2017-12-15 version 1.12.10 Usability 2017-08-01 version 1.12.9 Mitigated "express.exe.log" permissions conflict 2017-06-01 version 1.12.8 qub.mandelics.com edition 2017-05-18 version 1.12.7 Compatibility with QUB Online 2017-01-24 version 1.12.6 Scripting: QubX.Modeling.MacRates.data_prep.datas[i].get_buffer()[:,2] has properly scaled log likelihood 2017-01-17 version 1.12.5 Open a .qmj model file by drag and drop added global RejectMacModels([qubx.fast.PModel]) -> True to reject as an optimizer step for MacRates 2016-11-14 version 1.12.4 Added Minimum Description Length (MDL) idealization to Modeling:Idealize panel. See: Gnanasambandam, Nielsen, Nicolai, Sachs, Hofgaard, Dreyer. 2016. Unsupervised idealization of ion channel recordings by Minimum Description Length: Application to human PIEZO1-channels 2016-09-24 version 1.12.3 DurHist: Fit all exponentials: shows LLR of last successful step 9 Landowne simplification 2016-09-12 version 1.12.2 DurHist: to import a log10-binned histogram table for fitting, click the blue folder next to "Fit all exponentials" DurHist: Fit all exponentials: experimental "Step 11"--remove any tiny components that remain, then re-fit 2016-09-06 version 1.12.1 HJCFIT ignores initial and final closed events, rather than complaining scripting bug fixes 2016-08-07 version 1.12.0 Added Modeling:HJCFIT plugin, thanks to David Colquhoun et al for providing open source Fixed some other plugins on MacOS 2016-08-05 version 1.11.11 Disabled stdout on Mac OS; writing to it eventually hangs the app 2016-08-04 version 1.11.10 Accumulating console output from "Fit All Exponentials" offscreen until finished, to address crash reports on Mac OS 2016-07-20 version 1.11.9 DurHist bug fixes: fitted exponentials were shifted by one bin "Fit All Exponentials" was improperly discarding some components Extract bug fix: saving idealized data "Fit All Exponentials" significance level can be adjusted with a script variable: >>> qubx_single.dur_hist.ALL_EXPONENTIALS_SIGNIFICANCE = 0.05 2016-06-15 version 1.11.8 List table: added "Add field" button DurHist: after "Fit All Exponentials", runs "Fit" once more to ensure convergence DFP optimizer: added "perturb" option to randomly adjust parameters before fitting, so it generates better error estimates 2016-04-17 version 1.11.7 States table: added "Plot" button 2016-04-16 version 1.11.6 States table: new columns computed from rate constants, using stimulus values from highlighted data (or from the Constants table, if no stimulus signal) Peq: equilibrium occupancy probability TimeConstant: average lifetime, = 1/sum(exit rates) Drag and drop a .py file to open it in the Scripts panel 2016-03-31 version 1.11.5 MacRates: Multi-data: to set model channel count per data file: add a constant named "Channel Count" (exact capitalization) to the "Constants" table Curve fitting: fixed editing parameter "High" limit downgraded Windows installer to Python 2.6 due to broken clipboard in newer pygtk installers 2016-03-14 version 1.11.4 Windows bug fix: MacRates of selection (and other curve-fitting of data selections) 2016-02-23 version 1.11.3 Windows bug fix: double-click-to-zoom in data panel 2016-02-22 version 1.11.2 Workflow:ColumnFit helps automate curve fitting of all columns in a text file Figures:Charts: added "edit bounds, all charts" to top-left menu more grid labels, customizable color 2016-02-22 version 1.11.1 added grid labels in some charts added "y" as a variable for weighted curve fitting 2016-02-09 version 1.11.0 upgraded Windows installer to Python 2.7 2016-02-08 version 1.10.3 bug fix: reading tab-separated tables that have some blank cells 2016-01-29 version 1.10.2 after idealizing with SKM or Viterbi, Figures:AmpHist shows pdf curves - mean and std are from the final SKM iteration - areas are proportional to idealized occupancy "GaussianUnit" function for curve fitting -- normalizes so sum of components is 1 2016-01-28 version 1.10.1 bug fix: working with raw binary files in Windows 2016-01-13 version 1.10.0 bug fix: reading ABF with waveform data 2016-01-08 version 1.9.12 bug fix: Extract from custom signals, processing the correct signal 2016-01-06 version 1.9.11 bug fix: constraints on k2 (pressure-dependence) 2015-10-19 version 1.9.10 Simulation:Presets: Paired pulse wizard sets up conditioning and test pulses with variable