Update documentation

NeuroML · Jul 26, 2023 · 12c9d0c · 12c9d0c
commit 12c9d0c
Show file tree

Hide file tree

Showing 536 changed files with 183,675 additions and 0 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 9ff3e23c5b55102a37bf77a2351673bc
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.nojekyll b/.nojekyll
diff --git a/404.html b/404.html
diff --git a/CNAME b/CNAME
@@ -0,0 +1 @@
+docs.neuroml.org
diff --git a/Devdocs/DevSOP.html b/Devdocs/DevSOP.html
diff --git a/Devdocs/Devdocs.html b/Devdocs/Devdocs.html
diff --git a/Devdocs/InteractionOtherBits.html b/Devdocs/InteractionOtherBits.html
diff --git a/Devdocs/ReleaseProcess.html b/Devdocs/ReleaseProcess.html
diff --git a/Devdocs/UpdatingStandard.html b/Devdocs/UpdatingStandard.html
diff --git a/Events/2012-Edinburgh.html b/Events/2012-Edinburgh.html
diff --git a/Events/202103-Harmony.html b/Events/202103-Harmony.html
diff --git a/Events/202107-CNS2021.html b/Events/202107-CNS2021.html
diff --git a/Events/202108-INCF-Training-Week.html b/Events/202108-INCF-Training-Week.html
diff --git a/Events/202109-COMBINE.html b/Events/202109-COMBINE.html
diff --git a/Events/202204-Harmony.html b/Events/202204-Harmony.html
diff --git a/Events/20220630-CNS2022.html b/Events/20220630-CNS2022.html
diff --git a/Events/PastEvents.html b/Events/PastEvents.html
diff --git a/Landing.html b/Landing.html
diff --git a/NeuroMLOrg/Board.html b/NeuroMLOrg/Board.html
diff --git a/NeuroMLOrg/BoardHistory.html b/NeuroMLOrg/BoardHistory.html
diff --git a/NeuroMLOrg/BoardMeetingReports.html b/NeuroMLOrg/BoardMeetingReports.html
diff --git a/NeuroMLOrg/CoC.html b/NeuroMLOrg/CoC.html
diff --git a/NeuroMLOrg/CommunicationChannels.html b/NeuroMLOrg/CommunicationChannels.html
diff --git a/NeuroMLOrg/Contributors.html b/NeuroMLOrg/Contributors.html
diff --git a/NeuroMLOrg/Funding.html b/NeuroMLOrg/Funding.html
diff --git a/NeuroMLOrg/History.html b/NeuroMLOrg/History.html
diff --git a/NeuroMLOrg/OutreachTraining.html b/NeuroMLOrg/OutreachTraining.html
diff --git a/NeuroMLOrg/ScientificCommittee.html b/NeuroMLOrg/ScientificCommittee.html
diff --git a/NeuroMLOrg/Standards.html b/NeuroMLOrg/Standards.html
diff --git a/Reference/Glossary.html b/Reference/Glossary.html
diff --git a/Reference/zBibliography.html b/Reference/zBibliography.html
diff --git a/Userdocs/Conventions.html b/Userdocs/Conventions.html
diff --git a/Userdocs/CreatingNeuroMLModels.html b/Userdocs/CreatingNeuroMLModels.html
diff --git a/Userdocs/ExtendingNeuroMLv2.html b/Userdocs/ExtendingNeuroMLv2.html
diff --git a/Userdocs/FAQ.html b/Userdocs/FAQ.html
diff --git a/Userdocs/FindingNeuroMLModels.html b/Userdocs/FindingNeuroMLModels.html
diff --git a/Userdocs/GettingStarted.html b/Userdocs/GettingStarted.html
diff --git a/Userdocs/ImportingMorphologyFiles.html b/Userdocs/ImportingMorphologyFiles.html
diff --git a/Userdocs/IzhikevichNetworkExample.html b/Userdocs/IzhikevichNetworkExample.html
diff --git a/Userdocs/LEMS.html b/Userdocs/LEMS.html
diff --git a/Userdocs/LEMSExample1.html b/Userdocs/LEMSExample1.html
diff --git a/Userdocs/LEMSExample2.html b/Userdocs/LEMSExample2.html
diff --git a/Userdocs/LEMSExample3.html b/Userdocs/LEMSExample3.html
diff --git a/Userdocs/LEMSExample4.html b/Userdocs/LEMSExample4.html
diff --git a/Userdocs/LEMSExample5.html b/Userdocs/LEMSExample5.html
diff --git a/Userdocs/LEMSExample6.html b/Userdocs/LEMSExample6.html
diff --git a/Userdocs/LEMSExample7.html b/Userdocs/LEMSExample7.html
diff --git a/Userdocs/LEMSExample8.html b/Userdocs/LEMSExample8.html
diff --git a/Userdocs/LEMSOverview.html b/Userdocs/LEMSOverview.html
diff --git a/Userdocs/LEMSSchema.html b/Userdocs/LEMSSchema.html
diff --git a/Userdocs/LEMSSimulation.html b/Userdocs/LEMSSimulation.html
diff --git a/Userdocs/LEMS_elements/DefiningComponents.html b/Userdocs/LEMS_elements/DefiningComponents.html
diff --git a/Userdocs/LEMS_elements/Definingcomponenttypes.html b/Userdocs/LEMS_elements/Definingcomponenttypes.html
diff --git a/Userdocs/LEMS_elements/Dynamics.html b/Userdocs/LEMS_elements/Dynamics.html
diff --git a/Userdocs/LEMS_elements/Geometry.html b/Userdocs/LEMS_elements/Geometry.html
diff --git a/Userdocs/LEMS_elements/Modelstructure.html b/Userdocs/LEMS_elements/Modelstructure.html
diff --git a/Userdocs/LEMS_elements/Procedure.html b/Userdocs/LEMS_elements/Procedure.html
diff --git a/Userdocs/LEMS_elements/Simulation.html b/Userdocs/LEMS_elements/Simulation.html
