** + + + + + + + + + + + + + + + + Specifies a single input to a **target,** optionally giving the **segmentId** ( default 0 ) and **fractionAlong** the segment ( default 0. 5 ). + + + + + + + + + + + Specifies input lists. Can set **weight** to scale individual inputs. +\n +:param weight: +:type weight: none + + + + + + + + + + + + + + + Base type of any PyNN standard cell model. Note: membrane potential **v** has dimensions voltage, but all other parameters are dimensionless. This is to facilitate translation to and from PyNN scripts in Python, where these parameters have implicit units, see http://neuralensemble.org/trac/PyNN/wiki/StandardModels +\n +:param cm: +:type cm: none +:param i_offset: +:type i_offset: none +:param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_E: none +:param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_I: none +:param v_init: +:type v_init: none + + + + + + + + + + + + + + + + Base type of any PyNN standard integrate and fire model +\n +:param tau_refrac: +:type tau_refrac: none +:param v_thresh: +:type v_thresh: none +:param tau_m: +:type tau_m: none +:param v_rest: +:type v_rest: none +:param v_reset: +:type v_reset: none +:param cm: +:type cm: none +:param i_offset: +:type i_offset: none +:param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_E: none +:param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_I: none +:param v_init: +:type v_init: none + + + + + + + + + + + + + + + + Base type of conductance based PyNN IaF cell models +\n +:param e_rev_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type e_rev_E: none +:param e_rev_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type e_rev_I: none +:param tau_refrac: +:type tau_refrac: none +:param v_thresh: +:type v_thresh: none +:param tau_m: +:type tau_m: none +:param v_rest: +:type v_rest: none +:param v_reset: +:type v_reset: none +:param cm: +:type cm: none +:param i_offset: +:type i_offset: none +:param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_E: none +:param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_I: none +:param v_init: +:type v_init: none + + + + + + + + + + + + + Leaky integrate and fire model with fixed threshold and alpha-function-shaped post-synaptic current +\n +:param tau_refrac: +:type tau_refrac: none +:param v_thresh: +:type v_thresh: none +:param tau_m: +:type tau_m: none +:param v_rest: +:type v_rest: none +:param v_reset: +:type v_reset: none +:param cm: +:type cm: none +:param i_offset: +:type i_offset: none +:param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_E: none +:param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_I: none +:param v_init: +:type v_init: none + + + + + + + + + + + Leaky integrate and fire model with fixed threshold and decaying-exponential post-synaptic current +\n +:param tau_refrac: +:type tau_refrac: none +:param v_thresh: +:type v_thresh: none +:param tau_m: +:type tau_m: none +:param v_rest: +:type v_rest: none +:param v_reset: +:type v_reset: none +:param cm: +:type cm: none +:param i_offset: +:type i_offset: none +:param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_E: none +:param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_I: none +:param v_init: +:type v_init: none + + + + + + + + + + + Leaky integrate and fire model with fixed threshold and alpha-function-shaped post-synaptic conductance +\n +:param e_rev_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type e_rev_E: none +:param e_rev_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type e_rev_I: none +:param tau_refrac: +:type tau_refrac: none +:param v_thresh: +:type v_thresh: none +:param tau_m: +:type tau_m: none +:param v_rest: +:type v_rest: none +:param v_reset: +:type v_reset: none +:param cm: +:type cm: none +:param i_offset: +:type i_offset: none +:param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_E: none +:param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_I: none +:param v_init: +:type v_init: none + + + + + + + + + + + Leaky integrate and fire model with fixed threshold and exponentially-decaying post-synaptic conductance +\n +:param e_rev_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type e_rev_E: none +:param e_rev_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type e_rev_I: none +:param tau_refrac: +:type tau_refrac: none +:param v_thresh: +:type v_thresh: none +:param tau_m: +:type tau_m: none +:param v_rest: +:type v_rest: none +:param v_reset: +:type v_reset: none +:param cm: +:type cm: none +:param i_offset: +:type i_offset: none +:param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_E: none +:param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_I: none +:param v_init: +:type v_init: none + + + + + + + + + + + Adaptive exponential integrate and fire neuron according to Brette R and Gerstner W ( 2005 ) with exponentially-decaying post-synaptic conductance +\n +:param v_spike: +:type v_spike: none +:param delta_T: +:type delta_T: none +:param tau_w: +:type tau_w: none +:param a: +:type a: none +:param b: +:type b: none +:param e_rev_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type e_rev_E: none +:param e_rev_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type e_rev_I: none +:param tau_refrac: +:type tau_refrac: none +:param v_thresh: +:type v_thresh: none +:param tau_m: +:type tau_m: none +:param v_rest: +:type v_rest: none +:param v_reset: +:type v_reset: none +:param cm: +:type cm: none +:param i_offset: +:type i_offset: none +:param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_E: none +:param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_I: none +:param v_init: +:type v_init: none + + + + + + + + + + + + + + + + Adaptive exponential integrate and fire neuron according to Brette R and Gerstner W ( 2005 ) with alpha-function-shaped post-synaptic conductance +\n +:param v_spike: +:type v_spike: none +:param delta_T: +:type delta_T: none +:param tau_w: +:type tau_w: none +:param a: +:type a: none +:param b: +:type b: none +:param e_rev_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type e_rev_E: none +:param e_rev_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type e_rev_I: none +:param tau_refrac: +:type tau_refrac: none +:param v_thresh: +:type v_thresh: none +:param tau_m: +:type tau_m: none +:param v_rest: +:type v_rest: none +:param v_reset: +:type v_reset: none +:param cm: +:type cm: none +:param i_offset: +:type i_offset: none +:param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_E: none +:param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_I: none +:param v_init: +:type v_init: none + + + + + + + + + + + Single-compartment Hodgkin-Huxley-type neuron with transient sodium and delayed-rectifier potassium currents using the ion channel models from Traub. +\n +:param gbar_K: +:type gbar_K: none +:param gbar_Na: +:type gbar_Na: none +:param g_leak: +:type g_leak: none +:param e_rev_K: +:type e_rev_K: none +:param e_rev_Na: +:type e_rev_Na: none +:param e_rev_leak: +:type e_rev_leak: none +:param v_offset: +:type v_offset: none +:param e_rev_E: +:type e_rev_E: none +:param e_rev_I: +:type e_rev_I: none +:param cm: +:type cm: none +:param i_offset: +:type i_offset: none +:param tau_syn_E: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_E: none +:param tau_syn_I: This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell +:type tau_syn_I: none +:param v_init: +:type v_init: none + + + + + + + + + + + + + + + + + + + + Base type for all PyNN synapses. Note, the current **I** produced is dimensionless, but it requires a membrane potential **v** with dimension voltage +\n +:param tau_syn: +:type tau_syn: none + + + + + + + + + + + + Conductance based synapse with instantaneous rise and single exponential decay ( with time constant tau_syn ) +\n +:param e_rev: +:type e_rev: none +:param tau_syn: +:type tau_syn: none + + + + + + + + + + + + Alpha synapse: rise time and decay time are both tau_syn. Conductance based synapse. +\n +:param e_rev: +:type e_rev: none +:param tau_syn: +:type tau_syn: none + + + + + + + + + + + + Current based synapse with instantaneous rise and single exponential decay ( with time constant tau_syn ) +\n +:param tau_syn: +:type tau_syn: none + + + + + + + + + + + + Alpha synapse: rise time and decay time are both tau_syn. Current based synapse. +\n +:param tau_syn: +:type tau_syn: none + + + + + + + + + + + + Spike source, generating spikes according to a Poisson process. +\n +:param start: +:type start: time +:param duration: +:type duration: time +:param rate: +:type rate: per_time + + + + + + + + + + + + + + + + + + Base element without ID specified *yet*, e.g. for an element with a particular requirement on its id which does not comply with NmlId (e.g. Segment needs nonNegativeInteger). + + + + + + Anything which can have a unique (within its parent) id, which must be an integer zero or greater. + + + + + + + + + + Anything which can have a unique (within its parent) id of the form NmlId (spaceless combination of letters, numbers and underscore). + + + + + + + + + + Elements which can stand alone and be referenced by id, e.g. cell, morphology. + + + + + + + + + + + + + + + + diff --git a/docs/Cells.html b/docs/Cells.html index a4bb835..1ff7e50 100644 --- a/docs/Cells.html +++ b/docs/Cells.html @@ -15,7 +15,7 @@ - NeuroML v2.1 Component Types + NeuroML v2.2 Component Types
  • Cells
    • @@ -36,11 +36,11 @@
    Component Types
    -baseCell
    +baseCell
       > baseSpikingCell
    -      > baseCellMembPot
    +      > baseCellMembPot
             > cell
    @@ -56,17 +56,17 @@                      ++ specificCapacitances specificCapacitance
    -                     ++ populations baseChannelPopulation
    +                     ++ populations baseChannelPopulation
    -                        > channelPopulation
    +                        > channelPopulation
    -                        > channelPopulationNernst
    +                        > channelPopulationNernst
    -                     ++ channelDensities baseChannelDensity
    +                     ++ channelDensities baseChannelDensity
                            > baseChannelDensityCond
    -                           > channelDensity
    +                           > channelDensity
                                  > channelDensityVShift
    @@ -78,9 +78,9 @@                         > channelDensityNonUniform
    -                           + variableParameter
    +                           + variableParameter
    -                              + inhomogeneousValue
    +                              + inhomogeneousValue
                            > channelDensityNonUniformNernst
    @@ -96,23 +96,23 @@             + morphology
    -               ++ segments segment
    +               ++ segments segment
    -                  + parent
    +                  + parent
    -                  + distal
    +                  + distal
    -                  + proximal
    +                  + proximal
    -               ++ segmentGroups segmentGroup
    +               ++ segmentGroups segmentGroup
    -                  + notes
    +                  + notes
    -                  + annotation
    +                  + annotation
    -                     + rdf:RDF rdf_RDF
    +                     + rdf:RDF rdf_RDF
    -                        + rdf:Description rdf_Description
    +                        + rdf:Description rdf_Description
                               + bqbiol:encodes bqbiol_encodes
    @@ -146,21 +146,21 @@                            + bqmodel:isDerivedFrom bqmodel_isDerivedFrom
    -                     ++ property
    +                     ++ property
                      ++ members member
                      ++ paths path
    -                     + from
    +                     + from
    -                     + to
    +                     + to
                      ++ subTrees subTree
    -                  ++ includes include
    +                  ++ includes include
    -                  ++ inhomogeneousParameter
    +                  ++ inhomogeneousParameter
                         + proximal proximalProperties
    @@ -172,9 +172,9 @@                   ++ specificCapacitances specificCapacitance
    -                  ++ populations baseChannelPopulation
    +                  ++ populations baseChannelPopulation
    -                  ++ channelDensities baseChannelDensity
    +                  ++ channelDensities baseChannelDensity
                   + intracellularProperties
    @@ -182,13 +182,13 @@          > baseCellMembPotCap
    -            > pointCellCondBased
    +            > pointCellCondBased
    -               ++ populations baseChannelPopulation
    +               ++ populations baseChannelPopulation
    -            > pointCellCondBasedCa
    +            > pointCellCondBasedCa
    -               ++ populations baseChannelPopulation
    +               ++ populations baseChannelPopulation
                   ++ concentrationModels concentrationModel
    @@ -218,7 +218,7 @@          > pinskyRinzelCA3Cell
    -      > baseCellMembPotDL
    +      > baseCellMembPotDL
             > fitzHughNagumo1969Cell
    @@ -227,21 +227,21 @@
    -