recovery time in between can assign different rate constants for rest, conditioning, and test phases 2015-10-07 version 1.9.9 bug fixes: preserving idealization when segment 2 is the first idealized saving large session (QSF) files reading the final segment (episode) of ABF files 2015-10-03 version 1.9.8 More responsive during rate optimization 2015-09-23 version 1.9.7 Admin:Seq: import and export script sequences Data: point at the low-res panel and press 'N' to add a baseline node bug fix: editing non-loop rate constants in a constrained cyclic model 2015-07-22 version 1.9.6 MacRates: switched eigenvectors from scipy to gsl 2015-07-17 version 1.9.5 bug fix 2015-07-15 version 1.9.4 MacRates: Gaussian fit display is optional (because it's slower) in the Data's Display menu bug fix: crash post-optimization 2015-06-17 version 1.9.3 Modeling tools menu: "Link to this model online" 2015-06-08 version 1.9.2 bug fix: Trials: Iterations now faster, more stable 2015-06-04 version 1.9.1 bug fix: building selection lists 2015-06-02 version 1.9.0 MIL, MacRates, etc: all iterations of the last optimization are stored in Tables, under Trials, e.g. as "MIL Iterations" optimization algorithms (Simplex, DFP) are highlighted in the sidebar while running Idealize (SKM): outputs observed transition probability matrix A (consider all the points idealized as state i: if, for one tenth of those points, the next point was idealized as state j, then A[i,j] == 0.1) 2015-05-23 version 1.8.6 Data display option: draw idealization with class colors bug fixes: balance loops handling models with noncontiguous classes, or where [class of state 0] != 0 2015-05-19 version 1.8.5 MacroR: by default showing MacRates (non-recursive) fit curve Model: Effective/overall K drawn on rates with stimulus sensitivity Model: "Balance loops" is now a checkbox in the "Kinetic Constraints" table bug fix: "balance loops" with pressure- and voltage-sensitivity Notebook: images in HTML output shrink to fit the window 2015-05-14 version 1.8.4 bug fixes: fixed crash when exceeding maximum columns in a table automatic Notebook "Data picture" figures now refer to the high-resolution data pane 2015-05-10 version 1.8.3 bug fix 2015-05-09 version 1.8.2 Added Pressure to the rate formula: k = k0 * Ligand * exp(k1 * Voltage + k2 * Pressure) MacRates: fit distribution drawn with Gaussian intensity MacRates: fixed slowdown when optimizing with "live" still checked Model: using unicode minus glyph for negative rate constants 2015-04-28 version 1.8.1 Data: Notebook: table of all items in List Model: read and write .qmj format (JSON notation) bug fixes: drawing more than 2 traces at a time measuring dose/response with no filter or normalization hang when viewing DurHist with an empty model 2015-03-26 version 1.8.0 Modeling tools: Plot Dose-Response, Find EC50 bug fix: repeated segment in some simulation stimulus protocols 2015-03-16 version 1.7.8 Compiled for Mac OS X 10.10 (Yosemite). Please report any issues. 2015-02-26 version 1.7.7 Idealize: By Delta (binary) -- splits in half until each region has std < delta By Delta (forward) -- simpler heuristic used by Modeling:Stimulus panel Notebook: Send to SciDAVis (requires SciDAVis version > 1D8 with Python engine bug fixes) bug fix: reading ABF files (Windows) 2014-12-16 version 1.7.6 bug fix: table Index column after "Delete rows" 2014-11-14 version 1.7.5 Rates: column "K" shows the computed rate constant, with stimulus values from highlighted data bug fixes: MacroR, check table rows by group 2014-11-12 version 1.7.4 bug fixes: redo idealization, delete checked rows, extract joined 2014-11-12 version 1.7.3 Data: Clone/erase tool Undo last idealization (hi-res data's Idealization menu) Figures:AmpHist: multi-file (by the Group column in the Data table) Tools:Extract: join segments (concatenation) Tables: Check rows if (select rows by criteria) 2014-10-23 version 1.7.2 Lists: Chop: option to (not) switch to the new list bug fix: scripting QubX.Modeling.Idealize.idealize() 2014-10-15 version 1.7.1 bug fix: re-idealizing with SKM 2014-10-14 version 1.7.0 Modeling:Idealize:By Delta Can read space-delimited text files Fixed Figures:DurHist 2014-10-10 version 1.6.8 Workflows:DoseResponse, Data:Measure:Measure Dose-Response, and Simulation:Presets:Stimulus ladder wizard 2014-10-05 version 1.6.7 Scripts: Explore: inspect the module hierarchy, including "INSTANCES" lists of objects' global names 2014-09-30 version 1.6.6 Simulation: add a low-pass filter to any stimulus signal Scripts: Explore: cleaned up hierarchical listing 2014-08-04 version 1.6.5 bug fix: QubX.Data.copy_list() in scripts 2014-08-04 version 1.6.4 bug fix: custom measurement scripts 2014-08-03 version 1.6.3 "Close all" in File menus Can hilight and copy text from non-editable table fields Scripting: access onscreen tables by name, e.g. QubX.Tables.States Scripting: generators e.g. idl_events_flc() to iterate over idealized events bug fixes: DurHist bin count, out-of-bounds selections, data hi/lo-res splitter position 2014-07-23 version 1.6.2 Tools:Kalman panel for linear Gaussian filtering 2014-06-27 version 1.6.1 Can "Re-grab" amplitudes from model's state menu; selections stored in the List called "Model-Grab" qubx.workflow.Workflow for html-like wizards with embedded scripts bug fixes 2014-06-16 version 1.6.0 Optional multi-window layout with smaller main window (in green triangle menu, upper left) 2014-06-06 version 1.5.5 Figures:Charts: histograms have new "Histogram" output in Notebook panel Admin:Seq: new panel for running sequences of scripts 2014-05-16 version 1.5.4 Admin:Scripts: if you edit the script in an outside editor, it will prompt to re-load it before running 2014-05-02 version 1.5.3 Admin:Scripts:Explore: added a button to "View in API" -- show the selected object's documentation in a web browser 2014-04-29 version 1.5.2 Figures:DurHist: automatically find and fit all significant exponentials, using the method of David Landowne, Bin Yuan, and Karl L. Magleby Biophysical Journal Volume 104 June 2013 2383-2391 Data: pressing 'N' to add a baseline node uses the high-res selection if available "Clear fit curves (onscreen)" in per-signal menu remembers the divider position between lo- and hi- resolution panels bug fixes: multi-component LogExponential curve fitting LogExponential display on histogram Layout menu: multi-window layouts include the main window's position Figures:DurHist remembers settings of bins, smooth, sqrt ordinate 2014-04-26 version 1.5.1 bug fix: "Center signal" 2014-04-25 version 1.5.0 Admin:Scripts: "Explore" button displays Python object hierarchy, or at the >>> prompt, for example: >>> explore() >>> explore('QubX', 'Models', 'file') >>> explore_one(QubX.Models, 'QubX.Models') # shows only QubX.Models and its children 2014-04-23 version 1.4.8 To keep QUB Express and its settings on an external drive (in Windows): First copy the program folder, e.g. C:\Program Files (x86)\QUB Express\ Then, either copy your local settings folder, e.g. C:\Users\Me\.qub-express (Windows XP: C:\Documents and Settings\Me\.qub-express) into your new copy of the QUB Express\ program folder, or make a new folder called ".qub-express" inside your new copy of the program folder. Simulation: "force Q" uses the Q-matrix method, which may be more accurate (By default, it can use the A-matrix method when that is likely to be faster, but it can suffer from rounding error when the rate constants span several orders of magnitude.) Figures:ListFigure: multi-file mode: draws data from all open files in a Group (set in the Data table) bug fixes: "show entire segment" button when "auto-scale" is on reading some large QDF files getting measurement captions from the Scope table rather than the Signals table error messages on quitting (windows) Figures:AmpHist was discarding some data in List or Whole file mode (since 1.4.2) Figures:ListFigure zero line when signal is inverted rare multi-threaded simulation glitches 2014-04-16 version 1.4.7 Figures:ListFigure: can draw zero line (baseline) on traces and/or stimulus 2014-04-16 version 1.4.6 bug fixes: Data: AMP cursor assumes "Channel count == 1" even if the model has a higher number Data: baseline node display (reversed end-points) Data: idealized display (after re-idealizing with fewer classes or channels) Tools:Extract: time-shifted idealization (when a segment begins with non-idealized data) 2014-04-15 version 1.4.5 bug fix: Figures:ListFigure: Zoom 2014-04-11 version 1.4.4 Moved Baum-Welch (AMP) to the main cursor bar in the Data panel bug fix: spacing of Figures:ListFigure: Notebook: Scale bars bug fix: properties of Modeling:Idealize: v-sensitive algorithms 