diff --git a/Userdocs/LEMS_elements/Structure.html b/Userdocs/LEMS_elements/Structure.html
diff --git a/Userdocs/LEMS_elements/Unitsanddimensions.html b/Userdocs/LEMS_elements/Unitsanddimensions.html
diff --git a/Userdocs/MissionAndAims.html b/Userdocs/MissionAndAims.html
diff --git a/Userdocs/MultiCompartmentOLMexample.html b/Userdocs/MultiCompartmentOLMexample.html
diff --git a/Userdocs/NML2_examples/HH_single_compartment.html b/Userdocs/NML2_examples/HH_single_compartment.html
diff --git a/Userdocs/NML2_examples/IzhikevichNetwork.html b/Userdocs/NML2_examples/IzhikevichNetwork.html
diff --git a/Userdocs/NML2_examples/NeuroML-DB.html b/Userdocs/NML2_examples/NeuroML-DB.html
diff --git a/Userdocs/NML2_examples/OLM.html b/Userdocs/NML2_examples/OLM.html
diff --git a/Userdocs/NML2_examples/SingleNeuron.html b/Userdocs/NML2_examples/SingleNeuron.html
diff --git a/Userdocs/NeuroMLv1.html b/Userdocs/NeuroMLv1.html
diff --git a/Userdocs/NeuroMLv2.html b/Userdocs/NeuroMLv2.html
diff --git a/Userdocs/NeuroMLv2AndLEMS.html b/Userdocs/NeuroMLv2AndLEMS.html
diff --git a/Userdocs/OptimisingNeuroMLModels.html b/Userdocs/OptimisingNeuroMLModels.html
diff --git a/Userdocs/Paths.html b/Userdocs/Paths.html
diff --git a/Userdocs/Publications.html b/Userdocs/Publications.html
diff --git a/Userdocs/QuantitiesAndRecording.html b/Userdocs/QuantitiesAndRecording.html
diff --git a/Userdocs/Schemas/Cells.html b/Userdocs/Schemas/Cells.html
diff --git a/Userdocs/Schemas/Channels.html b/Userdocs/Schemas/Channels.html
diff --git a/Userdocs/Schemas/Index.html b/Userdocs/Schemas/Index.html
diff --git a/Userdocs/Schemas/Inputs.html b/Userdocs/Schemas/Inputs.html
diff --git a/Userdocs/Schemas/Networks.html b/Userdocs/Schemas/Networks.html
diff --git a/Userdocs/Schemas/NeuroMLCoreCompTypes.html b/Userdocs/Schemas/NeuroMLCoreCompTypes.html
diff --git a/Userdocs/Schemas/NeuroMLCoreDimensions.html b/Userdocs/Schemas/NeuroMLCoreDimensions.html
diff --git a/Userdocs/Schemas/PyNN.html b/Userdocs/Schemas/PyNN.html
diff --git a/Userdocs/Schemas/Simulation.html b/Userdocs/Schemas/Simulation.html
diff --git a/Userdocs/Schemas/Synapses.html b/Userdocs/Schemas/Synapses.html
diff --git a/Userdocs/SimulatingNeuroMLModels.html b/Userdocs/SimulatingNeuroMLModels.html
diff --git a/Userdocs/SingleCompartmentHHExample.html b/Userdocs/SingleCompartmentHHExample.html
diff --git a/Userdocs/SingleNeuronExample.html b/Userdocs/SingleNeuronExample.html
diff --git a/Userdocs/Software/MatLab.html b/Userdocs/Software/MatLab.html
diff --git a/Userdocs/Software/NeuroML_API.html b/Userdocs/Software/NeuroML_API.html
diff --git a/Userdocs/Software/NeuroMLlite.html b/Userdocs/Software/NeuroMLlite.html
diff --git a/Userdocs/Software/Software.html b/Userdocs/Software/Software.html
diff --git a/Userdocs/Software/SupportingTools.html b/Userdocs/Software/SupportingTools.html
diff --git a/Userdocs/Software/Tools/Approaches.html b/Userdocs/Software/Tools/Approaches.html
diff --git a/Userdocs/Software/Tools/Arbor.html b/Userdocs/Software/Tools/Arbor.html
diff --git a/Userdocs/Software/Tools/Brian.html b/Userdocs/Software/Tools/Brian.html
diff --git a/Userdocs/Software/Tools/EDEN.html b/Userdocs/Software/Tools/EDEN.html
diff --git a/Userdocs/Software/Tools/MOOSE.html b/Userdocs/Software/Tools/MOOSE.html
diff --git a/Userdocs/Software/Tools/NEURON.html b/Userdocs/Software/Tools/NEURON.html
diff --git a/Userdocs/Software/Tools/NetPyNE.html b/Userdocs/Software/Tools/NetPyNE.html
diff --git a/Userdocs/Software/Tools/PyNN.html b/Userdocs/Software/Tools/PyNN.html
diff --git a/Userdocs/Software/jLEMS.html b/Userdocs/Software/jLEMS.html
diff --git a/Userdocs/Software/jNeuroML.html b/Userdocs/Software/jNeuroML.html
diff --git a/Userdocs/Software/libNeuroML.html b/Userdocs/Software/libNeuroML.html
diff --git a/Userdocs/Software/pyLEMS.html b/Userdocs/Software/pyLEMS.html
diff --git a/Userdocs/Software/pyNeuroML.html b/Userdocs/Software/pyNeuroML.html
diff --git a/Userdocs/Specification.html b/Userdocs/Specification.html
diff --git a/Userdocs/TestingNeuroMLModels.html b/Userdocs/TestingNeuroMLModels.html
diff --git a/Userdocs/UnitsAndDimensions.html b/Userdocs/UnitsAndDimensions.html
diff --git a/Userdocs/Usage.html b/Userdocs/Usage.html
diff --git a/Userdocs/ValidatingNeuroMLModels.html b/Userdocs/ValidatingNeuroMLModels.html
diff --git a/Userdocs/VisualisingCells.html b/Userdocs/VisualisingCells.html