    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 v2.1 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 v2.2 definitions, using the latest version of LEMS!
    - - + +

    Cells

    NeuroML2 ComponentType definitions from Cells.xml
    Original LEMS ComponentType definitions: Cells.xml
    Schema against which NeuroML based on these should be valid: NeuroML_v2.1.xsd
    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

      +

        extends baseStandalone

    + Base type of any cell (e.g. point neuron like izhikevich2007Cell, or a morphologically detailed ??? with segments) which can be used in a population
    baseCell -

        extends baseStandalone
    - Base type of any cell which can be used in a population
    @@ -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
    -

    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 v2.1 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 v2.2 definitions, using the latest version of LEMS!
    - - + +

    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 - + @@ -1883,7 +1883,7 @@ Child elements - + @@ -1977,10 +1977,10 @@ Child elements - + - + 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
    -

    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 v2.1 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 v2.2 definitions, using the latest version of LEMS!
    notesnotesnotes
    notesnotesnotes
    timeCourse baseVoltageDepTime notesnotesnotes
    annotationannotationannotation
    - - + +

    Inputs

    NeuroML2 ComponentType definitions from Inputs.xml
    Original LEMS ComponentType definitions: Inputs.xml
    Schema against which NeuroML based on these should be valid: NeuroML_v2.1.xsd
    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

