Changelog

Download Windows Berkeley Madonna 9.1.0 for Windows

Download Mac Berkeley Madonna 9.1.0 for macOS

Download Linux Berkeley Madonna 9.0.73 for Linux (beta)

Version 9.1.0 04/04/2018

Version 9 for Windows (stable) is out, with a new installer program and cryptographically signed binaries.

Version 9.1.0 04/04/2018

Version 9 for macOS (stable) is out.

You may get the error message "Berkeley Madonna is damaged and can't be opened. You should move it to the trash.". Don't move it to the trash. Open a Terminal and run "xattr -cr /Applications/BerkeleyMadonna.app" to allow the app to run. We are working to resolve some app signing issues, and will replace this version as soon as possible.

Version 9.0.128 11/07/2017

Release of cryptographically signed macOS application.

Version 9.0.127 09/21/2017

Maintenance release

Note: If you get the error message "Berkeley Madonna is damaged and can't be opened. You should move it to the trash.", there is nothing wrong with the build.

On newer macOS systems, open a Terminal and run "xattr -cr /Applications/BerkeleyMadonna.app" to allow the app to run. On older OS X systems, you may be able to allow Berkeley Madonna through system settings. Go to "System Preferences", and then choose "Security & Privacy". On the "General" tab there is a choice for "Allow applications downloaded from:" Set that choice to "anywhere". You can change it back after installing Madonna and running it once. We will get the app store registration soon.

Version 9.0.126 03/08/2017

Maintenance release

Version 9.0.124 02/24/2016

Maintenance release

Version 9.0.122 05/20/2015

Fixed undo in most flowchart operations.

Version 9.0.120 01/27/2015

Fixed problem of erroneously changing INIT concentrations in chemical reactions.

Version 9.0.118 04/01/14

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 03/17/14

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 02/13/14

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 01/30/14

Fixed a bug in sliders which caused a null pointer exception.

Version 9.0.113 01/28/14

Added edit menu shortcut to increase/decrease the equation panel text size

Version 9.0.112 10/16/13

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 07/29/13

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 07/23/13

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 04/22/13

Changed size of find/replace dialog. Fixed highlighting problem on Mac.

Version 9.0.108 04/02/13

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 02/21/13

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 02/20/13

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 02/02/13

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 01/22/13

Fixed some problems loading old model files.

Removed beta version warning at startup.

Removed registration warning at startup.

Version 9.0.103 01/07/13

Fixed bug preventing Calc Oscillations example from loading.

Version 9.0.102 01/06/13

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 8/22/12

Updated Windows release to 101.

Version 9.0.100 7/6/12

Made fixes to work with Mac OS X 10.7 (Lion)

Version 9.0.98 3/20/12

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 3/15/12

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 2/27/12

fixed crash bug when moving sliders rapidly 

Version 9.0.94 2/14/12

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 2/3/12

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 12/26/11

online translator for old flowchart documents

Version 9.0.90 11/18/11

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 08/30/11

Moved "difference equations" from flowchart icon dialog to flowchart menu, fixed generated equations

Started fix of flowchart scrollbars

Version 9.0.88 08/04/11

Windows version

Version 9.0.87 06/24/11

Removed file saving restriction.

Added 6 month time bomb.

Disabled automatic download of new version.

Fix bug in storing graph.

Fix bug in paste flowchart icons.

Version 9.0.86 04/26/11

Fixed cycling windows with control-'.

Made sure there is at least one selected document.

Version 9.0.85 04/25/11

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 04/20/11

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 04/15/11

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 04/01/11

Enabled separate labels on graphs through preference.

Version 9.0.73 04/30/10

Scrollbars added to flowchart icon dialogs, so that dialog windows don't grow larger than screen in large models

Version 9.0.72 04/21/10

Fixed loading of corrupted models with misplaced DocPanel tags

Version 9.0.71 04/07/10

Fixed focus issue with blue Run button

Version 9.0.70 03/31/10

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 03/28/10

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 03/14/10

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 03/05/10

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 02/24/10

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 02/22/10

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 02/18/10

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 02/07/10

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 02/02/10

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 1/22/10

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 1/20/10

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 1/19/10

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 01/17/10

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 01/15/10

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 12/30/09

MultiPanel GUI

(OSX)Java console

Version 9.0.54 12/28/09

(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