diff --git a/Userdocs/VisualisingChannels.html b/Userdocs/VisualisingChannels.html
diff --git a/Userdocs/VisualisingNeuroMLModels.html b/Userdocs/VisualisingNeuroMLModels.html
diff --git a/_downloads/54d9372f3c36e040552bd9cd5af44e43/Acnet-LEMS.png b/_downloads/54d9372f3c36e040552bd9cd5af44e43/Acnet-LEMS.png
diff --git a/_images/00c47a381be8909575f49b63cf951249f6769d66608b9b8c22c692156858b868.png b/_images/00c47a381be8909575f49b63cf951249f6769d66608b9b8c22c692156858b868.png
diff --git a/_images/1abe9667432989702a328bc8006d8b98d31514dd7276541530ac0d0e6f6cf802.png b/_images/1abe9667432989702a328bc8006d8b98d31514dd7276541530ac0d0e6f6cf802.png
diff --git a/_images/21da5d20d226f9ba010af0c85727743b7d0f604a11d927ff7b85e04705273bf6.png b/_images/21da5d20d226f9ba010af0c85727743b7d0f604a11d927ff7b85e04705273bf6.png
diff --git a/_images/2e1bea36fe18d51db608aa0f8ab5ea17531213bda9b78245318583898b1049c5.png b/_images/2e1bea36fe18d51db608aa0f8ab5ea17531213bda9b78245318583898b1049c5.png
diff --git a/_images/349e5aaa552d4ce60f4e7573735b30cc0480ffd993c3c66298a665b5509fbda2.png b/_images/349e5aaa552d4ce60f4e7573735b30cc0480ffd993c3c66298a665b5509fbda2.png
diff --git a/_images/35240cec24494f1017c1d284c8f2adf6310a004f30810c5ac1b4cb029823b834.png b/_images/35240cec24494f1017c1d284c8f2adf6310a004f30810c5ac1b4cb029823b834.png
diff --git a/_images/35387de40bb3779c6e78fd8b3b87dcd64e3e7aafd3790055adfb904c42de8715.png b/_images/35387de40bb3779c6e78fd8b3b87dcd64e3e7aafd3790055adfb904c42de8715.png
diff --git a/_images/523586e534cca4ab457b29b08c7b91242a2585c1d118638969d1474917a40993.png b/_images/523586e534cca4ab457b29b08c7b91242a2585c1d118638969d1474917a40993.png
diff --git a/_images/5937371635ed8af22afea233c4121ee286296df71709a0c0d983c5ac54dbfb3e.png b/_images/5937371635ed8af22afea233c4121ee286296df71709a0c0d983c5ac54dbfb3e.png
diff --git a/_images/7d2474292dcb2b6a573030e67d9af7d7e579e2c3d8e56c1e32a56d343a0becb7.png b/_images/7d2474292dcb2b6a573030e67d9af7d7e579e2c3d8e56c1e32a56d343a0becb7.png
diff --git a/_images/835df6149b6b3319d86e9763543ede3eed51b41e7c84b4c27259cc7a3c31af1f.png b/_images/835df6149b6b3319d86e9763543ede3eed51b41e7c84b4c27259cc7a3c31af1f.png
diff --git a/_images/863e38be94469bb4b14bd4bbcac5d8261faee3be515526c6d407dc954dab6c5e.png b/_images/863e38be94469bb4b14bd4bbcac5d8261faee3be515526c6d407dc954dab6c5e.png
diff --git a/_images/8d7b1262d5990fefa06c4b90cadf12e907aee4eeb988f8819ba40ae8a5e031bb.png b/_images/8d7b1262d5990fefa06c4b90cadf12e907aee4eeb988f8819ba40ae8a5e031bb.png
diff --git a/_images/8e8e3bf3e6fc4280c36795b162a61d25f69c8b77e952822708f4dc55f8fc8b15.png b/_images/8e8e3bf3e6fc4280c36795b162a61d25f69c8b77e952822708f4dc55f8fc8b15.png
diff --git a/_images/91256f1e9c93f0531d06136550395bb8faa3ed1232cb3260fbd8011f46d57767.png b/_images/91256f1e9c93f0531d06136550395bb8faa3ed1232cb3260fbd8011f46d57767.png
diff --git a/_images/9308d45b4b48ba7575d551d4156fbe740b8d01a0096dcd96eb46b31ba11fe126.png b/_images/9308d45b4b48ba7575d551d4156fbe740b8d01a0096dcd96eb46b31ba11fe126.png
diff --git a/_images/9ecc288583f6019e3e8f6976760d24ce605a6876d383b19b897a3bcac6d80fe7.png b/_images/9ecc288583f6019e3e8f6976760d24ce605a6876d383b19b897a3bcac6d80fe7.png
diff --git a/_images/Acnet-matrix-1.png b/_images/Acnet-matrix-1.png
diff --git a/_images/Acnet-matrix-2.png b/_images/Acnet-matrix-2.png
diff --git a/_images/Acnet-matrix-3.png b/_images/Acnet-matrix-3.png
diff --git a/_images/Acnet-matrix-4.png b/_images/Acnet-matrix-4.png
diff --git a/_images/Acnet-matrix-5.png b/_images/Acnet-matrix-5.png
diff --git a/_images/Acnet-medium-graph-level1.png b/_images/Acnet-medium-graph-level1.png
diff --git a/_images/Acnet-medium-graph-level5.png b/_images/Acnet-medium-graph-level5.png
diff --git a/_images/Acnet-medium.net.png b/_images/Acnet-medium.net.png
diff --git a/_images/Acnet-medium.povray.png b/_images/Acnet-medium.povray.png
diff --git a/_images/EUS_200px.gif b/_images/EUS_200px.gif
diff --git a/_images/Figure6a.png b/_images/Figure6a.png
diff --git a/_images/HH_example_k_channel_1.png b/_images/HH_example_k_channel_1.png
diff --git a/_images/HH_example_k_channel_2.png b/_images/HH_example_k_channel_2.png
diff --git a/_images/HH_example_na_channel_1.png b/_images/HH_example_na_channel_1.png
diff --git a/_images/HH_example_na_channel_2.png b/_images/HH_example_na_channel_2.png
diff --git a/_images/HH_single_compartment_example_sim-i.png b/_images/HH_single_compartment_example_sim-i.png