      +

        extends baseStandalone

    - +
    basePointCurrent -

        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 +spikesspike
    + 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 @@ - + - + - + @@ -1044,7 +1178,7 @@ - + @@ -1083,7 +1217,7 @@ + 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 @@ +

        extends basePointCurrentDL

    + 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 - + - + @@ -1185,24 +1319,24 @@ +

        extends basePointCurrentDL

    + 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 - + - + - + @@ -1210,7 +1344,7 @@ - + @@ -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. Scaled by weight, if set - + - + - + - + - + @@ -1327,30 +1461,30 @@ +

        extends basePointCurrentDL

    + 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 - + - + - + - + - + @@ -1358,7 +1492,7 @@ - + @@ -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. Scaled by weight, if set - + - + - + - + - + @@ -1478,30 +1612,30 @@ +

        extends basePointCurrentDL

    + 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 - + - + - + - + - + @@ -1509,7 +1643,7 @@ - + @@ -1555,7 +1689,7 @@ +

        extends baseVoltageDepPointCurrent

    - + - + - + - + @@ -1591,7 +1725,7 @@ - + @@ -1634,7 +1768,7 @@ +

        extends baseVoltageDepPointCurrent

    - + - + - + - + - + - + - + @@ -1679,7 +1813,7 @@ - + @@ -1717,140 +1851,6 @@
    Parameters amplitudeamplitude
        Amplitude of current pulse    		 current
    delaydelay
        Delay before change in current. Current is zero prior to this.    		 time
    durationduration
        Duration for holding current at amplitude. Current is zero after delay + duration.    		 time
    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
    - Generates a current which is the sum of all its child basePointCurrent elements
    compoundInputDL -

        extends basePointCurrentDL
    - Generates a current which is the sum of all its child basePointCurrentDL elements
    currentsbasePointCurrentDLbasePointCurrentDL
    Exposures I    (from basePointCurrentDL)I    (from basePointCurrentDL) Dimensionless
    pulseGeneratorDL -

        extends basePointCurrentDL
    - Dimensionless equivalent of pulseGenerator. Generates a constant current pulse of a certain amplitude for a specified duration after a delay
    Parameters amplitudeamplitude
        Amplitude of current pulse    		 Dimensionless
    delaydelay
        Delay before change in current. Current is zero prior to this.    		 time
    durationduration
        Duration for holding current at amplitude. Current is zero after delay + duration.    		 time
    Exposures I    (from basePointCurrentDL)I    (from basePointCurrentDL) Dimensionless
    - 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.
    Parameters amplitudeamplitude
        Maximum amplitude of current    		 current
    delaydelay
        Delay before change in current. Current is zero prior to this.    		 time
    durationduration
        Duration for holding current at amplitude. Current is zero after delay + duration.    		 time
    periodperiod
        Time period of oscillation    		 time
    phasephase
        Phase (between 0 and 2*pi) at which to start the varying current (i.e. at time given by delay)    		 Dimensionless
    sineGeneratorDL -

        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.
    Parameters amplitudeamplitude
        Maximum amplitude of current    		 Dimensionless
    delaydelay
        Delay before change in current. Current is zero prior to this.    		 time
    durationduration
        Duration for holding current at amplitude. Current is zero after delay + duration.    		 time
    periodperiod
        Time period of oscillation    		 time
    phasephase
        Phase (between 0 and 2*pi) at which to start the varying current (i.e. at time given by delay)    		 Dimensionless
    Exposures I    (from basePointCurrentDL)I    (from basePointCurrentDL) Dimensionless
    - Generates a ramping current after a time delay, for a fixed duration. During this time the current steadily changes from startAmplitude to finishAmplitude.
    Parameters baselineAmplitudebaselineAmplitude
        Amplitude of current before time delay, and after time delay + duration    		 current
    delaydelay
        Delay before change in current. Current is baselineAmplitude prior to this.    		 time
    durationduration
        Duration for holding current at amplitude. Current is baselineAmplitude after delay + duration.    		 time
    finishAmplitudefinishAmplitude
        Amplitude of linearly varying current at time delay + duration    		 current
    startAmplitudestartAmplitude
        Amplitude of linearly varying current at time delay    		 current
    rampGeneratorDL -

        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.
    Parameters baselineAmplitudebaselineAmplitude
        Amplitude of current before time delay, and after time delay + duration    		 Dimensionless
    delaydelay
        Delay before change in current. Current is baselineAmplitude prior to this.    		 time
    durationduration
        Duration for holding current at amplitude. Current is baselineAmplitude after delay + duration.    		 time
    finishAmplitudefinishAmplitude
        Amplitude of linearly varying current at time delay + duration    		 Dimensionless
    startAmplitudestartAmplitude
        Amplitude of linearly varying current at time delay    		 Dimensionless
    Exposures I    (from basePointCurrentDL)I    (from basePointCurrentDL) Dimensionless
    voltageClamp -

        extends baseVoltageDepPointCurrent
    @@ -1566,16 +1700,16 @@ Parameters delaydelay
        Delay before change in current. Current is zero prior to this.    		 time
    durationduration
        Duration for attempting to keep parent at targetVoltage. Current is zero after delay + duration.    		 time
    simpleSeriesResistancesimpleSeriesResistance
        Current will be calculated by the difference in voltage between the target and parent, divided by this value    		 resistance
    targetVoltagetargetVoltage
        Current will be applied to try to get parent to this target voltage    		 voltage
    Requirements v    (from baseVoltageDepPointCurrent)v    (from baseVoltageDepPointCurrent) voltage
    voltageClampTriple -

