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 idx = tests2idx(db, dim_num, tests)

% tests2idx - Find dimension indices from a test names/numbers specification.
%
% Usage:
% idx = tests2idx(db, dim_num, tests)
%
% Description:
%
%   Parameters:
%	db: A tests_db object.
%	dim_num: Number between 1-3 to choose dimension: row, column, or page.
%	tests: Either a single or array of column numbers, or a single
%		test name or a cell array of test names. If ':', all
%		tests. For name strings, regular expressions are
%		supported if quoted with slashes (e.g., '/a.*/')
%		
%   Returns:
%	idx: Array of column indices.
%
% Example:
% >> cols = tests2idx(a_db, 2, {'col1', '/col2+/'});
% will return indices of col1 and columns like col2, col22, col22, etc.
%
% See also: tests_db, tests2cols, regexp
%
% $Id$
%
% Author: Cengiz Gunay <cgunay@emory.edu>, 2004/10/07

% Copyright (c) 2007 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.

% note: page_idx only exists in tests_3D_db
%dim_name_str = struct('row', 1, 'col', 2, 'page', 3);

if ~ isnumeric(dim_num) || dim_num < 1 || dim_num > 3
  error('dim_num must be within [1,3]');
end

dim_names = {'row', 'col', 'page'};
dim_name = dim_names{dim_num};

%strmatch(dim_name, possible_dim_names, 'exact');
% $$$ try 
% $$$   dim_num = dim_name_str.(dim_name);
% $$$ catch
% $$$   % sanity check
% $$$   %if isempty(dim_num)
% $$$   lasterror
% $$$   names = strcat(fieldnames(dim_name_str)', ', ')';
% $$$   error([ 'dim_name "' dim_name '" not recognized. It can only be one of these: ' ...
% $$$           strcat(names{:}) '.' ] );
% $$$ end


% Parse tests
idx = [];
if ischar(tests) && strcmp(tests, ':')
  idx = 1:dbsize(db, dim_num);
elseif islogical(tests)
  idx = find(tests);
elseif isnumeric(tests) 
  idx = tests;
elseif ischar(tests)
  ind_struct = db.([ dim_name '_idx']);
  % check if regexp first
  if tests(1) == '/'
    idx = findRegExpIdx(tests, fieldnames(ind_struct)');
  else
    idx = getfuzzyfield(ind_struct, tests, NaN, 1);
    if isempty(idx) || isnan(idx)
      error(['Field ''' tests ''' not found in db']);
    end
  end
elseif iscell(tests)
  tests={tests{:}}; % add by Li Su, change the array to a row vector.
  ind_struct = db.([ dim_name '_idx']);
  all_names = fieldnames(ind_struct);
  for test1=tests
    test = test1{1}; % unwrap the cell
    if ischar(test)
      if test(1) == '/'
        ind = findRegExpIdx(test, all_names');
      else
        ind = getfuzzyfield(ind_struct, test, NaN, 1);
        if isempty(ind) || isnan(ind)
          error(['Field ''' test ''' not found in db']);
        end
      end
    elseif isnumeric(test)
      ind = test;
    else
      display(test);
      error('Test not recognized.');
    end

    idx = [idx, ind];
  end
else
  error(['tests can either be '':'', column number or array of numbers,'...
	 ' column name or cell array of names.']);
end

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