diff --git a/_images/HH_single_compartment_example_sim-iden.png b/_images/HH_single_compartment_example_sim-iden.png
diff --git a/_images/HH_single_compartment_example_sim-v.png b/_images/HH_single_compartment_example_sim-v.png
diff --git a/_images/IzNet-1.gv.png b/_images/IzNet-1.gv.png
diff --git a/_images/IzNet.gv.png b/_images/IzNet.gv.png
diff --git a/_images/LEMS_example_izhikevich2007network_sim.png b/_images/LEMS_example_izhikevich2007network_sim.png
diff --git a/_images/MorphologyNeuroML2.png b/_images/MorphologyNeuroML2.png
diff --git a/_images/NML-DB.png b/_images/NML-DB.png
diff --git a/_images/NaTa.png b/_images/NaTa.png
diff --git a/_images/NeuroML2_LEMS_Overview_web.svg b/_images/NeuroML2_LEMS_Overview_web.svg
diff --git a/_images/OSBv1.png b/_images/OSBv1.png
diff --git a/_images/a1682c582020f26638525d4a812f97aa362beb8da262ef32b308547024d5a802.png b/_images/a1682c582020f26638525d4a812f97aa362beb8da262ef32b308547024d5a802.png
diff --git a/_images/a99093d06e333047267dd3684cf78ee807373312af857f41ac59f908fb9803ad.png b/_images/a99093d06e333047267dd3684cf78ee807373312af857f41ac59f908fb9803ad.png
diff --git a/_images/andrew.jpg b/_images/andrew.jpg
diff --git a/_images/angus.png b/_images/angus.png
diff --git a/_images/ankur.png b/_images/ankur.png
diff --git a/_images/arbor.png b/_images/arbor.png
diff --git a/_images/avrama.jpg b/_images/avrama.jpg
diff --git a/_images/b3d46ea6b1e6c953f728decc53999ad59c77361d64a19a9257570a608a6852c3.png b/_images/b3d46ea6b1e6c953f728decc53999ad59c77361d64a19a9257570a608a6852c3.png
diff --git a/_images/bbsrc.gif b/_images/bbsrc.gif
diff --git a/_images/bhalla.png b/_images/bhalla.png
diff --git a/_images/biosimulators.png b/_images/biosimulators.png
diff --git a/_images/boris.jpg b/_images/boris.jpg
diff --git a/_images/brian2.png b/_images/brian2.png
diff --git a/_images/catmaid.png b/_images/catmaid.png
diff --git a/_images/cfdab35a33a4eefbef69291732f46c4a8827c8331a537a168f760487e0ccdde1.png b/_images/cfdab35a33a4eefbef69291732f46c4a8827c8331a537a168f760487e0ccdde1.png
diff --git a/_images/cgunay.JPG b/_images/cgunay.JPG
diff --git a/_images/combine.png b/_images/combine.png
diff --git a/_images/crook2007-morphml-figure1.png b/_images/crook2007-morphml-figure1.png
diff --git a/_images/cx3d.png b/_images/cx3d.png
diff --git a/_images/d81d290a075f80d4e3f73cb193e521f4ff087e3384d4092a426b52022b0acfb3.png b/_images/d81d290a075f80d4e3f73cb193e521f4ff087e3384d4092a426b52022b0acfb3.png
diff --git a/_images/ec193126c160d9b3a694a430ec1c3ce01ff44331eb30ff5cecfa6f5b966145d2.png b/_images/ec193126c160d9b3a694a430ec1c3ce01ff44331eb30ff5cecfa6f5b966145d2.png
diff --git a/_images/endorsed.png b/_images/endorsed.png
diff --git a/_images/example-single-izhikevich2007cell-sim-v.png b/_images/example-single-izhikevich2007cell-sim-v.png
diff --git a/_images/example_izhikevich2007network_sim-spikes.png b/_images/example_izhikevich2007network_sim-spikes.png
diff --git a/_images/f1d8583360566fe9d8b2e47c778612433a72d4ff36e0357412e47f9beb6a4c96.png b/_images/f1d8583360566fe9d8b2e47c778612433a72d4ff36e0357412e47f9beb6a4c96.png
diff --git a/_images/f1f31e8eafdc8d95c2b008aeb75148bba8424ec39f507a61d2e6431218acfcc2.png b/_images/f1f31e8eafdc8d95c2b008aeb75148bba8424ec39f507a61d2e6431218acfcc2.png
diff --git a/_images/fce843b119e9ef931e2fb37076f9f8b9a2f35cda36396498580c7374c2b8a456.png b/_images/fce843b119e9ef931e2fb37076f9f8b9a2f35cda36396498580c7374c2b8a456.png
diff --git a/_images/fec0f325150b43c7a02cc9ff8f07fa8a1e324904e18f2c28707a143e6343c5a1.png b/_images/fec0f325150b43c7a02cc9ff8f07fa8a1e324904e18f2c28707a143e6343c5a1.png
diff --git a/_images/fitted_izhikevich_fitness.png b/_images/fitted_izhikevich_fitness.png
diff --git a/_images/fitted_izhikevich_hist.png b/_images/fitted_izhikevich_hist.png
diff --git a/_images/fitted_izhikevich_output.png b/_images/fitted_izhikevich_output.png
diff --git a/_images/fitted_izhikevich_scatter.png b/_images/fitted_izhikevich_scatter.png
diff --git a/_images/fitted_izhikevich_screenshot_nwbexplorer.png b/_images/fitted_izhikevich_screenshot_nwbexplorer.png
diff --git a/_images/fitted_izhikevich_sim-exp-v.png b/_images/fitted_izhikevich_sim-exp-v.png
diff --git a/_images/genesis.png b/_images/genesis.png
diff --git a/_images/geppetto.png b/_images/geppetto.png
diff --git a/_images/hugo.png b/_images/hugo.png