        extends baseVoltageDepPointCurrent
    @@ -1645,25 +1779,25 @@ Parameters activeactive
        Whether the voltage clamp is active (1) or inactive (0).    		 Dimensionless
    conditioningVoltageconditioningVoltage
        Target voltage before time delay    		 voltage
    delaydelay
        Delay before switching from conditioningVoltage to testingVoltage.    		 time
    durationduration
        Duration to hold at testingVoltage.    		 time
    returnVoltagereturnVoltage
        Target voltage after time duration    		 voltage
    simpleSeriesResistancesimpleSeriesResistance
        Current will be calculated by the difference in voltage between the target and parent, divided by this value    		 resistance
    testingVoltagetestingVoltage
        Target voltage between times delay and delay + duration    		 voltage
    Requirements v    (from baseVoltageDepPointCurrent)v    (from baseVoltageDepPointCurrent) voltage
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    - 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 -spikesspike
    - 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 -timetime
    - 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
    -
    -
    -
diff --git a/docs/Networks.html b/docs/Networks.html index fcea4cd..7265723 100644 --- a/docs/Networks.html +++ b/docs/Networks.html @@ -15,7 +15,7 @@ - NeuroML v2.1 Component Types + NeuroML v2.2 Component Types
  • Cells
    • @@ -36,31 +36,31 @@
    Component Types
    -network
    +network
    -   > networkWithTemperature
    +   > networkWithTemperature
       ++ regions region
          + rectangularExtent
    -   ++ populations basePopulation
    +   ++ populations basePopulation
    -      > population
    +      > population
    -      > populationList
    +      > populationList
             ++ instances instance
    -            + location
    +            + location
    -      + notes
    +      + notes
    -      + annotation
    +      + annotation
    -         + rdf:RDF rdf_RDF
    +         + rdf:RDF rdf_RDF
    -            + rdf:Description rdf_Description
    +            + rdf:Description rdf_Description
                   + bqbiol:encodes bqbiol_encodes
    @@ -94,7 +94,7 @@                + bqmodel:isDerivedFrom bqmodel_isDerivedFrom
    -         ++ property
    +         ++ property
       ++ projections projection
    @@ -128,30 +128,30 @@    ++ explicitInputs explicitInput
    -   ++ inputs inputList
    +   ++ inputs inputList
    -      ++ inputs input
    +      ++ inputs input
             > inputW
    -

    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 v2.1 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 v2.2 definitions, using the latest version of LEMS!
    - - + +

    Networks

    NeuroML2 ComponentType definitions from Networks.xml
    Original LEMS ComponentType definitions: Networks.xml
    Schema against which NeuroML based on these should be valid: NeuroML_v2.1.xsd
    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

      +

        extends baseStandalone

    + Network containing: populations (potentially of type populationList, and so specifying a list of cell locations); projections (with lists of connections) and/or explicitConnections; and inputLists (with lists of inputs) and/or explicitInputs. Note: often in NeuroML this will be of type networkWithTemperature if there are temperature dependent elements (e.g. ion channels). @@ -162,7 +162,7 @@ - + @@ -180,7 +180,7 @@ - +
    network -

        extends baseStandalone
    - Network containing populations, projections and lists of explicitConnections (either directly between components of the populations or via synapses)
    region
    populationsbasePopulationbasePopulation
    projections projectionexplicitInput
    inputsinputListinputList
    @@ -189,11 +189,11 @@ networkWithTemperature -

        extends network

    +

        extends network

    - Network containing populations, projections and lists of explicitConnections (either directly between components of the populations or via synapses), and an explicit temperature + Same as network, but with an explicit temperature for temperature dependent elements (e.g. ion channels) @@ -210,11 +210,11 @@ basePopulation -

        extends baseStandalone

    +

        extends baseStandalone

    - A population of cells (anything which extends baseCell) + A population of multiple instances of a specific component, which anything which extends baseCell. @@ -222,7 +222,7 @@ Component References component - baseCell + baseCell @@ -230,17 +230,17 @@ Child elements notes - notes + notes annotation - annotation + annotation Children elements property - property + property @@ -249,18 +249,18 @@ population -

        extends basePopulation

    +

        extends basePopulation

    - A population of components, with just one parameter for the size + A population of components, with just one parameter for the size, i.e. number of components to create. Note: quite often this is used with type=populationList which means the size is determined by the number of instances (with locations) in the list. The size attribute is still set, and there will be a validation error if this does not match the number in the list. Parameters - size + size
        Number of instances of this Component to create when the population is instantiated Dimensionless @@ -270,11 +270,11 @@ populationList -

        extends basePopulation

    +

        extends basePopulation

    - An explicit list of the cells in the population. + An explicit list of instances (with locations) of components in the population. @@ -302,7 +302,7 @@ - Specifies a single instance of a component in a population (placed at location). + Specifies a single instance of a component in a population (placed at location). @@ -310,7 +310,7 @@ Child elements location - location + location @@ -323,7 +323,7 @@ - Specifies location of a single instance of a component in a population + Specifies the (x,y,z) location of a single instance of a component in a population @@ -653,7 +653,7 @@ - To enable connections between populations through gap junctions. Populations need to be of type populationList and contain instance and location elements. + To enable connections between populations through gap junctions. Populations need to be of type populationList and contain instance and location elements. @@ -696,7 +696,7 @@ - To enable connections between populations through gap junctions. Populations need to be of type populationList and contain instance and location elements. Includes setting of weight for the connection + To enable connections between populations through gap junctions. Populations need to be of type populationList and contain instance and location elements. Includes setting of weight for the connection @@ -747,10 +747,10 @@ Component References presynapticPopulation - population + population postsynapticPopulation - population + population @@ -798,7 +798,7 @@ - An instance of a connection in a continuousProjection between presynapticPopulation to another postsynapticPopulation through a preComponent at the start and postComponent at the end. Populations need to be of type populationList and contain instance and location elements. Can be used for analog synapses. + An instance of a connection in a continuousProjection between presynapticPopulation to another postsynapticPopulation through a preComponent at the start and postComponent at the end. Populations need to be of type populationList and contain instance and location elements. Can be used for analog synapses. @@ -844,7 +844,7 @@ - An instance of a connection in a continuousProjection between presynapticPopulation to another postsynapticPopulation through a preComponent at the start and postComponent at the end. Populations need to be of type populationList and contain instance and location elements. Can be used for analog synapses. Includes setting of weight for the connection + An instance of a connection in a continuousProjection between presynapticPopulation to another postsynapticPopulation through a preComponent at the start and postComponent at the end. Populations need to be of type populationList and contain instance and location elements. Can be used for analog synapses. Includes setting of weight for the connection @@ -895,10 +895,10 @@ Component References presynapticPopulation - population + population postsynapticPopulation - population + population @@ -961,7 +961,7 @@ - An explicit list of inputs. Not yet stable... + An explicit list of inputs to a population. @@ -984,7 +984,7 @@ Children elements inputs - input + input @@ -997,7 +997,7 @@ - Specifies input lists. + Specifies a single input to a target, optionally giving the segmentId (default 0) and fractionAlong the segment (default 0.5). @@ -1024,7 +1024,7 @@ inputW -

