Models
The following are a number of published models which have been converted to NeuroML. They are available as either a zip file containing just the NeuroML elements, or as a neuroConstruct project file, which can be used to map the NeuroML elements onto NEURON, GENESIS, etc.
These have been converted to NeuroML from published biophysically detailed cell and network models. Some examples more abstract examples of models illustrating support for NeuroML in neuroConstruct can be found here.
There are also a number of standalone examples of NeuroML files available on this website.
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Project name: CA1PyramidalCell Conversion of CA1 cell from Migliore et al 2005: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=55035. This model can currently be executed in NEURON, GENESIS, MOOSE and PSICS. |
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Project name: GranuleCell A project illustrating the behaviour of the Granule Cell model from: Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a Detailed Network Model of the Cerebellar Granule Cell Layer J Neurophysiol, Nov 1998; 80: 2521 - 2537. Based on scripts obtained from: http://www.tnb.ua.ac.be/models/network.shtml. This project shows how a cell model with multiple active conductances can produce the same behaviour on NEURON and GENESIS through the specification of channel mechanisms in ChannelML. |
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Project name: GranCellLayer An extension in 3D of the Granule Cell Layer model from: Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a Detailed Network Model of the Cerebellar Granule Cell Layer J Neurophysiol, Nov 1998; 80: 2521 - 2537. The default Simulation Configuration replicates the 1D 75 granule cell example from: http://www.tnb.ua.ac.be/models/network.shtml |
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Project name: MainenEtAl_PyramidalCell Implementation of the Mainen et al. pyramidal cell model from: Mainen ZF, Joerges J, Huguenard JR, Sejnowski TJ (1995) A model of spike initiation in neocortical pyramidal neurons. Neuron 15:1427-39. This project is based on scripts obtained from: http://senselab.med.yale.edu/senselab/modeldb/ShowModel.asp?model=8210 |
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Project name: SolinasEtAl_GolgiCell Multicompartmental model of cerebellar Golgi cell from: Solinas S, Forti L, Cesana E, Mapelli J, De Schutter E, D'Angelo E. (2007) Computational reconstruction of pacemaking and intrinsic electroresponsiveness in cerebellar Golgi cells. Front Cell Neurosci. 2007;1:2. Based on implemetation in NEURON taken from: http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=112685 |
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Project name: Thalamocortical This is a project implementing cells from the thalamocortical network model of Traub et al 2005 in NeuroML. Based on the NEURON implementation from: http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=45539. This model can be run on NEURON, GENESIS and MOOSE (though not yet PSICS as calcium dynamics aren't supported). It can also be used to generate a smaller version of the Layer 2/3 network model described in Cunningham et al 2004. The Default Simulation Configuration contains a single compartment cell model containing all of the 22 active channels (plus a passive conductance and a calcium pool) as used in the more detailed cell models. To run this simulation through the neuroConstruct interface, click on tab Generate, select Default Simulation Configuration, press Generate, go to tab Export -> NEURON, press Create hoc simulation, and run the simulation (or do the equivalent at tab GENESIS; MOOSE can be generated at that tab too). |
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Project name: VervaekeEtAl-GolgiCellNetwork Network of electrically coupled cerebellar Golgi cells, as described in Vervaeke et al. Rapid Desynchronization of an Electrically Coupled Interneuron Network with Sparse Excitatory Synaptic Input, Neuron 2010. |
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