diff --git a/_images/incf.png b/_images/incf.png
diff --git a/_images/izhikevich-binder.png b/_images/izhikevich-binder.png
diff --git a/_images/izhikevich-google.png b/_images/izhikevich-google.png
diff --git a/_images/izhikevich-livecode.png b/_images/izhikevich-livecode.png
diff --git a/_images/izhikevich-rocket-options.png b/_images/izhikevich-rocket-options.png
diff --git a/_images/izhikevich-rocket.png b/_images/izhikevich-rocket.png
diff --git a/_images/jupyter-download.png b/_images/jupyter-download.png
diff --git a/_images/jupyterbook-issue.png b/_images/jupyterbook-issue.png
diff --git a/_images/justas.jpg b/_images/justas.jpg
diff --git a/_images/lems-figure2.png b/_images/lems-figure2.png
diff --git a/_images/lems_example4.png b/_images/lems_example4.png
diff --git a/_images/lems_example6.png b/_images/lems_example6.png
diff --git a/_images/lems_example7.png b/_images/lems_example7.png
diff --git a/_images/lems_nml_files.png b/_images/lems_nml_files.png
diff --git a/_images/lfpy.png b/_images/lfpy.png
diff --git a/_images/libneuroml.png b/_images/libneuroml.png
diff --git a/_images/lyle.png b/_images/lyle.png
diff --git a/_images/mdf.png b/_images/mdf.png
diff --git a/_images/michael.png b/_images/michael.png
diff --git a/_images/moose.jpg b/_images/moose.jpg
diff --git a/_images/moose_mod.png b/_images/moose_mod.png
diff --git a/_images/mrc.jpg b/_images/mrc.jpg
diff --git a/_images/myokit.png b/_images/myokit.png
diff --git a/_images/netpyne.png b/_images/netpyne.png
diff --git a/_images/neuroconstruct.png b/_images/neuroconstruct.png
diff --git a/_images/neuron.png b/_images/neuron.png
diff --git a/_images/neuronland.png b/_images/neuronland.png
diff --git a/_images/neuronvisio.png b/_images/neuronvisio.png
diff --git a/_images/nih.gif b/_images/nih.gif
diff --git a/_images/nml-db-morphology.png b/_images/nml-db-morphology.png
diff --git a/_images/nmllite-example.png b/_images/nmllite-example.png
diff --git a/_images/nsf.gif b/_images/nsf.gif
diff --git a/_images/olm-cell-fi.png b/_images/olm-cell-fi.png
diff --git a/_images/olm-cell-subthresholdVi.png b/_images/olm-cell-subthresholdVi.png
diff --git a/_images/olm-cell-voltage-traces.png b/_images/olm-cell-voltage-traces.png
diff --git a/_images/olm.cell.png b/_images/olm.cell.png
diff --git a/_images/olm.cell.xy.png b/_images/olm.cell.xy.png
diff --git a/_images/olm_example_sim_seg0_soma0-v.png b/_images/olm_example_sim_seg0_soma0-v.png
diff --git a/_images/openworm.png b/_images/openworm.png
diff --git a/_images/openworm2-mod.png b/_images/openworm2-mod.png
diff --git a/_images/osb-conversion.png b/_images/osb-conversion.png
diff --git a/_images/osb-morphology.png b/_images/osb-morphology.png
diff --git a/_images/osbnivo_mod2.png b/_images/osbnivo_mod2.png
diff --git a/_images/padraig2.jpeg b/_images/padraig2.jpeg
diff --git a/_images/pynml-channelanalysis.png b/_images/pynml-channelanalysis.png
diff --git a/_images/pynml_jnml.svg b/_images/pynml_jnml.svg
diff --git a/_images/pynn.png b/_images/pynn.png
diff --git a/_images/robertmcdougal.png b/_images/robertmcdougal.png
diff --git a/_images/rsz_crook.jpg b/_images/rsz_crook.jpg
diff --git a/_images/salva.png b/_images/salva.png
diff --git a/_images/single_hh_cell_network.gv.png b/_images/single_hh_cell_network.gv.png
diff --git a/_images/single_olm_cell_network.gv.png b/_images/single_olm_cell_network.gv.png
diff --git a/_images/test_morphology_plot_2d_Cell_497232312_cell_nml_xy.png b/_images/test_morphology_plot_2d_Cell_497232312_cell_nml_xy.png
diff --git a/_images/test_morphology_plot_3d_Cell_497232312_cell_nml.png b/_images/test_morphology_plot_3d_Cell_497232312_cell_nml.png
diff --git a/_images/trakem2.png b/_images/trakem2.png
diff --git a/_images/trees.png b/_images/trees.png
diff --git a/_images/tvb.png b/_images/tvb.png
diff --git a/_images/wtlogo.png b/_images/wtlogo.png
diff --git a/_sources/404.md b/_sources/404.md
@@ -0,0 +1,5 @@
+# Page not found
+
+Sorry, the page you were looking could not be found.
+Please use the search function to look for information in the documentation.
+For any issues, please {ref}`contact us <contact>`.
diff --git a/_sources/Devdocs/DevSOP.md b/_sources/Devdocs/DevSOP.md
@@ -0,0 +1,124 @@
+(devdocs:devsop)=
+# Contribution guidelines
+
+Thank you for your interest in contributing to NeuroML.
+Welcome!
+
+This page documents the contribution guidelines for all NeuroML related repositories.
