 ds2mdd | Convert DynaSim data structure to xp format |
| dsAll2mdd | |
| dsAnalyzeStudy | dsAnalyzeStudy - Apply an analysis function to DynaSim data, optionally saving data |
| dsApplyModifications | APPLYMODIFICATIONS - Apply modifications to DynaSim specification or model structure |
| dsAutoMergeVarieds | [data_new, variedname_merged, varied_vals ] = mergeVarieds(data,varied_fields) |
| dsCalcACF | CALCACF - Calculate the autocorrelation function. |
| dsCalcAverages | CALCAVERAGES - Average fields in a DynaSim data struct across neurons |
| dsCalcCellProperties | CALCCELLPROPERTIES - calculates the intrinsic electrophysiological properties of all cells in one or more populations |
| dsCalcCurrentPosthoc | data = calcCurrentPosthoc(data, mechanism_prefix, current_equation, additional_fields, additional_constants, current_suffix, varargin) |
| dsCalcFR | CALCFR - Calculate firing rage for DynaSim data |
| dsCalcFRmulti | CALCFRMULTI - extends dsCalcFR to get SUA and MUA firing rates |
| dsCalcISI | CALCISI - Calculate the interspike interval. |
| dsCalcPower | CALCPOWER - Compute spectral analysis of DynaSim data |
| dsCalcSpikeSync | CALCSPIKESYNC - Compute spike synchronization between spiketrains |
| dsCalcSumOverFields | CALCSUMOVERFIELDS - Creates a new field in data that is the sum of a bunch of other fields |
| dsCheckCovary | CHECKCOVARY - TODO I assume this checks if any varied parameters are covaried? |
| dsCheckCovaryWrapper | Calls checkCovary and handles all the set up automagically. |
| dsCheckData | CHECKDATA - Standardize data structure and auto-populate missing fields |
| dsCheckHostPaths | CHECKHOSTPATHS - Compare paths on host to those set in studyinfo when batch was created |
| dsCheckModel | CHECKMODEL - Standardize model structure and auto-populate missing fields |
| dsCheckOptions | CHECKOPTIONS - organize key/value pairs in structure with default or user-supplied values according to a schema |
| dsCheckSolverOptions | CHECKSOLVEROPTIONS - standardize simulation options appended to params.mat |
| dsCheckSpecification | CHECKSPECIFICATION - standardize specification structure and auto-populate missing fields |
| dsCheckStudyinfo | CHECKSTUDYINFO - Standardize studyinfo structure and auto-populate missing fields |
| dsCheckVersion | % dsCheckVersion - checks dynasim version against github |
| dsClassifyEquation | CLASSIFYEQUATION - use regular expressions to classify model expressions in STRING |
| dsCollectVariedParams | COLLECTVARIEDPARAMS - Gathers info on parameters that have been varied in a batch |
| dsCombineModels | COMBINEMODELS - combine subfields in two DynaSim model structures |
| dsCompareSolveFiles | COMPARESOLVEFILES - look for an equivalent file in same directory |
| dsComputeRaster | dsComputeRaster - Use a threshold to find spiketrain for a voltage trace |
| dsCreateBatch | CREATEBATCH - create and submit jobs to run sets of simulations or analyses. |
| dsCropData | CROPDATA - Crops DynaSim data structre |
| dsData2Table | Converts DynaSim structure to 1D cell array format. Later can use to |
| dsDataField2Table | Converts DynaSim structure to 1D cell array format. Later can use to |
| dsDecimateData | DOWNSAMPLEDATA - Downsamples DynaSim data structre data |
| dsDownloadFiles | dsDownloadFiles - Downloads data from the web (utility function) |
| dsDynasim2odefun | Purpose: prepare ODEFUN for use with built-in Matlab solvers. |
| dsEditModelFiles | |
| dsExportData | EXPORTDATA - export DynaSim data structure in various formats. |
| dsGenerateDocumentation | GENERATEDOCUMENTATION - Build DynaSim function documentation |
| dsGenerateModel | GENERATEMODEL - Parse DynaSim specification and organize model data in DynaSim model structure |
| dsGetConfig | GETCONFIG - returns the value of the variable specificed as string in argument |
| dsGetLinearIndependentDs | [Asubs, Abasis, Abasisi] = getLinearIndependentDs(data,ignore_constant_shift,varargin) |
| dsGetNamespaces | Purpose: retrieve namespaces for all objects in specification |
| dsGetOutputCounts | GETOUTPUTCOUNTS - determine how many copies of each state variable and monitor will be produced by simulating the model. |
| dsGetParentNamespace | GETPARENTNAMESPACE - determine parent namespace from namespace specified in namespace |
| dsGetPopSizeFromName | Purpose: reverse engineer the appropriate population size from the name |
| dsGetRootPath | getRootPath - get path to main ds directory |