2014-04-04 version 1.4.3 bug fix: Data panel's Idealization menu: Run Idealizer 2014-04-03 version 1.4.2 Figures:AmpHist: fixed bug with non-auto bounds; also, faster Clarification: events with duration of exactly Tdead are not dropped 2014-03-25 version 1.4.1 Faster SKM and Viterbi idealization Figures:DurHist sidebar shows Time constants and Tcrit (dividing line between components) 2014-03-24 version 1.4.0 Baum-Welch idealization (a.k.a. AMP): - in Data panel's Idealization menu -- highlight data to estimate single-channel conductance - in Modeling:Idealization Idealization plugin framework; see qubx/idealize.py or >>> help(QubX.Modeling.Idealize) Notebook: save as comma-separated text bug fix: crash simulating from a model with no states 2014-03-17 version 1.3.0 Simulation: "Extra noise" options optionally don't reset state occupancies at the beginning of each segment "File" reads a waveform from disk for use as a stimulus signal For a shape property such as "Amp", there are two ways to make it vary each segment: (the old way, still works:) "Incr"ementing it: adding a quantity each semgment, or multiplying it by a "Factor" (the new way:) enter an explicit list of values, separated by commas (e.g.: 1, 2, 5, 10, 20, 50, 100) Save data as CSV (comma-separated values) text file Model: Notebook display options: state area proportional to occupancy Model: right-click a rate to make it ligand- or voltage- sensitive Figures:ListAverage: can limit display to rows with Group == i Figures:Hill bug fixes 2014-02-21 version 1.2.9 bug fix: simulation with no stimulus 2014-02-21 version 1.2.8 Model: "Picture options" in Notebook menu Model: "Edit menu" items moved to "Modeling tools" (by file menu) List of "Segments" automatically added to each data file Simulation no longer slows down with faster rate constants MacRates and MacroR no longer become unresponsive after "Stop Tasks" 2014-02-06 version 1.2.7 Notebook: Save pictures as TIFF (set the resolution--dots per inch--in the Admin:Notebook panel) 2014-02-04 version 1.2.6 Figures:ListAverage: more scale bar options 2014-01-16 version 1.2.5 Figures:ListAverage generates high-quality pictures of selection lists 2014-01-15 version 1.2.3 Figures:ListAverage generates high-quality pictures of selection lists Correctly read baseline nodes from QuB classic data files 2013-12-04 version 1.2.2 MacRates and MacroR: fixed occasional glitches 2013-11-22 version 1.2.1 MacroR: optimizes a model from ensemble (macroscopic) data, using Moffatt's algorithm (2007) font size now applies to all controls 2013-10-10 version 1.2.0 MacRates: multi-model fitting to the sum of several models' current distributions option to save data file's fit curves across sessions bug fixes: extract/add segments, data list curve fitting, plus layout issues and other quibbles 2013-10-04 version 1.1.4 bug fix: intermittent Modeling crashes (e.g. in MacRates) since v1.1.0 2013-10-01 version 1.1.3 bug fixes: keyboard focus to table cell upon selection, when Tables is in its own window memory leaks 2013-09-23 version 1.1.2 bug fixes: data curve fitting of list sometimes didn't go to the next selection correctly QDF files were wasting time on closing "Default layer foreground" and "mouseover" color prefs cleaned up the name "c" from globals, so it can be a curve fitting parameter 2013-09-19 version 1.1.1 bug fix: data curve fitting on windows (worked around bugs in multiprocessing module) 2013-09-19 version 1.1.0 Curve fitting in Data window: curve isn't drawn until you adjust its parameters or fit "Restore last fit" button when browsing a List of fitted selections accelerated on multi-core processors bug fixes: Extract: custom signals in presets main window can stay in background while working memory leaks 2013-09-10 version 1.0.9 fixed bugs: model constraints, saving model, closing empty data files 2013-09-07 version 1.0.8 Signals: Add computed signal: To re-create a stimulus signal that's missing from recorded data: - build the stimulus protocol using the Simulation panel - right-click the signal in the Simulation panel (or click into it, then click the green triangle menu button) - from the menu, choose "Add signal to data file" - "Save as" or "Extract" the data to a new file Save/extract/notebook/fit: data time column starts at 0.0 seconds bug fixes: missing panels in the left