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

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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]
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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;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: GENESIS;
Model Concept(s): Synaptic Integration;
Implementer(s): Jaeger, Dieter [djaeger at];
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;
.cvsignore *
Makefile *
- make latest SVN/GIT version available from somewhere!
- cleanup old files in GIT history (there are some abf files somewhere! r1190-1199)
- make function to save text file from trace!
- website options:
  - keep INCF and add more wikis. pros: professional place. cons: wiki files not in repo.
  - switch to github: wikis are in different repo, but versioned, nice
    web page support for projects.
  - make entry in Mathworks page. pros: associated with author name
  - best solution: keep all three, make github main place with web
    pages for all three projects: pandora, cgmplots, param_fitter.
    Keep everything in github, but push to SVN on INCF? NeuroTools
    keeps everything external.
- add support for neuroshare matlab import [isn't this done?]
- change names of major classes to make more sense
- modify license to include attribution in scientific publications
- add test suite?
- add more examples to lyx documentation. [doing wikis on incf instead]
- replace exist functions with a 'var' 2nd param [what? No!]
- add pclamp import function abf_atf_import from Matlab file exchange
  in the utils/ folder. [abf2load works now?]
	- make trace accept atf, abf and Spike2 formats 
	- use the neuroshare input specification?
- put license, add SQL export function, and publish package
- add neurosage hdf5 support
- ask to correct link on
  comes first in google when searched for "neuroscience software".
  also link to
- rename plot_abstract, joined_db to more meaningful names.
- generalize histogram_db to hold 2 and 3-dimensional histograms
- open tools/utils dir and move needed stuff from cen_matlab and alftoolbox into there.
- make a paper production class capable of generating figures for paper automatically
- make plan and requisites for version procession
- put ItemIndex as param
- improve visualization of cip_traces
- create custom class to eliminate high-variance neurons? how to get sdb?
- plot matches that vary a lot in parameter values, but same outcome
- move multi_fileset_gpsim_cns2005 into djlab
+ move plotfICurve to model_ct_bundle
- make comparisonReport use reportCompareModelToPhysiolNeuron
+ for version 0.6:
	- add new physiology dataset loader
+ for version 0.7:
	+ new AP thr method, and look at all spikes
	+ also look at phys spikes, needs some smoothing
	+ rename displayRow to displayRows
	+ fix SE calc
- for version 0.8:
	+ move props to bottom of params_tests_dataset and tests_db
	+ remove redundant props from subclasses
- for version 1.0:
	+ add dataset connection to tests_db [created the bundle concept]
		- make version-aware loader?
		X put it in props for now?
	- put params in dataset, params_results_profile [?]
- fix fillederrorbar with new Matlab
- Make tests_db save and load its dataset on request
	- overload saveobj and loadobj methods
- tests_db
	+ add arithmetic operations that operate on the data matrix [can add columns]
	+ add horzcat, vertcat methods to concat rows or columns (!)
	+ print column numbers in display
	+ define all operations as row logical functions
	+ complex subsref for tests_db. 
- add plot-frame and docgen classes
  - plot_bars puts too much x-margin space
	- move plot_bars to utils/?
  - make plot_superpose return correct errorbar extents
  - allow adding insets to plots
  - clustering histograms?
  + fix varboxplot to return correct y-axis limits
  + add a PaperPosition property to figures to make printable figures.
  + allow fontsize change to fit more on a single page [can use export size for that]
  + Replace older plot methods with plotFigure(plot_abstract(.)) combinations
	- what to do with Interpreter=None stuff?
  + matrix color plot
  + allow adjusting location of title in stack plots
  + invar param value should be indicated on plotPages
  + classes should have function that returns plot_abstract
  + @plot_abstract is one x-y plot w/ legends, etc.
  + @plot_stack, places plots on subplots.
  + sortrows in histograms.m
  + histograms should have same axis limits
  + @plot_abstract/superposePlots, superposes plots on same axis, and 
    return a new plot_abstract object
- objects don't take more space when they're used again, has implications on design:
  - put links to previous db's for a chain of operations, but they must not be saved!
  + put link to dataset from db [made bundles]
- comparing physiology data
  - improve convenience by adding custom functions to bundle classes
  - cluster params of best matches
  - collect params of all best matches and cluster
  + allow easily choosing subset of measures
  + made color-coded error distance display
  + make tabular display
- Make params_tests_profile to use arrays rather than cell arrays
  - do for rest of profile elements
  + had to remove size member function
  + may need to modify subsref [if an array is passed, then call built-in function]
  + then make plot methods operate on arrays and return plot arrays
- update documentation 
  - perl doclet generator
  - make first description no longer than one line on all constructors
  - make sure an example accompanies each function
  - Make PDF with code design
	- add class diagram with converter methods
	- add diagram for bundles
  + update README
- high-order methods:
	+ factor analysis
	+ shuffle predicition
	- pca
	- ica
	- clustering (use for finding multiple solutions?)
		- need this for finding parameter clusters matching phys data?
		- no, use hierarchical clustering to find number of clusters and centers
		- use PCA to display clustering results
		- use ANOVA for showing significance of separation
+ make dualcip a new db and make it load profiles, etc. [made multi_fileset]
+ add method in dataset to load item by reading database row or in db vice-versa.
	- use db id for the prof id
+ ignore all parameters in comparisons?
+ plot average neuron comparison matches.
+ remove DAHPMag from depol_tests
+ remove not-a-spikes from spikes object
+ analyze each spike individually, then generate mean, mode, median, and unimodality score
+ add an addItem method to datasets
+ new subclass for custom analysis
	- add plotTestStats function to group things together [?]

  - present CVS, start using it
  - move this repository to djlab account?
+ add min ahp time to DB
+ replace '_' in latex outputs
+ ignore NeuronId while comparison and do the comparison again
+ profile:
	+ make a converter method from params_tests_db to get the profile
	+ make the profile constructor simple
	+ put all test results into the results structure
	+ overload the get method to look into the results structure
+ matrix stack plot
+ new plot & data type for mean and stds of each test and param value
	+ swapRowsPages, then find statsMeanStd
	+ statsMeanStd needs page-capable mean and std funcs
	+ create special plot with vectors and errorbars
	+ do it over all parameters in the profile
	+ then plot a test for all parameters in the same way
	+ use boxplots
+ poster size: 1.75x1.1 m^2, 68"x43"
+ sortrows(tests_db) only sorts one page and applies to all?
	+ invarValues should've been sorted already? [no, only other columns are sorted]
+ add calcSlowInact to @cip_trace
+ add cip_trace_fileset class
+ make abstract profile class to describe the getResults method
+ Make Matlab contents file
+ getResults for @spikes, @trace
+ Make README file
+ make spike checks in cip_trace_profile
+ make specialized directory for brute_aug_04, move cip_trace_profile there
	+ first make a general cip_trace_profile which takes ready-made objs
+ remove conflicting classes from the cen_matlab module