Version 9.2.1 2020-05-08
Force the use of "." instead of "," as a decimal separator. This fixes a bug that prevents resetting parameters in the parameter window. Proper international entry and display of number formats will be supported in a future release.
Version 9.2.0 2020-05-01
Progress bars will now appear for long running models, batch runs and writing saving large tables to disk.
New histogram feature available on all graphs.
New graph high resolution toolbar icons.
Prevent users from overwriting built-in example models by forcing "Save As" instead of "Save".
On Windows, to improve the responsiveness when moving or resizing models, only the window outline will be shown.
Saving large tables to disk is now much faster.
Selecting Edit -> Copy Image will now work correctly, copying the current graph to the clipboard.
Fixed several issues related to display of NaN and infinity in graphs, the parameter window, tables, and exported tables.
Dataset names are no longer case-sensitive: #v and #V refer to the same dataset.
Fixed several bugs relating to loading and saving models.
Version 9.1.19 2019-07-02
Bug fix for batch runs and for graphs with more than 8 lines which could cause plotting to fail. Bug fix error when discarding some or all runs under some circ*mstances. Improved color selection for new lines to reduce duplicates. Fix for bug in log sliders introduced in 9.1.17.
Version 9.1.18 2019-04-01
Minor bug fix for display of datasets.
Version 9.1.17 2019-03-31
Major bug fix for flowcharts using difference equations: In versions 9.0 through 9.1.16, the difference equation for a reservoir R with total inward flow J was: R(t+dt) = J. In version 9.1.17, the difference equation generated from a flowchart has been corrected to R(t+dt) = R(t) + J. This change makes difference equations match the behavior of version 8.3.
Optional Inputs lists in flowchart dialogs for reservoirs, flows, functions now correctly display only the variables defined in the Globals section. Invalid terms from the Globals section will no longer show up in these lists.
The delete button on the flowchart toolbar will no longer disappear when the window is made narrower than the full width toolbar.
Log-scale sliders now work correctly. Going from 10x to 1x sliders no longer modifes the parameter. Increased number of digits in slider readout. In some positions, the slider right arrow button would not increment the parameter.
Variable names in dialogs should no longer become invisible when selecting or removing a variable from a plot in the "Choose Variables" dialog.
Curve fit parameters are now saved to the model file. Curve fit parameters are preserved when the model is modified between curve fits.
Crosshairs readout has been clarified and number of significant digits increased.
Increased number of significant digits in the list of parameter values between the start and stop values in the parameter plot dialog.
Fixed a bug where creating a new parameter set and editing a parameter in the dialog would not always update the parameter in the Parameter panel when the dialog was closed.
Added import and export of parameter sets. Exported sets are saved in the same format as model (.mmd) files. We may support other formats in the future. To import or export a parameter set, hit the "New" or "Edit" button in the Parameters panel (bottom right of document window).
Supressed excess compiler error messages when sliders are defined. After a compiler error, move the mouse cursor near the error.
Manually set Right Y Axes ranges are now correctly read from model files, instead of producing NaNs.
The datasets panel now has toggles for displaying a 1D dataset using point and/or lines. These operate independently from the selections in the drop-down menu under the "Line Appearances" button on graphs.
Y axis labels for datasets are now the same color as the ploted data.
Version 9.1.14 2019-01-10
Bug fix for parameter plots.
Version 9.1.13 2019-01-07
Bug fixes and improvements: 1) Models could fail if you added new constants to a model in an earlier position than some already plotted variables. 2) Sometimes the wrong graph would close when clicking the "x" on a graph or notes/flowchart/equation help page. 3) Models with datasets would fail to plot the datasets if TIME was renamed. 4) There was a bug in handling non-square 2D datasets which could cause crashes. 5) The variable lists in the Monte Carlo dialog did not have scroll bars, so if the model had many variables, only the first 10 or 12 variables could be selected. 6) Fixed a bug which prevented discarding of flowcharts. 7) Color table choice is now saved to the model file. 8) Added toggling of plot lines, just like you can toggle plot points.
Version 9.1.9 2018-10-16
Improved the default color table for line plots, and included a few alternative color tables, including a color table for users with color vision deficiencies. Click the line style button on a graph to switch color tables. Minor improvements to parameter sets. Added drag and drop support for .mmd files.
Version 9.1.6 2018-07-20
Fixed bug with datasets on Windows. macOS fix will be released as soon as possible. You can use datasets in your model. For example, for dataset '#v', use: y = #v(time) or y = #v([arbitrary expression]).