sidebar SampleInitScripts/qubx_remote_ctl (to control QUB Express from another process) memory leaks 2013-09-03 version 1.0.7 Data: adjusted auto-scaling Model: faster undo (after optimizing rates) Signals: Add computed signal: the expression can be the name of a global numpy.array MILRates: faster, bug fixes Figures: Charts: more colors scripting: MacRates.OnLiveLL event 2013-08-20 version 1.0.6 Auto-scale (in Data's Display menu (grid icon)) MILRates bug fixes Windows: panel resize bug fix 2013-08-12 version 1.0.5 Fixed issue opening Patchmaster files with interleaved data Faster duration histograms 2013-07-26 version 1.0.4 Fixed curve fitting with ODE systems 2013-07-08 version 1.0.3 MILRates can accelerate MSL using OpenCL on certain GPUs DFP optimizer fixes 2013-04-26 version 1.0.2 Fixed MacRates: use GPU 2013-04-25 version 1.0.1 Modeling:MILRates: improved handling of complex models; set Constants:Tdead if you want to 0 to disable missed events correction Figures:DurHist: 2d layout when there are several classes in the model, fixed bug on empty data 2013-04-11 version 1.0.0 MIL/MacRates: automatically run multiple optimizers in sequence (e.g. Simplex then DFP) scripting: QubX.Modeling.MacRates.wait_for_fits() bug fixes: Reading QDF files MacRates Pop-out Tables window 2013-03-22 version 0.15.3 Faster kinetic constraints in model; fixed some UI glitches bug fixes: threshold idealization, copy table rows to table 2013-02-01 version 0.15.2 "Plot Mean v. Std" (instead of variance) Data: opens Patchmaster "bundled" .dat files, makes Lists of the series MacRates (multi-file) optimizes each file's channel count separately, in the Constants table bug fixes: opening some data files hide controls of hidden signals 2013-01-15 version 0.15.1 Plot Mean v. Variance (in Data's "..." menu) Multi-line data is an option (in Data's Display [grid] menu) List table options re-organized into a pop-up menu List table menu: added "Split selections by Group" Tools:Extract: option to limit to segments or selections of a particular Group bug fixes: Signal 0 can be used for Stimulus display of List controls at top of data MILRates with equilibrium prob. un-checked Extract: averaging or adding segments with different lengths Curve fitting: Weight expressions, parameter Low and High baseline tools 2013-01-10 version 0.15.0 Data (lo-res -- upper pane): multi-line display when you enlarge upper pane relative to lower Model: "Modeling Tools" menu featuring Model Merge Idealize and MIL Rates with Channel Count > 1 (not too large; it gets very slow) Idealize: displays log-likelihood bug fixes: optimization with completely constrained rates; add plugin; restore layout proportions ported classic qubopt and qubtree libraries 2012-10-12 version 0.14.6 bug fix: Idealize with baseline tracking (since v0.14.2) 2012-09-26 version 0.14.5 "Add computed signal" to a data file via the Signals table bug fix: "Measure onscreen" 2012-09-25 version 0.14.4 Model: add multiple scale constraints at once Bug fixes: table: del row, data baseline node display, extract resampled, global names in custom extracted signal func 2012-09-19 version 0.14.3 Reset all settings / restore defaults (in green top-left menu) Bug fixes: data display, opening large files, baseline menu checkmarks 2012-09-08 version 0.14.2 Idealize with Channel Count > 1 2012-09-07 version 0.14.1 4- and 5- component curve fitting presets "First latency" in idealized stats Bug fixes: list header menus, multi-file optimization 2012-09-05 version 0.14.0 Data baseline menu: select whole file baseline List table: menu of all measurement scripts Bug fixes: display glitches, simulation with nonzero baseline 2012-09-04 version 0.13.5 Builds List of series when opening Patchmaster/PUL files 2012-09-01 version 0.13.4 Faster data drawing Bug fixes: multi-file optimization, measurements, preset management 2012-08-27 version 0.13.3 Bug fixes: curve-fitting param bounds, MacRates "live", Modeling:Stimulus, memory leaks 2012-08-23 version 0.13.2 Modeling:Utils:Perturb -- tests stability of optimized parameters Modeling:Utils:ModelSearch -- tests each way of connecting states in the model Bug fixes: baseline node subtraction, Ligand- and Voltage- sensitive models 2012-08-19 version 0.13.1 Data: default tool is Measure Data: Idealization menu in hi-res toolbar Lists: Replace