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

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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;
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codes
pandora-matlab-1.4compat2
classes
@tests_db
private
.cvsignore *
abs.m
addColumns.m
addLastRow.m
addRow.m
allocateRows.m
anyRows.m
approxMappingLIBSVM.m
approxMappingNNet.m
approxMappingSVM.m
assignRowsTests.m
checkConsistentCols.m
compareRows.m
corrcoef.m
cov.m
crossProd.m
dbsize.m
delColumns.m
diff.m
display.m
displayRows.m
displayRowsCSV.m
displayRowsTeX.m
end.m
enumerateColumns.m
eq.m
factoran.m
fillMissingColumns.m
ge.m
get.m *
getColNames.m
groupBy.m
gt.m
histogram.m
invarValues.m
isinf.m
isnan.m
isnanrows.m
joinRows.m
kmeansCluster.m
le.m
lt.m
matchingRow.m
max.m
mean.m
meanDuplicateRows.m
min.m
minus.m
mtimes.m
ne.m
noNaNRows.m
onlyRowsTests.m
physiol_bundle.m
plot.m
plot_abstract.m
plot_bars.m
plotBox.m
plotCircular.m
plotCovar.m
plotImage.m
plotrow.m
plotrows.m
plotScatter.m
plotScatter3D.m
plotTestsHistsMatrix.m
plotUITable.m
plotUniquesStats2D.m
plotUniquesStatsBars.m
plotUniquesStatsStacked3D.m
plotXRows.m
plotYTests.m
plus.m
princomp.m
processDimNonNaNInf.m
rankMatching.m
rdivide.m
renameColumns.m
rop.m
rows2Struct.m
set.m *
setProp.m *
setRows.m
shufflerows.m
sortrows.m
sqrt.m
statsAll.m
statsBounds.m
statsMeanSE.m
statsMeanStd.m
std.m
subsasgn.m
subsref.m
sum.m
swapRowsPages.m
tests_db.m
tests2cols.m
tests2idx.m
tests2log.m
testsHists.m
times.m
transpose.m
uminus.m
unique.m
uop.m
vertcat.m
                            
function a_pm = plotTestsHistsMatrix(a_db, title_str, props)

% plotTestsHistsMatrix - Create a matrix plot of test histograms.
%
% Usage:
% a_pm = plotTestsHistsMatrix(a_db, title_str, props)
%
% Parameters:
%   a_db: One or more params_tests_db object. Multiple databases in an
%	  array will produce vertical stacks.
%   title_str: (Optional) A string to be concatanated to the title.
%   props: A structure with any optional properties, passed to plot_abstract.
%     orient: Orientation of the plot_stack. 'x', 'y', or 'matrix' (default).
%     histBins: Number of histogram bins.
%     quiet: Don't put the DB id on the title.
%     plotProps: Props passed to individual plots.
%     stackProps: Passed to vertical plot stacks.
% 
% Returns:
%   a_pm: A plot_stack with the plots organized in matrix form.
%
% Description:
%   Skips the 'ItemIndex' test. If no axisLimits is given in stackProps, 
% y-ranges are the maximal found from db.
%
% See also: params_tests_profile, plotVar
%
% $Id$
%
% Author: Cengiz Gunay <cgunay@emory.edu>, 2004/10/17

% Copyright (c) 2007-2011 Cengiz Gunay <cengique@users.sf.net>.
% This work is licensed under the Academic Free License ("AFL")
% v. 3.0. To view a copy of this license, please look at the COPYING
% file distributed with this software or visit
% http://opensource.org/licenses/afl-3.0.php.

% TODO:

if ~ exist('title_str', 'var')
  title_str = '';
end

if ~ exist('props', 'var')
  props = struct;
end

stack_props = getFieldDefault(props, 'stackProps', struct);

if isfield(props, 'histBins')
  hist_pars = {a_db, props.histBins};
else
  hist_pars = {a_db};
end

num_tests = dbsize(a_db(1), 2);

if ~ isfield(props, 'quiet')
  all_title = ['Measure histograms for ' get(a_db(1), 'id') title_str ];
else
  all_title = title_str;
end

num_dbs = length(a_db);
if num_dbs > 1
  hists_cell = testsHists(hist_pars{:});
  [all_pm(1:num_tests)] = deal(plot_stack);
  for test_num=1:num_tests
    plots = plot_abstract(hists_cell(test_num, :), '', ...
			  mergeStructs(getFieldDefault(props, 'plotProps', ...
                                                              struct), ...
                                       struct('rotateXLabel', 10)));
    % find maximal y-axis value
    hists = hists_cell(test_num, :);
    max_val = -Inf;
    for db_num=1:num_dbs
      max_val = max(max_val, ...
		    max(get(onlyRowsTests(hists(db_num), ':', 'histVal'), ...
			    'data'), [], 1));
    end

      extra_props = ...
          mergeStructs(stack_props, struct('xLabelsPos', 'bottom', 'xTicksPos', 'bottom'));

      % no need for this, controlled by final stack props
% $$$     if test_num == 1
% $$$     else
% $$$       extra_props = ...
% $$$           mergeStructs(stack_props, struct('xLabelsPos', 'bottom', 'xTicksPos', 'bottom', ...
% $$$                                            'yLabelsPos', 'none'));
% $$$       % Change to 'none' if 'yTicksPos'='left' is given in stackProps
% $$$       if strcmp(getFieldDefault(stack_props, 'yTicksPos', ''), 'left')
% $$$         extra_props = ...
% $$$             mergeStructs(struct('yTicksPos', 'none'), extra_props);
% $$$       end
% $$$     end

    if isfield(stack_props, 'axisLimits')
      axis_limits = stack_props.axisLimits;
    else
      axis_limits = repmat(Inf, 1, 4);
      axis_limits(3:4) = [0 max_val];
    end

    % vertical histogram stack for each test
    all_pm(test_num) = plot_stack(plots, axis_limits, 'y', '', ...
				  extra_props);
  end
  % final horizontal stack
  a_pm = plot_stack(num2cell(all_pm), [], 'x', ...
                    all_title, mergeStructs(props, ...
                                            struct('xLabelsPos', 'bottom', 'xTicksPos', 'bottom', ...
                                                   'yLabelsPos', 'left')));
else % num_dbs > 1
  plots = plot_abstract(testsHists(hist_pars{:}), '', ...
                        mergeStructs(props, struct('rotateXLabel', 10)));
  
  if isfield(props, 'orient') && strcmp(props.orient, 'x')  
    extra_props = struct('yLabelsPos', 'left');
  else
    extra_props = struct;
  end

  if isfield(props, 'orient') && (strcmp(props.orient, 'x')  || ...
                                  strcmp(props.orient, 'y'))
    a_pm = plot_stack(plots, ...
                      getFieldDefault(stack_props, 'axisLimits', []), props.orient, ...
                      all_title, ...
                      mergeStructs(props, ...
                                   mergeStructs(stack_props, extra_props)));
  else
    a_pm = matrixPlots(plots, {}, all_title, props);
  end

end

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