+
+Please do remember that these are *guidelines* but not rules that must be strictly followed.
+We think these are reasonable ideas to follow and they help us maintain a high code quality while making it easier and more efficient for all of us to work together.
+However, there may be cases where they can not be followed, and that's fine too.
+
+(devdocs:devsop:coc)=
+## Code of conduct
+
+All NeuroML projects are governed by the {ref}`Code of Conduct <coc>`.
+By participating, you are expected to uphold this code.
+Please report unacceptable behaviour to the moderators of the communication channel you are in.
+
+(devdocs:devsop:repos)=
+## Structure of repositories
+
+- All NeuroML repositories use the [Git](https://git-scm.com/) version control system.
+- Contributions are made using [pull requests](https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests).
+- Each NeuroML software tool resides in its own GitHub repository under the [NeuroML GitHub Organization](https://github.com/NeuroML), apart from [libNeuroML](https://github.com/NeuralEnsemble/libNeuroML) which is developed in collaboration with the [NeuralEnsemble community](http://neuralensemble.org/) and so lives under their GitHub organization.
+- LEMS repositories are housed under the [LEMS GitHub Organization](https://github.com/LEMS).
+
+You can find links to these on the respective pages for each {ref}`software tool <userdocs:software>`.
+
+The NeuroML standard itself (schema and ComponentType definitions) is housed in its own repository [here](https://github.com/NeuroML/NeuroML2).
+
+(devdocs:devsop:repos:zenhub)
+### Kanban board on Zenhub
+
+An overview of the various repositories, tasks, issues, and so on can be seen on the [NeuroML Kanban board on Zenhub](https://app.zenhub.com/workspaces/neuroml-development-605c92c7c670460016e497ab/board?filterLogic=any&repos=7225220,6579766,7225426,299352189,78101103,129064858,8460738,6171449,6171626,27832592,78100679,6171646,3740176,4614078,7146844,4326891&showPipelineDescriptions=false).
+
+
+(devdocs:devsop:versioning)=
+## Versioning
+
+All NeuroML repositories (including the standard) follow [Semantic versioning](https://semver.org/).
+This means that the version string consists of three components: `MAJOR.MINOR.PATCH`:
+
+- the MAJOR version is incremented when incompatible API changes are made,
+- the MINOR version is incremented when functionality is added in a backwards compatible manner, and
+- the PATCH version is incremented when backwards compatible bug fixes are made.
+
+(devdocs:devsop:branches)=
+## Git branches
+
+- Please develop against the `development` branch in all repositories.
+  This branch is merged into `master` via a pull request when a new release is made.
+  This ensures that all tests are run at each step to verify correctness.
+  As a result, the `master` branch of all repositories holds the stable version of the standard and tools, while the `development` branch holds the next, unstable version that is being worked upon.
+
+- For branch names, please consider using the [Git flow](https://nvie.com/posts/a-successful-git-branching-model/) naming convention (not mandatory but strongly suggested):
+
+  - prefix feature branches with `feat/` or `enh/` (for enhancement)
+  - prefix bugfix branches with `bugfix/` or `fix/`
+  - pull requests addressing specific tickets may also mention them in the branch name. E.g., `bugfix/issue-22`.
+
+(devdocs:devsop:commits)=
+## Git commits
+
+Git commit messages are extremely important because they allow us to nicely track the complete development history of the project.
+Here are some guidelines on writing good commit messages:
+
+- Each commit should ideally only address one issue.
+  It should be self-contained (should not group together lots of changes).
+  Tip: use `git add -p` to break your work down into logical, small commits).
+- Write good commit messages.
+  Read [this post](https://chris.beams.io/posts/git-commit/) to see how to write meaningful, useful commit messages and why they are important.
+- We strongly suggest using the [Conventional Commit](https://www.conventionalcommits.org/en/v1.0.0/#summary) specification.
+  In short:
+
+  - Each commit is of the form `<type>[optional scope]: description`, followed by the text body of the commit after a blank line, and then any optional references etc. as footer.
+  - The `type` can be one of: `fix`, `feat`, `build`, `chore`, `ci`, `docs`, `refactor`, `perf`, `test`, and so on depending on what the commit is doing.
+  - Any backwards incompatible, breaking change must be clearly noted in the commit using the `BREAKING CHANGE` phrase.
+    This corresponds to a major version update (as noted above in the versioning section).
+
+(devdocs:devsop:style:java)=
+## Code style: Java
+
+TODO
+
+(devdocs:devsop:style:python)=
+## Code style: Python
+
+- While Python 2 is still supported even though it is [no longer supported by the Python community](https://pythonclock.org), given that most Python modules (numpy/scipy/matplotlib/sphinx) have dropped support for this deprecated Python version, NeuroML will also drop support in the near future.
+  Therefore, we strongly suggest using Python 3.
+- For Python repositories, please use [Black](https://black.readthedocs.io/) to format your code before committing and submitting a pull request.
+- We also strongly suggest linting using [flake8](https://flake8.pycqa.org/).
+- Please use [type hints](https://docs.python.org/3/library/typing.html?highlight=type%20hint) in your code and run [mypy](https://mypy.readthedocs.io/en/stable/) to test it for correctness.
+  You can see the [mypy cheatsheet](https://mypy.readthedocs.io/en/stable/cheat_sheet.html) to quickly see how to do this.
+  Since NeuroML is currently still supporting Python 2, we use the Python 2 style to maintain compatibility (this also works with Python 3).
+- Deprecations should be clearly noted in the code, and in the commit message.
+  You may use the [Sphinx deprecated directive](https://www.sphinx-doc.org/en/master/usage/restructuredtext/directives.html#directive-deprecated) along with the Python [DeprecationWarning](https://docs.python.org/3/library/exceptions.html#DeprecationWarning), for example.
+
+(devdocs:devsop:docs)=
+## Documentation
+
+All tools include their own documentation in their repositories.
+Please feel free to improve this documentation and submit pull requests.