Version 9.1.3 2018-05-10
Bug fix for converting old models with spaces in the file name or path name. Flowchart size configurable in Preferences. Larger flowchart by default.
Version 9.1.3 2018-05-10
Flowchart size configurable in Preferences. Larger flowchart by default.
Version 9.1.0 2018-04-04
New stable Windows release with a new installer and signed binaries.
Version 9.1.0 2018-04-04
New stable macOS release. Some users may have problems with the app signature. We are working to replace this version. In the meantime, use the solution above to allow the app to run.
Version 9.0.128 2017-11-07
Signed the macOS version so that macOS does not complain about a damaged application.
Version 9.0.127 2017-09-21
Maintenance release
Version 9.0.126 2017-03-08
Maintenance release
Version 9.0.125 2016-10-11
Maintenance release
Version 9.0.124 2016-02-24
Maintenance release
Version 9.0.122 2015-05-20
Fixed undo in most flowchart operations.
Version 9.0.120 2015-01-27
Fixed problem of erroneously changing INIT concentrations in chemical reactions.
Version 9.0.118 2014-04-01
Fixed saving of flowchart files - sub model location was not being set.
Fixed typing into globals panel so it updates equations panel correctly.
Version 9.0.117 2014-03-17
Fixed a crash bug which occurred when multiple documents were open and one or more were closed.
Made the panel close boxes require the user to press the control key.
Added "Copy Image" to the edit menu for copying the image of the flowchart.
Stop activating a document after closing a document.
Fix improper enabling in the window menu.
Fix making flowchart elements with unique names.
Fix chemical reactions in flowchart document don't update equation panel
Fix parameter plots.
Version 9.0.115 2014-02-13
Fixed a bug in opening old JMadonna files which had multiple views in graphs. The graphs were coming up empty and had to be deleted.
Version 9.0.114 2014-01-30
Fixed a bug in sliders which caused a null pointer exception.
Version 9.0.113 2014-01-28
Added edit menu shortcut to increase/decrease the equation panel text size
Version 9.0.112 2013-10-16
show/hide middle panel from window menu
show/hide equation panel from window menu
show/hide parameter panel from window menu
Add scrollbars to icon dialog required inputs/optional inputs to prevent the dialog from getting too large.
Disable autoscale in graph if run from sliders
Version 9.0.111 2013-07-29
Windows version - this version includes a separate translator program "madonnaconvert.exe" which converts old binary model file formats into the new XML format.
When a file is imported, if it is an old version, the translator is invoked and the file is converted, such as "a.mmd" is converted to "a.out.mmd".
It currently has trouble with files which contain spaces, so get rid of any spaces in filenames, like change "a big file.mmd" to "a_big_file.mmd".
The Mac translator is not yet done, so if you have Mac files, convert them on a Windows machine.
Version 9.0.110 2013-07-23
Mac version - this fixes a crash using the DELAY model. It will only run on Lion and Mountain Lion, and requires JDK1.7.
Version 9.0.109 2013-04-22
Changed size of find/replace dialog. Fixed highlighting problem on Mac.
Version 9.0.108 2013-04-02
Macintosh release - fixed engine for Mountain Lion (10.8.2, 10.8.3) and for Lion (10.7) because of changes to Xcode after Mountain Lion.
Version 9.0.107 2013-02-21
Windows release - rearranged examples, how do i, jython directories to match Macintosh version
Made document windows open at 95% of height of application window in order to show iconized documents at bottom.
Version 9.0.106 2013-02-20
Added a preference (default true) to the General Panel: FullScreen - to open application fullscreen.
In the preferences under the General tab, there is a preference called "Open Docs Maximized" (default is true). If "Open Docs Maximized" is true, then JMadonna will open all documents to be maximized inside the application window.
Version 9.0.105 2013-02-02
Made the Macintosh installer more Mac-like.
Hid all the extras (Examples, How Do I, EquationHelp.htm, etc) inside the application.
Version 9.0.104 2013-01-22
Fixed some problems loading old model files.
Removed beta version warning at startup.
Removed registration warning at startup.
Version 9.0.103 2013-01-07
Fixed bug preventing Calc Oscillations example from loading.
Version 9.0.102 2013-01-06
Fixed undo in flowchart.
Note: For Mountain Lion version, if you get an error message that the app is damaged and can not be opened, here is a workaround.
