Robust transmission in the inhibitory Purkinje Cell to Cerebellar Nuclei pathway (Abbasi et al 2017)

 Download zip file 
Help downloading and running models
Accession:229279

References:
1 . Abbasi S, Hudson AE, Maran SK, Cao Y, Abbasi A, Heck DH, Jaeger D (2017) Robust Transmission of Rate Coding in the Inhibitory Purkinje Cell to Cerebellar Nuclei Pathway in Awake Mice PLOS Computational Biology
2 . Steuber V, Schultheiss NW, Silver RA, De Schutter E, Jaeger D (2011) Determinants of synaptic integration and heterogeneity in rebound firing explored with data-driven models of deep cerebellar nucleus cells. J Comput Neurosci 30:633-58 [PubMed]
3 . Steuber V, Jaeger D (2013) Modeling the generation of output by the cerebellar nuclei. Neural Netw 47:112-9 [PubMed]
4 . Steuber V, De Schutter E, Jaeger D (2004) Passive models of neurons in the deep cerebellar nuclei: the effect of reconstruction errors Neurocomputing 58-60:563-568
5 . Luthman J, Hoebeek FE, Maex R, Davey N, Adams R, De Zeeuw CI, Steuber V (2011) STD-dependent and independent encoding of input irregularity as spike rate in a computational model of a cerebellar nucleus neuron. Cerebellum 10:667-82 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Cerebellum;
Cell Type(s): Cerebellum deep nucleus neuron;
Channel(s): I h; I T low threshold; I L high threshold; I Na,p; I Na,t; I K,Ca; I K;
Gap Junctions:
Receptor(s): AMPA; NMDA; GabaA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: GENESIS;
Model Concept(s): Synaptic Integration;
Implementer(s): Jaeger, Dieter [djaeger at emory.edu];
Search NeuronDB for information about:  GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I K; I h; I K,Ca; Gaba; Glutamate;
/
codes
pandora-matlab-1.4compat2
.git
classes
doc
examples
functions
test_suite
README
README.cgmplot.dist
README.dist
.cvsignore *
.gitattributes
.gitignore
add_license.pl
ChangeLog
CHANGES *
configure
configure.ac
COPYING
CREDITS
Makefile *
Makefile.in
matlab-session_2008-02-11_load-extracellular-trace.log
matlab-session_2008-10-16_measure-timings.log
matlab-session_2012-04-03_class-materials.log
SUBSCRIBERS
TAGS
TODO
update_tags
                            
                              < M A T L A B >
                  Copyright 1984-2006 The MathWorks, Inc.
                         Version 7.3.0.298 (R2006b)
                              August 03, 2006

 
  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.
 
>> if usejava('jvm'), com.mathworks.services.Prefs.setBooleanPref('EditorGraphicalDebugging', false); end
>> cd /Raw/gpslice07/gps0727/
>> [a_ts, h5_info] = ...
    ns_load_tracesets('gps0727a.hdf5', ...
                      mergeStructs(struct('VmChan', 'Amp1 Vm', 'ImChan', 'Amp1 Im', ...
                                          'trials', [1:18 34:63 79:103]), def_props));
??? Undefined function or variable 'def_props'.

>> 
>> def_props = ...
      struct('addTreats', struct('kynacid', 1e-3, 'picrotx', 1e-4, 'ttx', 0, 'drug_4ap', 0), ...
             'renameTreats', struct('blocker_954AP', 'drug_4ap', ...
                                    'attr_954AP', 'drug_4ap'));
>> [a_ts, h5_info] = ...
    ns_load_tracesets('gps0727a.hdf5', ...
                      mergeStructs(struct('VmChan', 'Amp1 Vm', 'ImChan', 'Amp1 Im', ...
                                          'trials', [1:18 34:63 79:103]), def_props));
??? Undefined function or variable "log_num".

Error in ==> <a href="error:/djlab/shared/matlab/lisu/ns_file_info.m,316,1">ns_file_info at 316</a>
            for lg=1:log_num

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/functions/ns_load_tracesets.m,98,1">ns_load_tracesets at 98</a>
  [nfo h5] = ns_file_info(data_src, 'hc');

>> 
>> [a_ts, h5_info] = ...
    ns_load_tracesets('gps0727a.hdf5', ...
                      mergeStructs(struct('VmChan', 'Amp1 Vm', 'ImChan', 'Amp1 Im', ...
                                          'trials', [1:18 34:63 79:103]), def_props));
??? Undefined function or variable "log_num".

Error in ==> <a href="error:/djlab/shared/matlab/lisu/ns_file_info.m,316,1">ns_file_info at 316</a>
            for lg=1:log_num

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/functions/ns_load_tracesets.m,98,1">ns_load_tracesets at 98</a>
  [nfo h5] = ns_file_info(data_src, 'hc');

>> 
>> exit

M-Shell finished
 
                              < M A T L A B >
                  Copyright 1984-2006 The MathWorks, Inc.
                         Version 7.3.0.298 (R2006b)
                              August 03, 2006

 
  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.
 