        extends input

    +

        extends input

    diff --git a/docs/NeuroMLCoreCompTypes.html b/docs/NeuroMLCoreCompTypes.html index 48f6ebc..f539209 100644 --- a/docs/NeuroMLCoreCompTypes.html +++ b/docs/NeuroMLCoreCompTypes.html @@ -15,7 +15,7 @@ - NeuroML v2.1 Component Types + NeuroML v2.2 Component Types
    • Cells
      • @@ -36,13 +36,13 @@
      Component Types
      -notes
      +notes
      -annotation
      +annotation
      -   + rdf:RDF rdf_RDF
      +   + rdf:RDF rdf_RDF
      -      + rdf:Description rdf_Description
      +      + rdf:Description rdf_Description
               + bqbiol:encodes bqbiol_encodes
      @@ -76,25 +76,25 @@          + bqmodel:isDerivedFrom bqmodel_isDerivedFrom
      -   ++ property
      +   ++ property
      -baseStandalone
      +baseStandalone
      -baseBqbiol
      +baseBqbiol
      -   + rdf:Bag rdf_Bag
      +   + rdf:Bag rdf_Bag
      -      ++ rdf_li
      +      ++ rdf_li
      point3DWithDiam
      -

      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 v2.1 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 v2.2 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_v2.1.xsd
      Original LEMS ComponentType definitions: NeuroMLCoreCompTypes.xml
      Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd

        @@ -105,7 +105,7 @@ + Human readable notes/description for a Component
      - Human readable notes on a Component
      @@ -118,7 +118,7 @@ - Annotation... + A structured annotation containing metadata, specifically RDF or property elements @@ -126,14 +126,14 @@ Child elements rdf:RDF - rdf_RDF + rdf_RDF Children elements property - property + property @@ -146,7 +146,7 @@ - Property in Annotation... + A property (a tag and value pair), which can be on any baseStandalone either as a direct child, or within an ???. Generally something which helps the visual display or facilitates simulation of a Component, but is not a core physiological property. Common examples include: numberInternalDivisions, equivalent of nseg in NEURON; radius, for a radius to use in graphical displays for abstract cells (i.e. without defined morphologies); color, the color to use for a ??? or populationList of cells; recommended_dt_ms, the recommended timestep to use for simulating a ???, recommended_duration_ms the recommended duration to use when running a ??? @@ -168,7 +168,7 @@ - Base type of any component which will require notes, annotation, etc. + Base type of any Component which can have ???, ???, or a property list. @@ -176,17 +176,17 @@ Child elements notes - notes + notes annotation - annotation + annotation Children elements property - property + property @@ -199,7 +199,7 @@ - Work in progress... + Structured block in an annotation based on RDF. See https://github.com/OpenSourceBrain/OSB_API/blob/master/python/examples/grancelllayer.xml @@ -214,7 +214,7 @@ Child elements rdf:Description - rdf_Description + rdf_Description @@ -227,7 +227,7 @@ - Work in progress... + Structured block in an annotation based on RDF. @@ -300,7 +300,7 @@ - Work in progress... + Structured block in an annotation based on RDF. @@ -308,7 +308,7 @@ Child elements rdf:Bag - rdf_Bag + rdf_Bag @@ -317,7 +317,7 @@ bqbiol_encodes -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -330,7 +330,7 @@ bqbiol_hasPart -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -343,7 +343,7 @@ bqbiol_hasProperty -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -356,7 +356,7 @@ bqbiol_hasVersion -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -369,7 +369,7 @@ bqbiol_is -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -382,7 +382,7 @@ bqbiol_isDescribedBy -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -395,7 +395,7 @@ bqbiol_isEncodedBy -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -408,7 +408,7 @@ bqbiol_isHomologTo -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -421,7 +421,7 @@ bqbiol_isPartOf -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -434,7 +434,7 @@ bqbiol_isPropertyOf -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -447,7 +447,7 @@ bqbiol_isVersionOf -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -467,7 +467,7 @@ bqbiol_occursIn -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -480,7 +480,7 @@ bqbiol_hasTaxon -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -493,7 +493,7 @@ bqmodel_is -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -506,7 +506,7 @@ bqmodel_isDescribedBy -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -526,7 +526,7 @@ bqmodel_isDerivedFrom -

          extends baseBqbiol

      +

          extends baseBqbiol

      @@ -543,7 +543,7 @@ - Work in progress... + Structured block in an annotation based on RDF. @@ -564,7 +564,7 @@ - Annotation... + Structured block in an annotation based on RDF. @@ -591,16 +591,16 @@ Parameters - diameter + diameter
          Diameter of the ppoint. Note: no dimension used, see description of _point3DWithDiam_ for details. Dimensionless - x + x
          x coordinate of the point. Note: no dimension used, see description of _point3DWithDiam_ for details. Dimensionless - y + y
          y coordinate of the ppoint. Note: no dimension used, see description of _point3DWithDiam_ for details. Dimensionless - z + z
          z coordinate of the ppoint. Note: no dimension used, see description of _point3DWithDiam_ for details. Dimensionless diff --git a/docs/NeuroMLCoreDimensions.html b/docs/NeuroMLCoreDimensions.html index a170ebb..a596e83 100644 --- a/docs/NeuroMLCoreDimensions.html +++ b/docs/NeuroMLCoreDimensions.html @@ -15,7 +15,7 @@ - NeuroML v2.1 Component Types + NeuroML v2.2 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 v2.1 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 v2.2 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_v2.1.xsd
      Original LEMS ComponentType definitions: NeuroMLCoreDimensions.xml
      Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd

        diff --git a/docs/PyNN.html b/docs/PyNN.html index f47c693..a7c10d9 100644 --- a/docs/PyNN.html +++ b/docs/PyNN.html @@ -15,7 +15,7 @@ - NeuroML v2.1 Component Types + NeuroML v2.2 Component Types
      • Cells
        • @@ -71,17 +71,17 @@
      -

      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 v2.1 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 v2.2 definitions, using the latest version of LEMS!
      - - + +

      PyNN

      NeuroML2 ComponentType definitions from PyNN.xml
      Original LEMS ComponentType definitions: PyNN.xml
      Schema against which NeuroML based on these should be valid: NeuroML_v2.1.xsd
      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