1) Open System Preferences
2) Open Security & Privacy
3) Go to the General Tab
4) Change the "Allow applications downloaded from:" setting to "Anywhere"
This appears to be a security issue with Mountain Lion.
Version 9.0.101 2012-8-22
Updated Windows release to 101.
Version 9.0.100 2012-7-6
Made fixes to work with Mac OS X 10.7 (Lion)
Version 9.0.98 2012-3-20
In Mac version, move Madonna window menubar to the top of the screen, like most Mac applications.
In Mac version, fix version number reported by Finder.
Version 9.0.97 2012-3-15
make graph preference for axis font
make preference for parameter panel precision
make preference for parameter panel exponential notation
make equation font Serif and give no choice to the user in preferences
make equation font size choice (12, 14, 16, 18)
fix double click on axis messes with zoom
remove "Document Color" from preferences
change preference dialog to vertical flow layout
remove table background preference
fix sliders if current value is greater than the new maximum value
Version 9.0.95 2012-2-27
fixed crash bug when moving sliders rapidly
Version 9.0.94 2012-2-14
enable copy/select all in the Debug crash dialog.
fix loading of parameter plots (space problem)
keep sliders only with names so if the model is not compiled when loaded the sliders still work
make Chemical reactions size to fit so the contents don't get cut off it they are too long.
make run label larger
Version 9.0.93 2012-2-3
fixed graph.setTitle()
fixed run2.py to create a graph first if none exists, set the graph title of 3 graphs
fixed timer1.py to add setLocation so the frames are not on top of each other
fixed batchMeanMatrix to create a graph first if none exists
put "Run Script" in main menubar script menu
fixed getarray.py to print an error message if variable A does not exist
put "New Script" in main menubar script menu
put "Open Script" in main menubar script menu
support script for plotCurve
support script for plotPoints
Version 9.0.91 2011-12-26
online translator for old flowchart documents
Version 9.0.90 2011-11-18
Window selection for show all panels
Make nullcline a solid circle
Fix flowchart scrollbars
Fix histogram plotting from MonteCarlo
Help/Go To website download page
Slider automatic run with control key pressed.
Version 9.0.89 2011-08-30
Moved "difference equations" from flowchart icon dialog to flowchart menu, fixed generated equations
Started fix of flowchart scrollbars
Version 9.0.88 2011-08-04
Windows version
Version 9.0.87 2011-06-24
Removed file saving restriction.
Added 6 month timeout.
Disabled automatic download of new version.
Fix bug in storing graph.
Fix bug in paste flowchart icons.
Version 9.0.86 2011-04-26
Fixed cycling windows with control-'.
Made sure there is at least one selected document.
Version 9.0.85 2011-04-25
fixed load HH Axon (Submodels)SSSS.mmd - forbid duplicate flowchart panels
fixed load Thyroid.MDNA 2. The problem was loading CMadonna files created an extraneous MultiPanel.
prevent multiple jython consoles
renamed doc.getTopGraphTabPanel to doc.getTopGraph because graph no longer has tabs (relevant for scripts).
added jython menu to main menu bar
import dataset dialog should remember its directory
import dataset should automatically plot the data
Monte Carlo - remove variables from parameter list. The variables are now named "INIT A", etc
Version 9.0.84 2011-04-20
make all text entry fields accept scientific notation (chemical reactions)
getArrays() - creates Jython array variables for each Madonna variable and dataset
getDatasets() - creates Jython variables for each dataset
allow script to override preference of "plot data with circles" graph = doc.getTopGraphTabPanel(); graph.setAlwaysLines(1);
show sliders on each graph
make chemical reaction input accept scientific notation
getArray("variable") - return array of last run
Version 9.0.83 2011-04-15
Fixed Model Settings dialog to retain value of Fast Execution and Stop on Execution
Fixed graphing of infinite values
The middle window can now be split into left/right or top/bottom.
Enabled Window/Move Right, Window/Move Left to move tabs
Enabled Window/Vertical and Window/Horizontal to move tabs
Enabled dragging of tabs to rearrange the order
Command-shift-w closes current document
After run, the first graph window is displayed.
Version 9.0.82 2011-04-01
Enabled separate labels on graphs through preference.