>> if usejava('jvm'), com.mathworks.services.Prefs.setBooleanPref('EditorGraphicalDebugging', false); end
>> cd /Raw/gpslice07/gps0727/
>> def_props = ...
      struct('addTreats', struct('kynacid', 1e-3, 'picrotx', 1e-4, 'ttx', 0, 'drug_4ap', 0), ...
             'renameTreats', struct('blocker_954AP', 'drug_4ap', ...
                                    'attr_954AP', 'drug_4ap'))

def_props = 

       addTreats: [1x1 struct]
    renameTreats: [1x1 struct]

>> [a_ts, h5_info] = ...
    ns_load_tracesets('gps0727a.hdf5', ...
                      mergeStructs(struct('VmChan', 'Amp1 Vm', 'ImChan', 'Amp1 Im', ...
                                          'trials', [1:18 34:63 79:103]), def_props))
??? Error using ==> ns_file_info
Too many output arguments.

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/functions/ns_load_tracesets.m,98,1">ns_load_tracesets at 98</a>
  [nfo h5] = ns_file_info(data_src, 'hc');

>> exit

M-Shell finished

                              < M A T L A B >
                  Copyright 1984-2006 The MathWorks, Inc.
                         Version 7.3.0.298 (R2006b)
                              August 03, 2006

 
  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit www.mathworks.com.
 
>> if usejava('jvm'), com.mathworks.services.Prefs.setBooleanPref('EditorGraphicalDebugging', false); end
>> cd /Raw/gpslice07/gps0727/
>> def_props = ...
      struct('addTreats', struct('kynacid', 1e-3, 'picrotx', 1e-4, 'ttx', 0, 'drug_4ap', 0), ...
             'renameTreats', struct('blocker_954AP', 'drug_4ap', ...
                                    'attr_954AP', 'drug_4ap'))

def_props = 

       addTreats: [1x1 struct]
    renameTreats: [1x1 struct]

>> [a_ts, h5_info] = ...
    ns_load_tracesets('gps0727a.hdf5', ...
                      mergeStructs(struct('VmChan', 'Amp1 Vm', 'ImChan', 'Amp1 Im', ...
                                          'trials', [1:18 34:63 79:103]), def_props));
>> 
>> a_ts

a_ts = 

  Columns 1 through 2

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Columns 3 through 4

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Columns 5 through 6

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Columns 7 through 8

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Columns 9 through 10

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Columns 11 through 12

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Columns 13 through 14

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Columns 15 through 16

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Columns 17 through 18

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Columns 19 through 20

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Columns 21 through 22

    [1x1 physiol_cip_traceset]    [1x1 physiol_cip_traceset]

  Column 23

    [1x1 physiol_cip_traceset]

>> a_fs = ...
    physiol_cip_traceset_fileset([a_ts], [], [],...
                                 struct('profile_class_name', ...
                                        'getProfileAllSpikes', ...
                                        'neuronIdStart', 159))
physiol_cip_traceset_fileset, tracesets from  cell array

ans = 

              neuron_idx: [1x1 struct]
    params_tests_dataset: [1x1 params_tests_dataset]

params_tests_dataset, tracesets from  cell array

ans = 

     list: {1x23 cell}
       dt: []
       dy: []
       id: 'tracesets from  cell array'
    props: [1x1 struct]

Optional properties of params_tests_dataset:

ans = 

    profile_class_name: 'getProfileAllSpikes'
         neuronIdStart: 159

>> cip_trace(a_ts, 1)
??? Input argument "dy" is undefined.

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/classes/@cip_trace/cip_trace.m,67,1">cip_trace.cip_trace at 67</a>
  trace_obj = trace(datasrc, dt, dy, id, props);

>> a_ct = cip_trace(a_ts{1}, 1)
gps0727a_chan2(t1)

ans = 

    pulse_time_start: 300000
    pulse_time_width: 0
               trace: [1x1 trace]

>> plot(a_ct)

ans =

     1

>> a_ct.dt

ans =

   1.0000e-04

>> help physiol_cip_traceset/cip_trace
  cip_trace - Loads a cip_trace object from a raw data file in the traceset.
 
  Usage:
  a_cip_trace = cip_trace(traceset, trace_index, props)
 
  Description:
 
    Parameters:
 	traceset: A physiol_cip_traceset object.
 	trace_index: Index of file in traceset.
 	props: A structure with any optional properties.
 	  showParamsList: Cell array of params to add to id field.
 	  showName: Show the name of the cell in the id field (default=1).
 	  TracesetIndex: Indicates in the id field.
 		
    Returns:
 	a_cip_trace: A cip_trace object that holds the raw data.
 
