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]
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;
See ChangeLog or "svn log" for details of evolution.

Version history:

v1_3b: Cengiz Gunay, 2012/09/24. Public beta release.
	- More stable support for reading ABF and reading/writing
	Neuron binary and text files. 
	- Lots of new utility functions. 
	- Many bugfixes thanks to new users (e.g., Vladislav Sekulic,
	Anca Doloc-Mihu), so more options and stable operation for
	recordings from different organisms and systems. 
	- Took Readgenbin out as an independent tool (see it on
	- Support for voltage and current-clamp data as paired
	traces and related tools. VC data is used for Hodgkin-Huxley
	type channel data fitting.
	- Better unit support for data fitting and plots.
	- Better handling of NaNs in database operations.
	- New data measurements like "time to 1st spike".
	- Improved KL divergence calculation.
	- Optimized DB indexing and addressing operations, sped up 50x.
	- uniqueValues now preserves row order.
	- Improved use of NNet and SVM classifiers

v1_2b: Cengiz Gunay, 2008/10/31. Public beta "Halloween" release with
	bugfixes and support for NeuroShare-compatible files.
	- NeuroShare support to load many acquisition formats in Windows
	(see Included DLLs and utility functions.
	- Regular expression support in querying and indexing databases.
	- Added convenience 'group by' functionality similar to that of SQL's
	- Added citation reminder in license document
	- Included missing files for the filtering-based spike finder
	- Plot improvements: 
		- histogram bar plots
		- Blank plot objet are properly handled.
		- Workaround for compatibility with compiz-fusion.
		- Made CGMPLOT an optionally separate package (see website).
		- New stacked 3D image plot.
		- Proper handling of line colors in superposed plots.
	- Joins better handle NaNs and accept multiple pages.
	- Defaults changed for balancing classifier input probabilities.
	- website update, created example files for Neuroinformatics manuscript
	- Major bugfix to invarValues for asymmetric databases.
	- Improved HDF5 handling by Li Su and CG. Several changes and additions.
	- Can now merge old (PCDX) and new (HDF5) recorded bundles

v1_1b: Cengiz Gunay, 2008/02/11. Public beta bugfix and feature release. 
	Warning: old physiol_cip_traceset_fileset objects will be incompatible and will have to be re-created.
	- Added SQL import/export functions using Matlab Database Toolbox.
	- improved HDF5 acquisition data and metadata import with ns_load_traces.
	- simplified database + dataset bundle generation from raw physiology data.
	- Tom Sangrey added customized Butterworth filters for traces 
	  sampled at rates other than 10KHz.
	- Li Su provided bugfix to his improved findspikes routine.
	- Added examples to manual.
	- Added missing functions such as gettracelist2
	- improved plotting:
		- Improved chan_db plots.
		- Improved doc_plot, can reference using labels now.
		- histogram plots can normalize.
		- plot_stack can now find maximal ranges.
		- can display database values with boxplots.
		- Other miscellaneous plot enhancements.
	- Major bugfix for NaNs in compareRows, joinRows, princomp, and plotScatter
	- added several new overloaded operators to tests_db, such as unique, sqrt, uminus
	- Documentation update.
	- can make a database from matlab structure.
	- added spike width calculation at a fixed voltage.
	- changed the way joinRows uses parameters.
	- added tests_db/approxMappingNNet function that uses the Neural Network Toolbox.
		- added option to balance input probabilities of classes to map.

v1_0b: Cengiz Gunay, 2007/10/10. First public beta release
	- moved to subversion control from CVS
	- organized files into subdirectories
	- included all additional utilities
	- made a installable package available for download
	- added a Academic Free License and copyright statement
	- supports NeuroSAGE HDF5 input files for recorded physiology data
	- can load from subdirectories in params_tests_fileset
	- misc improvements of plotting functions (margins, titles, etc.)
	- added examples into manual
	- allow using covariance matrix for calculating Mahalonobis distance in ranking
	- new function to find a ll best matching neurons
	- support inset plots at arbitrary axis locations
	- extend querying to allow columns and pages. also better optimized.
	- added support for plotting channel variables
	- improved cluster job submission

v0_10b: Cengiz Gunay, 2007/03/22. Beta version.
	- automated function reference generation from Matlab source for PDF and HTML manuals
	- revamped plot generation by making plot_abstract solely responsible for frame
	- superposition of stacked plots now possible
	- several improvements to plotting
	- added algebraic operations to tests_db including transposition
	- improved comparative analysis of 3D DBs
	- started using arrays rather than cell arrays during analysis to simplify calls
	- new layouts for plotting neurons, flexible selection of traces to display
	- misc new database operations, such as enumerating unique values
	- improved firing frequency plot
	- generic 2D image plots
	- added parameter to load parameter files with different trial numbers
	- added a utils/ directory for external programs
	- added support for loading binary Neuron files, compressed Genesis files.

v0_9b: Cengiz Gunay, 2006/02/15. Beta version. 
	- Improved plotting in many ways including with self-resizing plots. 
	- Vectorized many functions to operate on multiple inputs. 
	- Improved spike shape measurements based on results from new morphologies. 
	- Optimized for memory usage in merging, joining and ranking databases.
	- Compatibility issues with Matlab R14.3 fixed.
	- Added the concept of a bundle of a dataset and DB.
	- Allow comments in physiol cell files by Tom Sangrey.
	- Moved props out of spike_shape, into base class trace.
	- Added automated document generators that can hold plots or tables, etc.
	- Organized and automated how ranking documents are generated and added more plots.
	- Added specialized plot that can do  f-I curves and similar plots.
	- Added script_array and subclasses to do automated analysis on the cluster.
	- Added .genflac support.
	- Allow adding files to existing filesets and loading DBs of added files only.
	- Added presets for comparing a limited set of measures and specify weighting.
	- Allow modifying DB contents with paren addressing rows and columns.

v0_8b: Cengiz Gunay, 2005/10/19. Beta version that has improved analysis and 
	plotting functionality, and documentation. Database object format
	has changed, which makes this revision binary incompatible with
	earlier created DB and dataset objects.

v0_7b: Cengiz Gunay, 2005/05/04. Beta version that analyzes each spike individually
	and uses improved threshold finding method.

v0_6b: Cengiz Gunay & Jeremy Edgerton, 2005/03/14. Beta version that can 
	load physiology filesets with pharmacology data.

v0_5b: Cengiz Gunay, 2005/01/25. Beta version that can work with PCDX files.

v0_4b: Cengiz Gunay, 2005/01/11. Beta version with pulse spike
	characteristics and database matching tools.

v0_2b: Cengiz Gunay, 2004/09/16. Beta version of fileset and db classes.

v0_1b: Cengiz Gunay, Aug, 2004. Beta version of base classes trace, spikes,
	spike_shape, period, and cip_trace.

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