Version 9.0.73 2010-04-30
Scrollbars added to flowchart icon dialogs, so that dialog windows don't grow larger than screen in large models
Version 9.0.72 2010-04-21
Fixed loading of corrupted models with misplaced DocPanel tags
Version 9.0.71 2010-04-07
Fixed focus issue with blue Run button
Version 9.0.70 2010-03-31
Open Recent submenu added
JM idle CPU usage improved
Connection timeout of 30 seconds for version check
Removed EquationSelector
Loading CM file and saving no longer loses equations if not flowchart
Version 9.0.69 2010-03-28
Save table as CSV
Hold down control when drawing arc to indicate whether it's excited or not; hold down option when drawing arc to indicate whether it's inhibitory or not; excited arc shows solid circle instead of arrow; inhibitory arc shows hollow circle instead of arrow
Remove dashed lines in graph
Fixed bug in storage of images inside Notes Panel
Add multiline notes to flowchart
Add text font/size to edit menu to change notes
Nullclines range adjusted
Version 9.0.68 2010-03-14
Fixed x-axis label coordinates when Variable Buttons missing
Adding/deleting variables from a compiled model, then running in same window no longer results in missing/zombie variable buttons
Choose Variables Dialog and graph's variable buttons are no longer out of sync with respect to visibility/right-axis status of variables
Plotter defaults to plotting variables governed by differential equations
No longer fails to save flowchart models created from parent CMadonna flowchart models
If equations are modified after a run (but not saved/recompiled/rerun), and the graph is temporarily obscured by a menu, the underlying areas on the graph are now redrawn correctly
Plotter colors: black, red, blue, gray, olive, teal -> black, red, blue, purple, orange
Modifying equation panel post-compile no longer clears graph
Color cycling bug that prevents colors other than black, blue, and olive from being used is now fixed
Fixed bug where if two variables start with same sequence of letters (for example, "I" and "InfectionRate"), both variable buttons light up with same color even if only one is selected
Plot.java's flag system rewritten
Anti-aliased graphs, to minimize jaggies in plot curves
The JMadonna.post_qmsg() methods should not be declared synchronized -- the single call to Vector.addElement is already synchronized
JMadonna.dispatch_qmsg()'s synchronized critical section that checks qmsg.isEmpty() and invokes qmsg.remove() should synchronize to qmsg, not qcs
Fixed nullclines
Default scale for FFT x-axis is log scale
Automatically moves registration.txt from old location ~/.madonna to ~/Library/Application Support/Berkeley Madonna so that users upgrading don't have to re-register
Make Mac-specific .madonna directory at ~/Library/Application Support/Berkeley Madonna
NPE in COutputFrame.showSlidersPanel
When the last document is closed, keystroke listener no longer stops responding
Cycle windows should cycle through Documents only
JMadonna.findActiveDocument() shoult not return console
Close model should not only close active document, should automatically find and activate next available document
Keystroke hints in menu set to black
Create a new MadonnaLog.txt for each day
Version 9.0.67 2010-03-05
Support added for OSX 10.5.8 Leopard users on x86_64 uarch (Core 2 and later)
Nullcline compute range extended by 25%
Dragging an object into a submodel no longer fails when submodel is surrounded by curves
Version 9.0.65 2010-02-24
Parameter plot fixed
Main toolbar moved to main menu bar
Flowchart/remove image fixed
Resizing of left/right panels in multipanel with minimum size
(OSX) Get Info should display version
Notes panel text initializes to top when opened from Examples/HowDoI menu
Subprograms fixed
Ctrl/Cmd-Shift-S hotkey for Save Model As...
