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.

Project last modified: Tuesday June 15, 2010

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neuroConstruct project

Project name: DentateGyrus

A recreation of the model Dentate Gyrus from: Santhakumar V, Aradi I, Soltesz I. Role of mossy fiber sprouting and mossy cell loss in hyperexcitability: a network model of the dentate gyrus incorporating cell types and axonal topography. J Neurophysiol. 2005. Based on model scripts obtained from: http://senselab.med.yale.edu/senselab/modeldb/ShowModel.asp?model=51781

Project last modified: Wednesday June 23, 2010

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neuroConstruct project

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.

Project last modified: Tuesday June 15, 2010

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neuroConstruct project

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, GENESIS and MOOSE through the specification of channel mechanisms in ChannelML. To run all 3 simulators side by side and test matching of the voltage trace of a single granule cell, run the Python based script in directory pythonScripts.

Project last modified: Friday August 13, 2010

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neuroConstruct project

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

Project last modified: Monday June 21, 2010

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neuroConstruct project

Project name: PurkinjeCell

An initial implementation in NeuroML of the Purkinje Cell model from De Schutter, E. and Bower, J. M. (1994). Based on Arnd Roth el al's conversion of the original GENESIS code to NEURON. Note: conversion not fully complete. Press Validate for details. Also, there are long standing issues about getting GENESIS and NEURON behaviour of the Purkinje cell to match. Contact P. Gleeson or A. Roth for more details on current status of this model.

Project last modified: Tuesday June 15, 2010

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neuroConstruct project

Project name: RothmanEtAl_KoleEtAl_PyrCell

A project which was used in Rothman et al. "Synaptic depression enables neuronal gain control" Nature 2009 to demonstrate gain control in realistic cell models. Based on cell model from Kole et al. 2008 (obtained from http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=114394). The main Simulation Configuration generates an example of the activity of the pyramidal cell receiving excitatory input from 400 cells (via a depressing synapse) and inhibitory input from 30 cells. To generate the graphs in the paper, the input frequencies were changed manually through the GUI and the firing frequencies of the pyramidal cell recorded (note that simulations of 2-10s were used to get these frequencies and the first ~500ms of the activity was ignored). Such a process for running multiple similar simulations can be facilitated by using the Python interface to control simulation generation and execution. See pythonnC/Ex5_MultiSimGenerate.py for an example.

Project last modified: Tuesday June 15, 2010

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neuroConstruct project

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

Project last modified: Friday August 13, 2010

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neuroConstruct project

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).

Project last modified: Wednesday August 25, 2010

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neuroConstruct project

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.

Project last modified: Friday August 13, 2010

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neuroConstruct project