selection, New list from sub-selection Baseline nodes are applied immediately "Edit Bounds" of charts Scripting: "with DeferredSideEffects():" context manager for faster inner loops 2012-08-12 version 0.13.0 Split Data panel into low- and high-resolution panes Added Data Source option (upper-right): List Added to Tools:Idealization: make list of events or transitions 2012-08-08 version 0.12.1 Panel menus (e.g. File) duplicated in sidebar; added Open Recent Appearance presets (in Admin:Settings) for black data on white background Data display option to "hide controls for hidden signals" Data keyboard shortcuts listed under Data panel's Display menu (grid icon) bug fixes: Idealize, saved display (Scope) settings, HTML notebook dialogs, ... 2012-06-05 version 0.12.0 Trials table holds output from Modeling optimizers - each row represents a model - viewable in the Models panel, as the document "" Data curve fitting can fit the List, either sequentially or together Some tables are sortable; click a column header Modeling:Idealize can add baseline nodes Better color names in Admin:Settings:Colors Text in model uses global font size bug fixes 2012-05-24 version 0.11.5 Tools:Extract saves unfiltered data by default Modeling:Idealize puts statistics into the List named "Idealized" Undo/redo for per-segment baseline offset Double-click in List table to zoom in bug fixes: notebook to Excel, bug reports, Extract 2012-05-22 version 0.11.4 Tables: Copy rows option: "checked" bug fixes: MacRates and Rates stability 2012-05-20 version 0.11.3 Zoom and pan controls for most figures Stability measurement (Tools:Idealization) with an N-event sliding window Data Notes subpanel (at right) for note-taking bug fixes: saving files, clicking in tables and lists 2012-05-16 version 0.11.2 Table rows have checkboxes, to edit several rows at once Figures:Average shows the average of selections in the List Faster output to MS Excel 2012-05-12 version 0.11.1 Modeling:Utils panel: Classify, Star, Chain active List item is outlined in white, rather than zoomed into offers to send bug reports windows opengl fix bug fixes 2012-05-02 version 0.11.0 Smaller, faster session files bug fixes 2012-04-29 version 0.10.10 Admin:Settings:Save all button also saves alt-key assignments bug fixes 2012-04-26 version 0.10.9 Per-segment baseline offset (in data baseline tool menu) Draw idealized above (option in per-signal menu) Extract: concatenate or average segments from a group of files Extract: subtract a trace from another file 2012-04-23 version 0.10.8 Drag-and-drop multiple files to open as sequence; can now drag to popped-out Data window Data Notebook: Pick signals to export Lists:Chop: option to discard initial/final time; shows progress Paste rows/columns into some tables Standardized Hill fitting and measurement with log10(x) vs. normalized y; fixed bugs 2012-04-12 version 0.10.7 Notebook -> MS Excel support under Windows (incomplete support for Figures:Charts) bug fixes: extracting custom signals, to various file types bug fix: Admin:Settings:Colors dialog 2012-04-05 version 0.10.6.2 Chop idealization: make list of events longer or shorter than burst terminator Fix for Extract, custom signals Script-recordable: choice of preset, table-editing by dialog (when Tables not on screen) 2012-03-15 version 0.10.6 Tools:Extract can build custom signals out of user-defined functions Admin:Scripts loads a default script at program start, where you can record common tasks when Tables are hidden, clicking a number edits it via a dialog box (Tables stay hidden) fixed Notebook: copy image on Windows 2012-03-12 version 0.10.5 Figures:Spectrum displays power spectrum density Modeling:MacRates: added parameter error estimates Modeling:Rates: added choice of algorithm MIL/MSL (MSL required for varying stimulus) more info in the "Data" context-panel (at right) bug fixes 2012-03-03 version 0.10.4 Monitor and stop scripts via the Tasks panel many bug fixes 2012-02-22 version 0.10.3 bug fixes: script execution, loading of duplicate plugins 2012-02-17 version 0.10.2 Data: new Display menu including presets for signals' Center, per div Data: File -> Open sequence: files are listed in the right-hand panel Data: option to save, auto-save session (.qsf) files Data: "Other" tool menu including "Join events", available to plugins Tables: Notebook menu -> Pick columns: exports partial tables bug fixes: Data: when using arrow keys to scroll data, doesn't go past the end Extract: subtracting baseline nodes from a long file Model: grab amps 2012-02-13 version 0.10.1 Edit and subtract baseline nodes (piecewise linear baseline correction) 2012-02-09 version 0.10.0 bug fixes: filtering, curve fitting of data 2012-02-05 version 0.9.9 "Idealized" statistics are now a measurement script Measure selection: subtracts baseline from "Data Source" signal only Scripts are more responsive Fixed memory leaks 2012-02-02 version 0.9.8 Tools:Extract saves 4-byte QDF files by default, for better dynamic range Adjusted AICc in Figures:Charts:X-Means Measure:List fix: subtracts baseline from "Data Source" signal only HTML notebook fix (fixed Linux/.deb packages) 2012-01-30 version 0.9.7 Data measurement (ruler cursor) is now a menu, and measurement is done by an editable script HTML notebook files can be culled in the browser Figures:Charts logarithms changed to base 10 2012-01-23 version 0.9.6 Scripts: stop, pause, and single-step; can record the saving of a model Highlighted rectangle around a panel indicates it has keyboard focus fixed: Data notebook menu was empty when curve-fitting fixed: crash/hang when stopping Rates and MacRates optimizers fixed: crash when simulating with no states in the model fixed: Rates and DurHist update when you change Constants:Tdead 2012-01-13 version 0.9.5 Tables: More options to "copy rows" or "copy sels" many keyboard shortcuts just about everything is recordable through Admin:Scripts bug fixes: extract with processing, script recording faster startup and shutdown 2012-01-04 version 0.9.4 most panels can pop out as a separate window Lists:Chop options: discard partial sels, clear existing list selection handles in the Lists bar are drawn with Index number some keyboard control in Data frame (+, -, arrow keys with shift and/or control) more script recording (Data, Model, Figures, Idealize) bug fix: Extract: List could save the wrong signal 2011-12-22 version 0.9.3 more script recording (model building, files, Tools:Extract and Idealization) new in Admin:Settings: "Line width" multiplier for data and charts bug fix: closing/removing a selection list 2011-12-19 version 0.9.2 Data: "Open Sequence" opens one file at a time; when you close it the next one opens Admin:AltKeys: assign alt-key combos to scripts or actions limited script recording (notebook, chop) Lists: Chop works on the Data Source (screen or whole file) bug fix: some notebook outputs weren't showing 2011-12-09 version 0.9.1 Extract: process (average, add or subtract traces) Charts: X-Means SSD plot can switch to show AICc (Akaike Information Criterion, corrected for small numbers) 2011-12-06 version 0.9.0 Data: Lists -- selections and labels - managed via List table or the top line of the Data panel - to add a selection, drag along the top line of the Data panel - "Chop" moved to Data:Lists menu (Chop makes a list, which Tools:Extract can save) Can read transition tables from TacFit as idealized data; Files must be renamed with extension .tacidl Scripts submenu in main (upper-left) menu -- executes .py files located in Scripts/ directory - searches system-wide (qub-express/Scripts) and per-user ($HOME/.qub-express/Scripts) folders - included script which exports the model to Neuron format, thanks to Aaron Luchko 2011-11-16 version 0.8.9 Notebook: send to QtiPlot (http://soft.proindependent.com/qtiplot.html) Simulated data includes idealization 2011-11-14 version 0.8.8 Modeling: Rates and MacRates: Multi-file option Drag and drop files onto the QUB Express window to open them Simulation is idealized (idealization of one channel, even if Channel count > 1) Hill curve as curve-fitting preset Can read legacy QuB .mdl model files Bug fix: display of simulation shape properties 2011-11-04 version 0.8.7 Modeling:Rates: error limits, also displayed in Rates table Data signals automatically colored, "Change color..." in each signal's menu Floating controls are shrunk to fit onscreen, if needed 2011-10-19 version 0.8.4 Bug fix: opening models with kinetic constraints OpenGL drawing is disabled by default; must re-start QUB Express after enabling 2011-10-17 version 0.8.2 Bug fixes: Extract, Data multi-segment curve fitting Snappier resizing and scrolling 2011-10-15 