        +

          extends baseCellMembPot

      - + - + @@ -129,7 +129,7 @@ - + @@ -202,7 +202,7 @@ - + @@ -240,10 +240,10 @@ - + - + @@ -281,7 +281,7 @@ - + @@ -354,7 +354,7 @@ - + @@ -474,7 +474,7 @@ - + @@ -600,7 +600,7 @@ - + @@ -726,7 +726,7 @@ - + @@ -875,7 +875,7 @@ - + @@ -1040,7 +1040,7 @@ - + @@ -1197,7 +1197,7 @@ - + @@ -1623,7 +1623,7 @@ +

          extends baseSpikeSource

      - + @@ -1687,7 +1687,7 @@ - + diff --git a/docs/Synapses.html b/docs/Synapses.html index 6343891..752913d 100644 --- a/docs/Synapses.html +++ b/docs/Synapses.html @@ -15,7 +15,7 @@ - NeuroML v2.1 Component Types + NeuroML v2.2 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 v2.1 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 v2.2 definitions, using the latest version of LEMS!
      basePyNNCell -

          extends baseCellMembPot
      @@ -98,10 +98,10 @@ i_offset Dimensionless
      tau_syn_Etau_syn_E
          This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell      		 Dimensionless
      tau_syn_Itau_syn_I
          This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell      		 Dimensionless
      v_initiSyn current
      v    (from baseCellMembPot)v    (from baseCellMembPot) voltage
      iSyn    (from basePyNNCell) current
      v    (from baseCellMembPot)v    (from baseCellMembPot) voltage
      cm    (from basePyNNCell) Dimensionless
      e_rev_Ee_rev_E
          This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell      		 Dimensionless
      e_rev_Ie_rev_I
          This parameter is never used in the NeuroML2 description of this cell! Any synapse producing a current can be placed on this cell      		 Dimensionless
      i_offset    (from basePyNNCell)iSyn    (from basePyNNCell) current
      v    (from baseCellMembPot)v    (from baseCellMembPot) voltage
      iSyn    (from basePyNNCell) current
      v    (from baseCellMembPot)v    (from baseCellMembPot) voltage
      iSyn    (from basePyNNCell) current
      v    (from baseCellMembPot)v    (from baseCellMembPot) voltage
      iSyn    (from basePyNNCell) current
      v    (from baseCellMembPot)v    (from baseCellMembPot) voltage
      iSyn    (from basePyNNCell) current
      v    (from baseCellMembPot)v    (from baseCellMembPot) voltage
      iSyn    (from basePyNNCell) current
      v    (from baseCellMembPot)v    (from baseCellMembPot) voltage
      wiSyn    (from basePyNNCell) current
      v    (from baseCellMembPot)v    (from baseCellMembPot) voltage
      wn Dimensionless
      v    (from baseCellMembPot)v    (from baseCellMembPot) voltage
      SpikeSourcePoisson -

          extends baseSpikeSource
      @@ -1676,7 +1676,7 @@ tnextUsed time
      tsince    (from baseSpikeSource)tsince    (from baseSpikeSource) time
      in Direction: in
      spike    (from baseSpikeSource)spike    (from baseSpikeSource) Direction: out
      - - + +

      Synapses

      NeuroML2 ComponentType definitions from Synapses.xml
      Original LEMS ComponentType definitions: Synapses.xml
      Schema against which NeuroML based on these should be valid: NeuroML_v2.1.xsd
      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