+
+When contributing fixes and enhancements, please remember to document your classes/functions and code in general.
+Not only does this allow others to understand your code, it also allows us to auto-generate documentation using various tools.
+
+- For the Java repositories, please use the standard [Javadoc](https://www.oracle.com/technical-resources/articles/java/javadoc-tool.html) syntax.
+- For the Python repositories, please document your code using the standard [Sphinx reStructuredText](https://www.sphinx-doc.org) system.
+  For functions and so on, you can use the provided [fields](https://www.sphinx-doc.org/en/master/usage/restructuredtext/domains.html?#python-signatures).
+
+Where applicable, please add examples and so on to the software documentation to ensure that users can find the information quickly.
+Additionally, please remember to consider if this primary NeuroML documentation here needs to be updated.
+
+Please use [Semantic Line Breaks](https://sembr.org/) wherever possible.
+
+(devdocs:devsop:testing)=
+## Testing
+
+- Before submitting a pull request, please run the various tests to confirm your changes.
+  You can see how they are run in the various GitHub workflow files (in the `.github/workflows/` folder in each repository).
+  They will be run on all pull requests automatically so you can also verify your changes there.
+- For a new feature addition, please remember to include a unit test.
+- For a bug fix, please include a regression test.
diff --git a/_sources/Devdocs/Devdocs.md b/_sources/Devdocs/Devdocs.md
@@ -0,0 +1,9 @@
+(devdocs:overview)=
+# Overview
+
+This section will contain information for those who wish to **contribute to the development** of the NeuroML standard and associated tools.
+
+An overview of the NeuroML **release process** can be found {ref}`here <devdocs:release>`.
+
+The relationship of NeuroML to a number of other tools and standards in computational neuroscience,
+and the practical steps taken thus far to ensure interoperability, can be found {ref}`here <devdocs:interaction>`.
diff --git a/_sources/Devdocs/InteractionOtherBits.md b/_sources/Devdocs/InteractionOtherBits.md
@@ -0,0 +1,40 @@
+(devdocs:interaction)=
+# Interaction with other languages and standards
+
+```{admonition} Needs work
+TODO: Add more information to each of these
+```
+
+(devdocs:interaction:pynn)=
+## PyNN
+
+[https://github.com/NeuroML/NeuroML2/issues/73](https://github.com/NeuroML/NeuroML2/issues/73)
+
+(devdocs:interaction:sbml)=
+## SBML
+
+[https://github.com/OpenSourceBrain/SBMLShowcase](https://github.com/OpenSourceBrain/SBMLShowcase)
+
+
+(devdocs:interaction:sonata)=
+## Sonata
+
+[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007696](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007696)
+
+
+(devdocs:interaction:nineml)=
+## NineML & SpineML
+
+[https://github.com/OpenSourceBrain/NineMLShowcase](https://github.com/OpenSourceBrain/NineMLShowcase)
+
+
+(devdocs:interaction:mdf)=
+## ModECI MDF
+
+[http://www.modeci.org/](http://www.modeci.org/)
+
+(devdocs:interaction:swc)=
+## SWC
+
+http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html
+http://www.neuromorpho.org/myfaq.jsp
diff --git a/_sources/Devdocs/ReleaseProcess.md b/_sources/Devdocs/ReleaseProcess.md
@@ -0,0 +1,43 @@
+(devdocs:release)=
+# Release Process
+
+## Overview
+
+In general, work is carried out in the **development** branches of the [main NeuroML repositories](https://github.com/NeuroML)
+and these are merged to **master** branches on a new major release, e.g. move from NeuroML v2.1 to v2.2.
+
+A single page showing the **status of the automated test** as well as any **open Pull Requests** on all of the core NeuroML repositories can be found [here](https://github.com/NeuroML/.github/blob/main/testsheet/README.md).
+
+## Steps for new major release
+
+These are the steps required for a new release of the NeuroML development tools.
+
+| Task | Version this was last done |
+| --- | --- |
+| Make releases (not just tag - generates DOI) previous development versions of individual repos | v2.2 |
+| Increment all version numbers - to distinguish release from previous development version | v2.2 |
+| Commit all work in development branches | v2.2 |
+| Test all development branches - rerun GitHub Actions at least once | v2.2 |
+| Recheck all READMEs & docs | v2.2 |
+| Run & check [test.py](https://github.com/NeuroML/NeuroML2/blob/master/test.py) in NeuroML2 repo | v2.2 |
+| Check through issues for closed & easily closable ones | v2.2 |
+| Update version in {ref}`documentation pages <userdocs:neuromlv2>` | v2.2 |
+| Update version on [COMBINE website](https://github.com/combine-org/combine-org.github.io/blob/master/content/authors/NeuroML/_index.md) | v2.2 |
+| Update NeuroML [milestones](https://github.com/NeuroML/NeuroML2/milestones) | v2.2 |
+| Update [HISTORY.md](https://github.com/NeuroML/NeuroML2/blob/master/HISTORY.md) in NeuroML2 | v2.2 |
+| pylems: Update README; Merge to master; Tag release; Release to pip | v2.2 |
+| libNeuroML:  Update README; Retest; Merge to master; Tag release; Release to pip; Check [installation docs](https://libneuroml.readthedocs.org/en/latest/install.html) | v2.2 |
+| pyNeuroML: Update Readme; Tag release; Release to pip | v2.2 |
+| NeuroMLlite: Update Readme; Tag release; Release to pip | v2.2 |
+| Java repositories ({ref}`jNeuroML <jNeuroML>`, org.neuroml.* etc.): Merge development to master; Tag releases | v2.2 |
+| Rebuild jNeuroML & commit to [jNeuroMLJar](https://sourceforge.net/p/neuroml/code/HEAD/tree/jNeuroMLJar/) and use latest for [jNeuroML for OMV](https://github.com/OpenSourceBrain/osb-model-validation/blob/master/omv/engines/getjnml.py#L8) | v2.2 |
+| Regenerate Cells.xml etc. on nml website & commit | v2.2 |
+| Update docs on [http://www.neuroml.org](https://www.neuroml.org) | v2.2 |
+| Add new binary release on [https://github.com/NeuroML/jNeuroML/releases](https://github.com/NeuroML/jNeuroML/releases) | v2.2 |
+| ANNOUNCE (mailing list, Twitter) | v2.2 |
+| Increment version numbers in all development branches | v2.1 |
+| DOI on [Zenodo](https://doi.org/10.5281/zenodo.4627568) | v2.1 |
+| New milestone in issues | v2.1 |
+| Update version used in [neuroConstruct](https://github.com/NeuralEnsemble/neuroConstruct) | v2.2 |
+| New release of neuroConstruct | v2.0 |
+| Test toolchain on Windows... | v2.0 |
diff --git a/_sources/Devdocs/UpdatingStandard.md b/_sources/Devdocs/UpdatingStandard.md
@@ -0,0 +1,74 @@
+(devdocs:updating_standard)=
+# Making changes to the NeuroML standard
+
+The NeuroML standard is stored in two sets of files, each serving a specific purpose:
+
+- the NeuroML [XML Schema Definition](https://en.wikipedia.org/wiki/XML_Schema_(W3C)) (XSD) file: this specifies the structure of a valid NeuroML XML file: what XML tags may be used and the how they are related
+- the NeuroML [LEMS](http://lems.github.io/LEMS/) ComponentType definition XML files: these include the definitions of the NeuroML standard ComponentTypes in LEMS constructs, which include the mathematical details underlying these ComponentTypes
+
+These files are housed in the [NeuroML](https://github.com/NeuroML/NeuroML2/) repository.