version 0.8.1 Bug fix: closing data files 2011-10-14 version 0.8.0 Renamed Charts to Figures Added Figures:Charts to plot and cluster info from Tables (like Select in QuB Classic) Added user-generated tables (New/Open Table... in main menu) 2011-09-22 version 0.7.4 Fixed bugs: Makefiles, plugin loading, MacRates with GPU 2011-09-21 version 0.7.3 Fixed bugs: reading ABF and PULSE files, reading model files with many states, modeling with no constraints, and MacRates live mode 2011-09-16 version 0.7.0 Curve fitting moved into data toolbar New layout options 2011-08-25 version 0.6.0 Curve fitting of data and histograms 2011-06-23 version 0.5.3 Reads Patchmaster/HEKA .pul files and QuB LDT files 2011-03-15 version 0.5.2 Faster data drawing with OpenGL 2011-03-03 version 0.5.1 Model channel count responds to scroll wheel Data drawing is a little faster Bug fixes: idealize (stats) 2011-03-02 version 0.5.0 Tools: Extract: chop and save data 2011-02-16 version 0.4.0 Tools: Idealization: statistics and other utilities Notebook facility writes figures as a web page, text files, to clipboard, etc. Data scope per-signal controls: added a menu: "Center signal" "Hide signal", "Clear fit curves" Bug fixes 2011-01-20 version 0.3.1 Can read *.acquire and *.dwt files Bug fixes 2011-01-14 version 0.3.0 Added "Single molecule" plugin: - Charts:DurHist -- duration histograms with log10(x axis) and model-based PDF curves - Modeling:Idealize -- detects single-molecule transitions in prep for Modeling:Rates - Modeling:Rates -- finds the most likely rate constants for idealized data Bug fixes 2011-01-04 version 0.2.4.1 Bug fixes: - fixed simulation protocol display glitch MacRates: - fixed GPU acceleration of models without I=f(V) - fixed hang/crash on "Stop Tasks" - fixed mapping between model variable names (e.g. "Ligand") and data signals 2010-12-30 version 0.2.4 MacRates: - GPU acceleration (OpenCL) for newer graphics cards - parameter standard error printout Faster data drawing 2010-12-09 version 0.2.2 bug fixes: - fixed crash on Stop Tasks - stopped MacRates resetting LL to 0.0 - made MacRates work with non-stimulated models (no Voltage- or Ligand- dependent rates) 2010-12-03 version 0.2.1 Different '?' behavior in the data; click to expand a signal; control-click to hide Data pane ignores single-click (rather than super zooming in) Model constraints are faster Mac "live" recomputes when you change Channel count, I=f(V), or Vrev simulation file can save as .qdf or .txt To remember scope and other settings, .qsf (qub session file) saved with each data file Switched to LAPACK for eigenvectors: more accurate with large and small rate constants Bug fixes: constraints, stimulus latency 2010-11-29 version 0.2.0 Reads raw binary data; bug fixes 2010-11-23 version 0.1.9.2 Reads ABF data (Axon binary -- Windows only), QDF (QuB Data) and .txt files 2010-11-01 version 0.1.8 Added "Macroscopic" plugin; provides Modeling:MacRates 2010-06-12 version 0.1.7 Model table: "K0 format" and "k1 Format"; Rates: "Format" - C-style formatting expressions; for example: %f 0.123455667 %.3f 0.123 [%.3f]! [0.123]! %.3g 1.234E-1 see http://www.cplusplus.com/reference/clibrary/cstdio/printf/ Bug fix: writing files with invalid data type 2010-06-06 version 0.1.6 Modeling:Stimulus -- prepares Ligand and Voltage signals for maximum likelihood algorithms (coming soon) Model: "Grab" mean current or conductance(s) from the Data Bug fixes including Save Data As... 2010-04-05 version 0.1.5 Simulation with unitary current as a function of voltage (I = f(V)) Charts:Model -- matrices including Q, A, Peq, delta free energy, and mean first passage Data source in upper right; controls what gets processed e.g. for Charts Low-pass filter Eraser cursor to exclude junk data 2010-02-10 version 0.1.4 Charts:Hill -- options for how to measure the simulated response (peak or equilibrium?) 2010-02-08 version 0.1.3 Renamed Histograms to Charts Added Charts:Hill -- plots dose-response and fits the Hill equation 2010-01-23 version 0.1.2 Lots of source code documentation qubfast.qub_raster_samples to speed up drawing 4X 2010-01-11 version 0.1.1 Improved aesthetics: - on first run, picks appropriate window sizes and font - tooltips on menu triangle buttons - window can resize smaller than 800x600 (barely) 2010-01-08 version 0.1 QUB Express for simulation