  See also: <a href="matlab:help itemResultsRow">itemResultsRow</a>, <a href="matlab:help params_tests_fileset">params_tests_fileset</a>, <a href="matlab:help paramNames">paramNames</a>, <a href="matlab:help testNames">testNames</a>

 
  $Id: cip_trace.m 919 2008-01-10 05:12:29Z cengiz $
 
  Author: Cengiz Gunay <cgunay@emory.edu>, 2005/07/13
 
  Modified by:
 	Li, Su <su.li@emory.edu>, 2007/06/10 for adding HDF5 compatibility.

>> a_ct = cip_trace(a_ts{1}, 1, struct('spike_finder', 2))
gps0727a_chan2(t1)

ans = 

    pulse_time_start: 300000
    pulse_time_width: 0
               trace: [1x1 trace]

>> a_sp = spikes(a_ct)
spikes, id=gps0727a_chan2(t1)

ans = 

          times: [1x136 double]
    num_samples: 300000
             dt: 1.0000e-04
             id: 'gps0727a_chan2(t1)'

>> plot(a_sp)

ans =

     2

>> methods(a_sp)


Methods for class spikes:


ISICV                periodWhole          spikeRateISI         
SFA                  plot                 spikes               
addSpikes            plotData             subsref              
display              plotFreqVsTime       vertcat              
get                  plotISIs             withinPeriod         
getISIs              set                  withinPeriodWOffset  
getResults           spikeAmpSlope        
intoPeriod           spikeRate            

>> figure; hist(getISIs(a_sp))
>> figure; hist(getISIs(a_sp, 100))
??? Attempt to reference field of non-structure array.

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/classes/@spikes/withinPeriodWOffset.m,29,1">spikes.withinPeriodWOffset at 29</a>
s.times = s.times(s.times > a_period.start_time & s.times <= a_period.end_time);

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/classes/@spikes/withinPeriod.m,33,1">spikes.withinPeriod at 33</a>
s = withinPeriodWOffset(s, a_period);

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/classes/@spikes/getISIs.m,34,1">spikes.getISIs at 34</a>
  s = withinPeriod(s, a_period);

>> getResults(a_sp)
??? Reference to non-existent field 'trace'.

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/classes/@spikes/getResults.m,36,1">spikes.getResults at 36</a>
if isempty(s.trace.data) 

>> getResults(a_sp, a_ct)
??? Reference to non-existent field 'trace'.

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/classes/@spikes/getResults.m,36,1">spikes.getResults at 36</a>
if isempty(s.trace.data) 

>> a_sp
spikes, id=gps0727a_chan2(t1)

ans = 

          times: [1x136 double]
    num_samples: 300000
             dt: 1.0000e-04
             id: 'gps0727a_chan2(t1)'

>> struct(a_sp)

ans = 

          times: [1x136 double]
    num_samples: 300000
             dt: 1.0000e-04
             id: 'gps0727a_chan2(t1)'

>> getResults(a_sp, a_ct)
??? Reference to non-existent field 'trace'.

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/classes/@spikes/getResults.m,44,1">spikes.getResults at 44</a>
ms_factor = 1e3 * s.trace.dt;

>> getResults(a_sp, a_ct)
??? Input argument "a_period" is undefined.

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/classes/@spikes/ISICV.m,30,1">spikes.ISICV at 30</a>
ISIs = getISIs(s, a_period);

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/classes/@spikes/getResults.m,49,1">spikes.getResults at 49</a>
results.ISICV = ISICV(s);

>> help spikes/ISICV
  ISICV - Calculates the coefficient of variation (CV) of the 
 	inter-spike-intervals (ISI).
 
  Usage:
  cv = ISICV(s, a_period)
 
  Description:
 
    Parameters:
 	s: A spikes object.
 	a_period: The period where spikes were found (optional)
 
    Returns:
 	cv: Coefficient of variation.
 
  See also: <a href="matlab:help spikes">spikes</a>, <a href="matlab:help period">period</a>

 
  $Id: ISICV.m 818 2007-08-28 20:28:51Z cengiz $
 
  Author: Cengiz Gunay <cgunay@emory.edu>, 2004/09/13

>> getResults(a_sp, a_ct)

ans = 

       spikeRate: 4.5333
    spikeRateISI: 4.5317
           ISICV: 0.0791

>> plotFigure(plotFreqVsTime(a_sp))

ans =

     2

>> getResults(a_ct)
??? Input argument "a_spikes" is undefined.

Error in ==> <a href="error:/djlab/private/cengiz/work/pandora/classes/@cip_trace/getResults.m,29,1">cip_trace.getResults at 29</a>
results = mergeStructs(getRateResults(a_cip_trace, a_spikes), ...

>> methods(trace)


Methods for class trace:


analyzeSpikesInPeriod   getDy                   setProp                 
calcAvg                 getResults              spike_shape             
calcMax                 getSpike                spikes                  
calcMin                 periodWhole             subsref                 
display                 plot                    trace                   
findFilteredSpikes      plotData                withinPeriod            
findFilteredSpikes-tom  plot_abstract           
get                     set                     

>> exit

M-Shell finished

Loading data, please wait...