+
+The XSD schema file is used to validate NeuroML XML files, as shown in the {ref}`page on validating NeuroML files <userdocs:validating_models>`.
+Further, the NeuroML Python model in {ref}`libNeuroML <libneuroml>` is also generated from the XSD file using the [generateDS](http://www.davekuhlman.org/generateDS.html) utility.
+
+The LEMS ComponentType definition XML files are also used for a series of additional validation tests, and since they include the details of the underlying dynamics for all ComponentTypes, they are also used for the simulation of NeuroML models either using the reference LEMS interpreter, {ref}`jLEMS <jlems>`, or through automated code generation for supported simulation platforms (via {ref}`jNeuroML <jneuroml>`).
+Additionally, the LEMS definition files are also used the generate the {ref}`human readable schema documentation <userdocs:neuromlv2>` included in this documentation resource.
+
+The two sets of files are therefore, tightly coupled.
+Any changes to the XSD file must also be followed by corresponding changes to the LEMS definition files.
+
+(devdocs:updating_standard:proc)=
+## Procedure
+
+```{admonition} PR waiting
+TODO: A pull request to include the `transfer_docs_to_xsd.py` script in the repository is in review here: https://github.com/NeuroML/NeuroML2/pull/172
+```
+
+The suggested way of making changes to these files is via pull requests to the NeuroML repository which will undergo review by the NeuroML editorial board and the development team.
+As noted in the {ref}`general contribution guidelines <devdocs:devsop>`, the `development` branch tracks the next release of the NeuroML standard.
+So, all pull request must be made against the `development` branch.
+
+- New ComponentTypes, and their elements (parameters, variables etc.) that are added in the LEMS definition XML files should be properly documented.
+- After both sets of files have been modified, please run the `transfer_docs_to_xsd.py` script in the `scripts` folder to copy documentation over from the XML files to the XSD schema file. This script will also run basic sanity checks to ensure that all ComponentTypes in the LEMS XML definition files are represented in the XSD schema file and vice-versa.
+- Please run `xmllint` on the files to ensure they are formatted correctly.
+- Please make individual commits for changes to the XSD file, and the XML files. This ensures that their change history is clearly maintained.
+
+(devdocs:updating_standard:schema_docs)=
+## Regenerating schema documentation
+
+Once the pull request has been merged in the NeuroML repository, the {ref}`human readable schema documentation included in this documentation resource <userdocs:neuromlv2>` must be updated.
+This is done by running the [generate-jupyter-ast.py](https://github.com/NeuroML/Documentation/blob/master/scripts/schemas/generate-jupyter-ast.py) script included in the [documentation source repository](https://github.com/NeuroML/Documentation).
+This will read the LEMS XML definition files and regenerate the corresponding documentation pages.
+A pull request can then be opened with the updated pages.
+
+
+
+(devdocs:updating_standard:org_neuroml_model)=
+## Updating the Java API: org.neuroml.model
+
+TODO: Document what needs to be done for https://github.com/NeuroML/org.neuroml.model
+
+
+
+(devdocs:updating_standard:libneuroml)=
+## Updating the Python API: libNeuroML
+
+```{admonition} PR waiting
+TODO: A pull request to include the `regenerate-nml.sh` script in the repository is in review here: https://github.com/NeuralEnsemble/libNeuroML/pull/110
+```
+
+Any changes to the XSD schema file require regeneration of the [Python object model in libNeuroML](https://github.com/NeuralEnsemble/libNeuroML/blob/development/neuroml/nml/nml.py):
+
+- copy over the updated XSD schema file to the `neuroml/nml/` directory in the `development` branch
+- commit the new XSD file
+- run the `regenerate-nml.sh` script to regenerate and reformat `nml.py`
+- build and install libNeuroML into a new virtual environment
+- run all tests using `pytest`
+- run all examples and ensure that they run correctly (please see the [GitHub actions workflow](https://github.com/NeuralEnsemble/libNeuroML/blob/master/.github/workflows/ci.yml#L44) for more information)
+- if all checks pass successfully, a pull request can be opened
+
+(devdocs:updating_standard:c_api)=
+## Updating the C++ API
+
+TODO: Document what needs to be done for https://github.com/NeuroML/NeuroML_API/
+