| dsGetSolveFile | GETSOLVEFILE - helper function that creates or retrieves the desired solver file. |
| dsGet_populations_from_meta | |
| dsGet_variables_from_meta | |
| dsImg2mdd | |
| dsImportCSV | IMPORTCSV - load CSV data into DynaSim formatted data structure. |
| dsImportModel | IMPORTMODEL - import model from raw equations, other program source, etc. |
| dsImportPlots | IMPORTPLOTS - load info about saved images (generated by SimulateMode or dsAnalyze) alongwith corresponding varied model components. |
| dsImportResults | IMPORTRESULTS - Import analysis result of a simulation |
| dsIndexToBlocks | INDEXTOBLOCKS - TODO unclear what this does |
| dsIsDevMode | check if _dev directory exists in main dynasim directory |
| dsLocateModelFiles | LOCATEMODELFILES - locate mechanism files associated with DynaSim specifications. |
| dsMakeDefaultConfig | dsMakeDefaultConfig - write default DS config vars to disk as text file in main DS dir. |
| dsMakeDefaultConfigJenkins | dsMakeDefaultConfig - write default DS config vars to disk as text file in main DS dir. |
| dsMdd2ds | % data=MDD2ds(obj,varargin) |
| dsMdd2dsImage | % data=MDD2ds(obj,varargin) |
| dsMergeData | MERGEDATA - Merge two Dynasim structures created from different simulations |
| dsMergeVarieds | [data_new, variedname_merged, varied_vals ] = mergeVarieds(data,varied_fields) |
| dsModifications2Vary | Adds fields tmpdata.varied and tmpdata.(varied{1}) ... |
| dsMonitorStudy | MONITORSTUDY - display information on study progress. |
| dsNameFromVaried | NAMEFROMVARIED - makes a filename based on the parameters in data.varied. |
| dsOptions2Keyval | OPTIONS2KEYVAL - Convert from options structure to a list of key/value pairs. |
| dsParseModelEquations | PARSEMODELEQUATIONS - parse equations and organize model data in DynaSim model structure |
| dsPlot2D | Purpose: display movie of 2D simulated data. |
| dsPlotFR | PLOTFR - plot spike rates in various ways depending on what data was provided. |
| dsPlotFR2 | PLOTFR2 - plot spike rates in various ways depending on what data was provided. |
| dsPlotStudy | PLOTSTUDY - Applies a user-specified plotting function to each element of data structure. |
| dsPlotWaveforms | PLOTWAVEFORMS - plot waveforms in various ways depending on what data was provided. |
| dsPrepareMEX | PREPAREMEX - take an m-file path and compile it using the Matlab coder. |
| dsProbeCellProperties | data = dsProbeCellProperties(model,'option1',option1,...) |
| dsProbeFI | % data=dsProbeFI(model,varargin) |
| dsPropagateFunctions | PROPAGATEFUNCTIONS - eliminate internal function calls from model ODEs, ICs, monitors, and conditionals. |
| dsPropagateNamespaces | PROPAGATENAMESPACES - namespace-establishing namespace substitutions. |
| dsPropagateParameters | PROPAGATEPARAMETERS - substitute parameter values or prepend parameter names with prefix across all model equations. |
| dsReadText | Purpose: read equations for DynaSim model from .mech, .eqns, or .m file. |
| dsRearrangeStudies2Neurons | REARRANGESTUDIES2NEURONS - Takes a DynaSim data structure that is the result of a parameter sweep and rearranges it into a single (1D) data structure. |
| dsRemoveKeyval | REMOVEKEYVAL - remove keys from keyvals_in. |
| dsSelectVariables | SELECTVARIABLES - determine what variables to plot |
| dsSetupStudy | SETUPSTUDY - Initialize DynaSim studyinfo structure, prepare list of output file names, and create output directories |
| dsSpecdiff | dsSpecDiff - Scans two DynaSim specs for differences |
| dsStrrep | STRREP - replace full words by new character strings, ignoring matches that appear as sub-strings. |
| dsStrrep2 | STRREP2 - replace full words by new character strings, WITHOUT ignoring matches that appear as sub-strings. |
| dsStudyinfoIO | STUDYINFOIO - use lock files to manage concurrent access to a shared studyinfo |
| dsThevEquiv | Calculates the Th�venin equivalent voltage and conductance for a |
| dsUnzipDemoData | dsUnzipDemoData - Unzips demo data (utility function) |
| dsUpdateStudy | UPDATESTUDY - helper function to keep track of study metadata when anything is saved |
| dsVary2Modifications | VARY2MODIFICATIONS - convert specification of things to vary into a set of modifications indicating how to vary the desired things. |
| dsWriteDynaSimSolver | WRITEDYNASIMSOLVER - write m-file that numerically inteegrates the model |
| dsWriteMatlabSolver | WRITEMATLABSOLVER - write m-file that numerically integrates the model |
| dsZipDemoData | ZIPDEMODATA - Zips demo data (utility function) |
Master index