Green eliminated as graph color
Compute stats moved next to variable buttons
Version 9.0.64 2010-02-22
Flowchart optional input list variables no longer rejected
Fixed help menu/CheckVersion so that it always reports the current version
If no document is open, equation help is disabled in help menu
Dataset - enable plot type (dots or lines)
Removed first seven buttons of toolbar
Removed toolbar "none" option fo rmiddle panel of multipanel
Removed equation panel run button
Docs always come up centered, not offset
Fonts taken off text dialog, use only sans-serif
Close box added to Notes panel
Notes Editor stored separately from Notes Panel to fix bug in saving when Notes Panel is closed
Removed "Show Parameters with Graph" preference
Graphs saved with empty pages no longer fails
Version 9.0.63 2010-02-18
New simplified multipanel
Option to remove toolbar nixed
(OSX) Cycle windows hotkey fixed
(OSX) Key bindings platform-independent
Paste hotkey no longer falls through when image not found in clipboard
Version 9.0.62 2010-02-07
Parameter plot indexing error for init, final, freq, ampl fixed
Parameter plots with renamed TIME variables fixed
UI parsing of rename TIME variables in single runs now case insensitive
(OSX) Copy and paste into register dialog fixed
Converted menu subpanel shortcuts to toggles (Dataset/Notes/Equation/Parameter Panels)
Colors cycle through black, dark blue, red, dark gray
Parameter panel occasionally did not appear after multipanel is resized smaller
Verison 9.0.61 2010-02-02
After discard flowchart, equations are editable
Equation panel locked for flowchart documents
Multipanel initializes as a ratio of desktop width/height
Duplicate graph duplicates variable buttons
Duplicate graph extra page tab bug fixed
Standard deviation added to histogram
(OSX) MadToolBar buttons reverted to toggles
(OSX) MMD file icons
(OSX) JM linked to MMD file extensions in OSX Plist database
(OSX) Java console moved to JInternalFrame
Registration file moved to user's home .madonna directory
Flowchart scaling disabled
Check version states reason for failure
Jython console checks for existence of jython2.2.1 directory
(Windows) Jython2.2.1 packaged
Text display in flowchart fixed
Graph colors changed
Flowchart loading of model files with submodel bug fixed
UITextDialog displays all fonts available on user's computer
(Windows) Release JEngine.dll packaged
Version 9.0.60 2010-1-22
This Windows version is released with the correct version of JEngine.dll. 9.0.59 had an incorrect Debug version of the JEngine.dll which prevented some users from launching the program.
Version check patched.
Version 9.0.59 2010-1-20
Application window and document windows bounded by monitor size on loading
Document panels reload with correct positions
Mac and Linux setup installers/scripts
Registration code added for students
Disabled File menu Jython console
Storage version 18 is first supported file format - error if loader finds <18
Server version enabled only by password
Version 9.0.58 2010-1-19
File/Close window - crash when trying to close console
Make graph on multipanel show when added
Fix zorder of loaded panels
When loading a flowchart model, compile the model before loading graphs.
Multipanel - if there is no graph, its container should be minimized
Create an installer for JMadonna windows. Notes: We will be making a Disk Image for the Mac, as it does not require a real installer. The Windows distribution WILL have an installer.
Version 9.0.57 2010-01-17
Equation Help opens in JMadonna HTML window
Document's internal windows saved as ratio of desktop size, to make saving/loading on different monitor sizes more natural
Equation Help opens in JMadonna HTML window
Drag and drop between editor panes
Paste images into Notes Panel (Edit->Paste)
Dragging into submodel when flowchart is scaled
Multipanel created fullsize
Models set to MMD file extension
Check Version moved to menu (Help->CheckVersion)
JVM Memory Limit removed
Loaded panels restore with saved bounds/dimensions
Version 9.0.56 2010-01-15
Flowchart window initializes to width that keeps all control icons visible
Nullclines added
Flowchart scalable
Insert image .PNG file filter
Notes panel scroll speed increased
(Linux)Batch runs window rendering issue fixed
About Dialog->Libraries window re-adjusted
Test modules removed from Examples/How Do I/User Library
JMadonna Equation Help (variance -> standard deviation)
Java console converted to JInternalFrame-like system
Document:getCurGraphTabPanel() and Document:getCurParamGraphTabPanel() routines updated
Parameter Panel initializes with appropriate size from toggle button
Parameter Plot storage
Parameter Plot toggle creates Parameter Panel if there is none
Check Version behavior tweaked
(OSX)Notes, Equations, Flowchart, Graph, Parameters toggle button redraw issues fixed
Sliders min/max range problem fixed
(Linux) Save dialog file filters issue fixed
Engine tokenizer code updated to maintain compatibility with GCC 4.1.2+ compilers
Fixed equation highlighter for error messages
Removed DockSliders, DockParameters
Graph Toolbar resizes to small icons if the user shrinks the toolbar
Version 9.0.55 2009-12-30
MultiPanel GUI
(OSX)Java console
Version 9.0.54 2009-12-28
(OSX)Exception in javax.swing.SwingUtilities fixed
Notes module includes image support, copy/paste support
Automatic error reporting
(OSX)Exception in java.awt.DefaultDesktopManager fixed
(OSX)Missing save directories are created
(Linux)Open Document dialog's file filter fixed
Console errors directed towards Jython Console
Boundary Value ODE's fixed
Java console redra