        @@ -145,7 +145,7 @@ - + @@ -174,7 +174,7 @@ - + @@ -232,10 +232,10 @@ - + - + @@ -300,10 +300,10 @@ - + - + @@ -351,13 +351,13 @@ - + - + - + @@ -411,7 +411,7 @@ - + @@ -491,7 +491,7 @@ - + @@ -1574,19 +1574,19 @@ - + - + - + - + diff --git a/docs/generate.py b/docs/generate.py index 1aff074..79813ec 100644 --- a/docs/generate.py +++ b/docs/generate.py @@ -24,7 +24,7 @@ # https://docs.python.org/3/library/decimal.html#module-decimal getcontext().prec = 7 -nml2_version = "2.1" +nml2_version = "2.2" nml2_branch = "master" col_width_left = "70" diff --git a/examples/NML2_AnalogSynapses.nml b/examples/NML2_AnalogSynapses.nml index 6d949de..f197c71 100644 --- a/examples/NML2_AnalogSynapses.nml +++ b/examples/NML2_AnalogSynapses.nml @@ -2,55 +2,47 @@ - + - + - + - + - + - - + + - + - + - + - - - - - - - - - - + + diff --git a/examples/NML2_AnalogSynapsesHH.nml b/examples/NML2_AnalogSynapsesHH.nml index 75db6c4..45c49d1 100644 --- a/examples/NML2_AnalogSynapsesHH.nml +++ b/examples/NML2_AnalogSynapsesHH.nml @@ -2,55 +2,47 @@ - + - - + + - - - + + + - + - + - - + + - + - - - - - - - - - - + + diff --git a/examples/NML2_FullCell.nml b/examples/NML2_FullCell.nml index fffc74f..a80c073 100644 --- a/examples/NML2_FullCell.nml +++ b/examples/NML2_FullCell.nml @@ -2,22 +2,21 @@ - + - + - + - + A Simple Spiking cell for testing purposes @@ -54,7 +53,7 @@ - + @@ -63,7 +62,7 @@ - + @@ -81,7 +80,7 @@ - + diff --git a/examples/NML2_GapJunctionInstances.nml b/examples/NML2_GapJunctionInstances.nml index 79f80c1..106f887 100644 --- a/examples/NML2_GapJunctionInstances.nml +++ b/examples/NML2_GapJunctionInstances.nml @@ -2,56 +2,48 @@ + This example shows the preferred usage with instance lists etc. --> - + - + - - + + - - + + - + - - + + - + - + - - - - - - - - diff --git a/examples/NML2_GapJunctions.nml b/examples/NML2_GapJunctions.nml index 7d44119..3ea7c8a 100644 --- a/examples/NML2_GapJunctions.nml +++ b/examples/NML2_GapJunctions.nml @@ -2,38 +2,30 @@ - + - + - + - - + + - + - + - + - - - - - - - - diff --git a/examples/NML2_InstanceBasedNetwork.nml b/examples/NML2_InstanceBasedNetwork.nml index d8a2e06..b0b963f 100644 --- a/examples/NML2_InstanceBasedNetwork.nml +++ b/examples/NML2_InstanceBasedNetwork.nml @@ -2,10 +2,10 @@ - + @@ -31,7 +31,7 @@ - @@ -46,16 +46,8 @@ - + - - - - - - - - diff --git a/examples/NML2_SegmentConnections.nml b/examples/NML2_SegmentConnections.nml index ebf2136..a36b791 100644 --- a/examples/NML2_SegmentConnections.nml +++ b/examples/NML2_SegmentConnections.nml @@ -2,11 +2,11 @@ - + @@ -26,10 +26,10 @@ - + - + @@ -50,7 +50,7 @@ - + @@ -65,11 +65,3 @@ - - - - - - - - diff --git a/examples/README.md b/examples/README.md index d9396bc..7fa4303 100644 --- a/examples/README.md +++ b/examples/README.md @@ -1,4 +1,5 @@ -Files starting with NML2_ in this folder will be valid against ../Schemas/NeuroML2/NeuroML_v2beta.xsd +Files starting with NML2_ in this folder will be valid against the latest +version of the NeuroML schema (and quite possibly a few earlier ones) in ../Schemas/NeuroML2/ To validate these files using `jnml`, run: @@ -25,4 +26,4 @@ this directory, use: for i in *.nml; do pynml $i -validate; done ``` -If the validation fails, please file an issue. +See also https://docs.neuroml.org/Userdocs/ValidatingNeuroMLModels.html. If the validation fails, please file an issue. diff --git a/pom.xml b/pom.xml index 561f9d5..bdfa999 100644 --- a/pom.xml +++ b/pom.xml @@ -8,7 +8,7 @@ neuroml2-base-definitionsorg.neuroml.core - 1.7.2 + 1.8.1 @@ -21,7 +21,7 @@ LEMSexamples/*.xml - + maven-remote-resources-plugin diff --git a/scripts/Readme.rst b/scripts/Readme.rst new file mode 100644 index 0000000..a349ca4 --- /dev/null +++ b/scripts/Readme.rst @@ -0,0 +1,7 @@ +Some scripts for ad-hoc tests. + +transfer_docs_to_xsd.py: + +Copies documentation from the XML Component definition files and adds it to the XSD file. +For best results, run xmllint on the XSD file before running the script, and then run xmllint on the resulting file too. +That ensures that the git diff shows the only relevant changes (without any formatting bits). diff --git a/scripts/format-xsd.sh b/scripts/format-xsd.sh new file mode 100755 index 0000000..b18a613 --- /dev/null +++ b/scripts/format-xsd.sh @@ -0,0 +1,23 @@ +#!/bin/bash + +# Copyright 2021 Ankur Sinha +# Author: Ankur Sinha +# File : format-xsd.sh +# +# format XSD file with xmllint + + +if [ "$#" -ne 1 ] +then + echo "Please provide the XSD file to format as an argument" + exit 1 +fi + +if [ -x "$(command -v xmllint)" ] +then + echo "Formatting $1" + xmllint --format "$1" -o "$1".formatted + mv "$1".formatted "$1" +else + echo "xmllint not found" +fi diff --git a/scripts/transfer_docs_to_xsd.py b/scripts/transfer_docs_to_xsd.py new file mode 100644 index 0000000..686f174 --- /dev/null +++ b/scripts/transfer_docs_to_xsd.py @@ -0,0 +1,240 @@ +#!/usr/bin/env python3 +""" +Copy over documentation from XML schema files to the XSD. + +File: transfer_docs_to_xsd.py + +Copyright 2021 Ankur Sinha +Author: NeuroML contributors +""" + + +import lxml.etree as ET +from lems.model.model import Model + + +xml_files = [ + "Cells.xml", + "NeuroML2CoreTypes.xml", + "Simulation.xml", + "Channels.xml", + "NeuroMLCoreCompTypes.xml", + "Synapses.xml", + "Inputs.xml", + "NeuroMLCoreDimensions.xml", + "Networks.xml", + "PyNN.xml" +] + + +def format_description(text): + """Format the description. + + This is too complex to be done in the Jinja template. It can be done, but + it'll be messy. + + - convert underscores in text to URLs and bold, + - no need to convert asterisk, since they're underline in myAST already, + - no need to format http:// URLs, since they're also handled automatically. + + :param text: text to process + :type text: string + :returns: converted string + + """ + if not text or len(text) == 0: + return "" + # Add spaces after these so we correctly split "(_gbase" type constructs + puncts = ["(", ",", ";", "."] + for punct in puncts: + text = text.replace(punct, punct + " ") + # Add spaces before these + for punct in [")"]: + text = text.replace(punct, " " + punct) + + # Remove spaces between dots and URL suffixes + # introduced by previous tweaks + suffixes = ["org", "com", "htm", "html"] + for suf in suffixes: + text = text.replace(". " + suf, "." + suf) + + words = text.split() + text2 = "" + for word in words: + if len(word) > 0: + if word.count('_') == 2: + pre = word[0:word.find('_')] + ct = word[word.find('_') + 1:word.rfind('_')] + post = word[word.rfind('_') + 1:] + word = "{} **{}** {}".format(pre, ct, post) + elif word[0] == '_': + word = "**{}** ".format(word[1:]) + + text2 = text2 + word + " " + return text2.rstrip() + + +def update_xsd(): + """Update the XSD documentation. + + This takes whatever is in the XML files and puts in the XSD, replacing + anything that may be in the XSD already. + """ + XSD_file = "../Schemas/NeuroML2/NeuroML_v2.2.xsd" + XSD_file_new = "../Schemas/NeuroML2/NeuroML_v2.2_docs.xsd" + try: + xsdtree = ET.parse(XSD_file) + xsdroot = xsdtree.getroot() + except ET.XMLSyntaxError as e: + print(f"Could not parse file {XSD_file}: {e}") + + xsdnamespaces = xsdroot.nsmap + xsdnsinfo = xsdnamespaces['xs'] + complex_types = xsdroot.findall(".