Models
1994 Purkinje Cell Model
The picture above shows the calcium concentration during a complex spike as simulated in the 1994 Purkinje cell model (PM9). The morphological data for the Purkinje cell model were provided by Rapp, Segev and Yarom (Hebrew University Jerusalem)
Explore this model in an interactive graphical interface:
the Purkinje cell tutorial.
Simulation scripts
Or else you can download the GENESIS2.1 scripts for this model
The tar file creates a PurkM9_model directory which contains scripts to run the following simulations:
- CLIMBSPINE9.g: simulates a complex spike in vivo.
- CLIMB9.g: simulates a complex spike in vitro.
- CURRENT9.g: simulates a somatic current injection protocol in vitro.
- ISPINE9.g: simulates irregular firing due to combined parallel fiber and inhibitory inputs in vivo.
- SYNCHRONORM9.g: simulates the firing response to a synchronous parallel fiber input in vivo.
- SYNCHROPASS9.g: simulates the EPSP evoked by a synchronous parallel fiber input in vivo.
All these scripts use additional script files:
- Purk_const.g: contains the most important parameters for the model.
- Purk_chan.g: sets up the channel kinetics. Symbolic link to: Purk_chansave.g: run this the first time, will create a set of binary (-> machine-dependent) .tab files with tabulated channel kinetics.
- Purk_chanload.g: once the .tab files are created you can link Purk_chan.g to this file. It runs much faster. Note: if you use GENESIS2.2 the .tab files are no longer machine-dependent.
- Purk_comp.g: sets up the prototype active compartments without synapses.
- Purk_icomp.g: sets up the prototype active compartments with only stellate cell synapses.
- Purk_cicomp.g: sets up the prototype active compartments with basket cell, climbing fiber and stellate cell synapses.
- Purk_spicomp.g: sets up the prototype compartments with a passive soma and active dendritic compartments including stellate cell synapses.
- Purk_syn.g: sets up the synaptic channel kinetics.
and an additional morphology file:
- Purk2M0.p: basic morphology file without channels and without spines.
- Purk2M0s.p: morphology file without channels but with one spine on each spiny dendrite compartment.
- Purk2M0sA.p: morphology file without channels but with one spine on each spiny dendrite compartment plus 200 spines for synchronous input distributed randomly.
- Purk2M9.p: basic morphology file with active channels but without spines.
- Purk2M9s.p: morphology file with channels and with one spine on each spiny dendrite compartment.
- Purk2M9s1.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #1 only.
- Purk2M9s10.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #10 only.
- Purk2M9s14.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #14 only.
- Purk2M9s19.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #19 only.
- Purk2M9s2.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #2 only.
- Purk2M9s25.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #25 only.
- Purk2M9s29.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #29 only.
- Purk2M9s3.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #3 only.
- Purk2M9s37.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #37 only.
- Purk2M9s4.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #4 only.
- Purk2M9s44.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #44 only.
- Purk2M9s45.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #45 only.
- Purk2M9s6.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 20 spines for synchronous input on branchlet #6 only.
- Purk2M9s8b.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 40 spines for synchronous input distributed over 8 different branchlets.
- Purk2M9sA.p: morphology file with channels and with one spine on each spiny dendrite compartment plus 200 spines for synchronous input distributed randomly.
Publications
The following papers describe the model and simulations using this model:
- De Schutter, E.: Dendritic voltage and calcium-gated channels amplify the variability of postsynaptic responses in a Purkinje cell model. Journal of Neurophysiology 80: 504-519 (1998).
- De Schutter E.: The Predictive Power of Detailed Biophysical Models: Experience with a Cerebellar Purkinje Cell Model. Abstracts of the 25th Goettingen Neurobiology Conference (1997).
- Jaeger D., De Schutter E., and Bower J.M.: The role of synaptic and voltage-gated currents in the control of Purkinje cell spiking: a modeling study. The Journal of Neuroscience 17: 91-106 (1997).
- De Schutter E.: A New Functional Role for Cerebellar Long Term Depression. Progress in Brain Research, C.I. De Zeeuw, J. Voogd, P. Strata editors, 114: 531-544 (1997).
- De Schutter E.: Dendritic calcium channels amplify the variability of postsynaptic responses. CSCC Annual Report 1994-1995 (1995).
- Leigh L., Vasilakis C.A., DeFanti T.A., Grossman R., Assad C., Rasnow B., Protopappas A., De Schutter E., and Bower J.M.: Virtual reality in computational neuroscience. in Virtual Reality Applications, R.A. Earnshaw, J.A. Vince and H. Jones editors, Academic Press, London. 293-306 (1995).
- Staub C., De Schutter E., and Knöpfel, T.: Voltage-imaging and simulation of effects of voltage and agonist activated conductances on soma-dendritic voltage coupling in cerebellar Purkinje cells. Journal of Computational Neuroscience 1: 301-311 (1994).
- De Schutter E.: Modelling the cerebellar Purkinje cell: experiments in computo. Progress in Brain Research, van Pelt J., Corner M.A., Uylings H.B.M. and Lopes da Silva F.H. editors, 102: 417-431 (1994).
- De Schutter E., and Bower J.M.: Simulated responses of cerebellar Purkinje cells are independent of the dendritic location of granule cell synaptic inputs. Proceedings of the National Academy of Sciences USA 91: 4736-4740 (1994c)
- De Schutter E., and Bower J.M.: An active membrane model of the cerebellar Purkinje cell. I. Simulation of current clamps in slice. Journal of Neurophysiology 71: 375-400 (1994a).
- De Schutter E., and Bower J.M.: An active membrane model of the cerebellar Purkinje cell: II. Simulation of synaptic responses. Journal of Neurophysiology 71: 401-419 (1994b).