A Model Description Language for Computational Neuroscience

These examples demonstrate the capabilities of the NeuroML v1.8.1 specifications.

For examples of models in NeuroML version 2.0 see here.

We highlight the following 4 examples to illustrate the key elements at the various Levels:

• Level 1: CablesIncluded.xml (More readable view) is an example of a cell with soma and dendrites specified in MorphML.
• Level 2: NaChannel_HH.xml (readable) is a ChannelML example of a sodium channel based on the Hodgkin Huxley squid model.
• Level 2: MossyCellBiophys.xml (readable) is a Level 2 cell description which includes the Biophysical properties of the cell.
• Level 3: CompleteNetwork.xml (readable) is a description of a full network model including cell, synaptic mechanisms and network connections (in NetworkML).

These files can be edited and revalidated or you can validate your own NeuroML files here.

Level 1: Anatomy only cells specified in MorphML

	Show HTML	Show XML	Current schema (v1.8.1)	All schemas
CablesIncluded.xml	View	Source	Validate	Validate
Simple.morph.xml	View	Source	Validate	Validate
SimpleNeuroML.xml	View	Source	Validate	Validate
L23PyrFRB.morph.xml	View	Source	Validate	Validate

Level 2: ChannelML and biophysical cell models

	Show HTML	Show XML	Current schema (v1.8.1)	All schemas
KCa_Channel.xml	View	Source	Validate	Validate
CaPool.xml	View	Source	Validate	Validate
NaF2_Chan.xml	View	Source	Validate	Validate
MossyCellBiophys.xml	View	Source	Validate	Validate
SK_KineticScheme.xml	View	Source	Validate	Validate
KChan_KineticScheme.xml	View	Source	Validate	Validate
NaChannel_HH.xml	View	Source	Validate	Validate
InhomogeneousBiophys.xml	View	Source	Validate	Validate
PyramidalCell.xml	View	Source	Validate	Validate
GranuleCell.xml	View	Source	Validate	Validate
KChannel_HH.xml	View	Source	Validate	Validate
Kc_fast_Chan.xml	View	Source	Validate	Validate
CaHVA_Chan.xml	View	Source	Validate	Validate
GateDepQ10.xml	View	Source	Validate	Validate
CellWithChannels.xml	View	Source	Validate	Validate
KA_Channel.xml	View	Source	Validate	Validate
IntFireMechanism.xml	View	Source	Validate	Validate
NaF_Chan.xml	View	Source	Validate	Validate
LeakConductance.xml	View	Source	Validate	Validate

Level 3: Networks of cells specified using NetworkML

	Show HTML	Show XML	Current schema (v1.8.1)	All schemas
SimpleNetworkInstance.xml	View	Source	Validate	Validate
ExtendNetSpec.xml	View	Source	Validate	Validate
DistributedNetwork.xml	View	Source	Validate	Validate
2DGridTemplate.xml	View	Source	Validate	Validate
SimpleNetworkTemplate.xml	View	Source	Validate	Validate
CompleteNetwork.xml	View	Source	Validate	Validate
Cerebellum.xml	View	Source	Validate	Validate
Spiral.xml	View	Source	Validate	Validate
NonSpatialGridTemplate.xml	View	Source	Validate	Validate

Miscellaneous XML files

	Show HTML	Show XML	Current schema (v1.8.1)	All schemas
BadMorphML.xml	View	Source	Validate	Validate
BadXML.xml	View	Source	Validate	Validate
OldChannelDesc.xml	View	Source	Validate	Validate

Level 2: ChannelML based synaptic mechanisms

	Show HTML	Show XML	Current schema (v1.8.1)	All schemas
STPSynapse.xml	View	Source	Validate	Validate
SingleExpSyn.xml	View	Source	Validate	Validate
DoubExpSyn.xml	View	Source	Validate	Validate
STDPSynapse.xml	View	Source	Validate	Validate
MultiDecaySyn.xml	View	Source	Validate	Validate
AlphaSyn.xml	View	Source	Validate	Validate
ElectSyn.xml	View	Source	Validate	Validate
NMDA.xml	View	Source	Validate	Validate

• @j6m8 Most of these APIs are generated from the XSD Schema: https://t.co/6K4SKEHAXf, so if there is an XSD->Go API converter...
• @j6m8 @j6m8 not yet... There are Java, Python, C++ and Matlab APIs though, see https://t.co/bKOCa4hyqN and https://t.co/NUZGm3Dwz5
• RT @TPVogels: Fun fact: Identically labeled #ion_channel #models create (sometimes very) different responses. Read it first at https://t.co…
• An update on latest developments with NeuroML: https://t.co/BjjPGAtKRs. Join our developers' Google Hangout, or che… https://t.co/CGa8ygDcpU
• NeuroML will be at the @HumanBrainProj Code Generation from Model Description Languages workshop at @fz_juelich https://t.co/rMXhvMinjJ
• RT @OSBTeam: Watch the @OpenWorm Open House today to see how @OSBTeam, @NeuroML & @GeppettoEngine help bring worm brains to life https://t.…
• The latest stable version of NeuroML 2 (v2beta4) has been released! For more details see https://t.co/F6j7UHH8xh https://t.co/BB4GUfOHU4
• RT @dagmarwaltemath: @NeuroML is now a core COMBINE standard. Hooray! #HARMONY16 @combine_coord
• @OSBTeam NeuroML will be there too! https://t.co/XJLCbH9yUJ
• RT @mhucka: #NeuroML is supported by many s/w tools these days — see https://t.co/0iJJVQvlWL — It’s come a long way. Kudos to the NeuroML c…
• RT @combine_coord: #NeuroML, a format to encode models of synapses, neurons and neuronal networks is now a COMBINE standard https://t.co/U0…
• Thanks @dwaithe. Check out https://t.co/NUZGm3Dwz5
• Congratulations @neuronJoy!
• RT @lenovere: "I know we agreed to standardise in green. But I don't like green. So I created a red standard, almost compatible with the g…
• RT @CompCancer: Sharon Crooks (Arizona State) talking about NeuroML. Lots of similarity to @MultiCellDS in terms of toolchain. #combine2015
• RT @SharCrook: @NeuroML is at COMBINE! @combine_coord Interesting talk on SBGN.
• @strawlab Have you seen http://t.co/MKUAuQZAE1 http://t.co/SWeX2PYwdd
• @strawlab It can represent some "abstract" networks without 3D info: https://t.co/UZVMjL66Ic, but probably not at the level you need...
• @strawlab NeuroML in current form is more suited to specific instances of nets with each neuron specified, e.g. http://t.co/cUuh0rpr1F
• Why should I convert my model to NeuroML 2 and put it on Open Source Brain? See http://t.co/PtT3nyQQny http://t.co/a0Z5nRhgZC

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