//xs:complexType", namespaces=xsdnamespaces) + + # iterate over all schema files + # find it in the XSD, make changes + for file in xml_files: + xmlfile = "../NeuroML2CoreTypes/" + file + print("Definitions: processing {}".format(xmlfile)) + model = Model(include_includes=False) + model.import_from_file(xmlfile) + + for comp_type in model.component_types: + ct_name = comp_type.name + ct_doc = format_description(comp_type.description) if comp_type.description is not None else "" + + # Add parameter documentation in the main complextype documentation + # itself so that it's formatted properly when put through + # generateds. + params = {} + for param in comp_type.parameters: + params[param] = comp_type.name + + extd_comp_type = None + extd_comp_type_name = None + extd_comp_type_name = comp_type.extends + for act in model.component_types: + if act.name == extd_comp_type_name: + extd_comp_type = act + break + + while extd_comp_type is not None: + current_comp_type = extd_comp_type + extd_comp_type = None + extd_comp_type_name = None + + for param in current_comp_type.parameters: + pk = params.copy().keys() + for pp0 in pk: + if pp0.name == param.name: + del params[pp0] + params[param] = current_comp_type.name + + # Next parent + extd_comp_type_name = current_comp_type.extends + for act in model.component_types: + if act.name == extd_comp_type_name: + extd_comp_type = act + break + + if len(params) > 0: + # this is required to get sphinx to correctly parse the + # parmeters. The :param: section must start after a blank line + # for sphinx to parse it correctly. + ct_doc += "\n" + ct_doc += "\\n" + ct_doc += "\n" + for p in params.keys(): + ct_doc += ":param {}: {}\n".format(p.name, format_description(p.description)) + ct_doc += ":type {}: {}\n".format(p.name, p.dimension) + + # find this in the XSD + for cxt in complex_types: + cxt_name = cxt.attrib['name'].lower() + + if cxt_name == ct_name.lower(): + # complex type documentation + doc_node = cxt.find("./xs:annotation/xs:documentation", + namespaces=xsdnamespaces) + # remove the existing doc node, we'll re-add a new one at + # the top of the complextype so that generateDS puts this + # documentation first in nml.py + if doc_node is not None: + if len(doc_node) > 1: + print("Warning: multiple doc elements found?") + for n in doc_node: + n.getparent().getparent().remove(n.getparent()) + else: + doc_node.getparent().getparent().remove(doc_node.getparent()) + + # sometimes existing documentation is in + # complexcontent/annotation/documentation + doc_node = cxt.find("./xs:complexContent/xs:annotation/xs:documentation", + namespaces=xsdnamespaces) + if doc_node is not None: + if len(doc_node) > 1: + print("Warning: multiple doc elements found?") + for n in doc_node: + n.getparent().getparent().remove(n.getparent()) + else: + doc_node.getparent().getparent().remove(doc_node.getparent()) + + # create new annotation at top of complextype + new_annotation = ET.Element('{' + xsdnsinfo + '}annotation') + cxt.insert(0, new_annotation) + doc_node = ET.SubElement(new_annotation, '{' + xsdnsinfo + '}documentation') + doc_node.text = ct_doc + '\n' + + # Remove any parameter documentation from the XSD + p_xsd_nodes = cxt.findall(".//xs:attribute", namespaces=xsdnamespaces) + for p_xsd_node in p_xsd_nodes: + p_doc_node = p_xsd_node.find("./xs:annotation/xs:documentation", + namespaces=xsdnamespaces) + if p_doc_node is not None: + p_doc_node.getparent().remove(p_doc_node) + + ET.indent(xsdtree) + xsdtree.write(XSD_file_new, encoding="UTF-8", method="xml", + xml_declaration=True, pretty_print=True) + print("New file written to {}".format(XSD_file_new)) + print("Please check the differences before replacing the main file.") + + +def compare_xml_xsd(): + """Compare what's defined in the XSD and in the XML.""" + + XSD_file = "../Schemas/NeuroML2/NeuroML_v2.2.xsd" + try: + xsdtree = ET.parse(XSD_file) + xsdroot = xsdtree.getroot() + except ET.XMLSyntaxError as e: + print(f"Could not parse file {XSD_file}: {e}") + + xsdnamespaces = xsdroot.nsmap + complex_types = xsdroot.findall(".//xs:complexType", namespaces=xsdnamespaces) + cxt_list = [ct.attrib['name'].lower() for ct in complex_types] + cxt_list = set(cxt_list) + + component_types = [] + for file in xml_files: + xmlfile = "../NeuroML2CoreTypes/" + file + try: + xmltree = ET.parse(xmlfile) + xmlroot = xmltree.getroot() + except ET.XMLSyntaxError as e: + print(f"Could not parse file {file}: {e}") + continue + xmlnamespaces = xmlroot.nsmap + component_types.extend(xmlroot.findall(".//ComponentType", namespaces=xmlnamespaces)) + ct_list = [ct.attrib['name'].lower() for ct in component_types] + ct_list = set(ct_list) + + print() + print("These are in the XSD but not in the XML: {}\n\n".format(cxt_list - ct_list)) + print("These are in the XML but not in the XSD: {}".format(ct_list - cxt_list)) + + +if __name__ == "__main__": + update_xsd() + compare_xml_xsd() diff --git a/test.py b/test.py index eea61ed..759189e 100644 --- a/test.py +++ b/test.py @@ -36,7 +36,7 @@ lems_exs_dir="LEMSexamples" lems_exs_list=os.listdir(lems_exs_dir) -lems_schema = "../LEMS/Schemas/LEMS/LEMS_v0.7.4.xsd" +lems_schema = "../LEMS/Schemas/LEMS/LEMS_v0.7.6.xsd" lems_schema_file = open(lems_schema) lems_xmlschema_doc = etree.parse(lems_schema_file) @@ -45,7 +45,7 @@ lems_master_ex_dir="../LEMS/examples" lems_master_ex_list=os.listdir(lems_master_ex_dir) -nml2_schema_name = "NeuroML_v2.1.xsd" +nml2_schema_name = "NeuroML_v2.2.xsd" nml2_schema = "Schemas/NeuroML2/%s"%nml2_schema_name nml2_schema_file = open(nml2_schema)
      Requirements vv
          The current may vary with the voltage exposed by the ComponentType on which this is placed      		 voltage
      Exposures I    (from basePointCurrentDL)I    (from basePointCurrentDL) Dimensionless
      Parameters ibaseibase
          Baseline current increase after receiving a spike      		 current
      tautau
          Time course for rise and decay      		 time
      Parameters ereverev
          Reversal potential of the synapse      		 voltage
      gbasegbase
          Baseline conductance, generally the maximum conductance following a single spike      		 conductance
      Parameters ereverev
          Reversal potential of the synapse      		 voltage
      gbase1gbase1
          Baseline conductance 1      		 conductance
      gbase2gbase2
          Baseline conductance 2      		 conductance
      gbase    (from baseConductanceBasedSynapse) conductance
      tauDecaytauDecay
          Time course of decay      		 time
      gbase    (from baseConductanceBasedSynapse) conductance
      tautau
          Time course of rise/decay      		 time
      Parameters VthVth
          The half-activation voltage of the synapse      		 voltage
      conductance conductance
      deltadelta
          Slope of the activation curve      		 voltage
      ereverev
          The reversal potential of the synapse      		 voltage
      kk
          Rate constant for transmitter-receptor dissociation rate      		 per_time