Download Berkeley Madonna 10.6.1 for Windows.

Download Berkeley Madonna 10.6.1 for macOS on x64 CPUs.

Download Berkeley Madonna 10.6.1 for macOS on arm64 M1/M2/M3 CPUs. This version will not work on Macs with Intel CPUs.

Download Berkeley Madonna 10.6.1 for linux.

User Guides and older versions can be found in our downloads directory.

Version 10.6.1 2023-11-09

Users should no longer be plagued by the dreaded "compiler failed" issue.
Models can be run in either interpreted "slow" mode or in compiled "fast" mode. By default, models run in fast mode,
but you can switch to slow mode via the Model -> Settings menu option.
If you are running a small model for a small number of time steps, slow and fast modes may take similar times.
If you are going to run a model many times (e.g., parameter plots or batch runs), or run a model for many iterations,
then fast mode should be 2 to 5 times faster than slow mode.
But the compiler can fail for a number of system dependent reasons, including installation issues, directory permissions,
anti-virus software, or bugs in our code. This release makes it possible to always run in slow mode when the compiler fails,
so you can still be productive. We have also improved the error messages when the compiler fails to help get to the source of the compiler problems.
The compiler should also work now for Windows users with "." characters in their account names.

Version 10.5.1 2023-04-25

Fixed a bug which prevented Berkeley Madonna versions 10.0 through 10.4 from running when Windows is configured to use assistive or accessibility technology, even if you are not currently using accessibility software.

Version 10.5.0 2023-04-12

Windows installer: Automatically install MSVC libraries on Windows. This should prevent first time installations
  on Windows from encountering the model compilation error. Some users may have to reboot after installation.

Critical bug fix: Fixed a bug which caused saved model files to be unreadable. In versions 10.4.4 and earlier, 
  if you saved a model with more than one copy of any particular flowchart tab open, the saved model could not
  be opened again. Now models with duplicate open tabs can be opened, though only one copy of each flowchart tab
  will be shown. If you must use 10.4.4 or earlier, you can avoid this bug by making sure that you do not have
  duplicate flowchart tabs open before saving models. If you can not open one of your models in 10.4.4 or earlier,
  try a newer version, or send us the model and we will repair it.

Critical bug fix: Fixed a bug in 10.4.3 which prevented parameter plots from recording and displaying the results
   under normal conditions. You can avoid this bug by in 10.4.3 by going to Model -> Settings and uncheck "Stop on Exception".

When duplicating graphs (Graph -> Duplicate Graph), preserve log/linear axes scales, auto/custom axes ranges, and normal/wide linewidths settings.
Added subticks on log scaled axes. Can be toggled on and off in the Graph tab of the Preferences menu.
Made it slightly harder to accidentally close a graph tab by narrowing the invisible area around the close button.
Parameter table: Sort parameters by name when clicking the name header. Sort by numerical value when clicking the value header.
Sliders: If you request a slider range that does not contain the current value of the parameter, instead the slider range will
  be expanded to include the current value. Fixed a rare bug that could make a slider unusable without resetting it.
Closing a graph tab or changing a flowchart background color now marks the model as modified, to ensure that those
  changes will be saved when the document is closed.

Version 10.4.4 2022-12-21 for Windows

Fixed compiler error for Windows users with non-ASCII characters in their user name. Now everyone should be able to use their own name, or any other valid Windows user name. 

Version 10.4.3 2022-12-21

Don't reset modified parameters every time the model changes. This fixes a bug introduced in in 10.4.2.
When you lock a graph, the "x" in the graph tab is changed a lock, and the graph can no longer be accidentially deleted.
Parameter plots can now be run for models with floating point exceptions. Go to Model -> Settings and uncheck Stop on Exception. Note that it is usually advisable to fix the model so that it does not trigger an exception.
When importing datasets from files containing dashes (minus signs), convert the dashes to underscores. Accept underscores when converting filenames to dataset names.
When zooming graphs, allow the initial point to be slightly outside of the graph.
When importing datasets, axes are required to be strictly increasing now. Duplicate axes values are not allowed.

Version 10.4.2 2022-10-14

macOS Catalina and later:
  Files in the Desktop, Documents and Downloads folders should be visible now when loading models, importing datasets, inserting images and importing and saving parameter sets.

Graph:
  More accurate, smoother, and higher resolution (sub-pixel) graphing.
  Nicer looking anti-aliased fonts for axis and tick labels, notes and legends.
  Better tick labels, formatted uniquely, with correct rounding and consistent minimal precision.
  Axes label and tick label fonts and sizes can be modified on the Graph tab in Preferences.
  Better positioning of tick labels and axis scale lines.
  Axis tick labels will no longer overlap their neighbors when graphs are shrunk, by only labeling some of the ticks.
  Parameters overlay: Precision set by the Parameters preferences. Better sizing. Built-in parameters skipped.
  Crosshairs for Graph readout and picking initial conditions improved.
  The "Visible" and "Right Axis" buttons in the Choose Variable dialog now work properly.
  Axis Settings dialog made wider so that ranges and labels are visible in the text boxes. 
  Graph tabs can be renamed by double-clicking on the tab name. New names must be unique, and can not start with the
    built-in tab names, such as "Equation",  "Notes", "Globals", "Datasets", "Histogram" and "Flowchart".
  Custom axis labels will no longer gain extra spaces on either end every saved and then loaded.
  Improved Readout calibration.
  Changed the illegible active graph tab foreground on macOS Catalina and above.

Graph Table:
  Graph table columns now resize automatically to fit the data. This is especially useful if
  you display the graph table with many digits of precision. (See the Table tab in Preferences.)

Saved Graphs:
  Graphs can now be saved to PNG format. Saved graphs will now better reflect the currently selected graph tab.
  We are planning on improvements to exported figure resolution, but for now, saved PNG files are a significant improvement over the JPG format.

Flowchart:
  Nicer looking, anti-aliased, lines and fonts in the flowchart.
  Fixed the multiline text tool, broken in versions 10.2.6 - 10.3.2.
  Eliminated duplicate error messages in dialogs.
  Fixed a bug in displaying the graph and table of data for graph statements defined in the flowchart.
  Changed the graph statement icon to match chemical reactions in color and resolution.

Preferences:
  The Preferences dialog should no longer be larger than the screen size on smaller devices.
  
General:
  Fixed a bug which prevented compilation of models containing many (>32) consecutive constant differential equations.
    E.g.: init x1 = 0 init x2 = 0 ... init x33 = 0 d/dt (x1) = 0 d/dt (x2) = 0 ... d/dt (x33) = 0.
  Made the error message more instructive for when there is not enough memory to run the model.
  Resetting a parameter with the Reset button now properly marks the model modified.
  Fixed truncation errors (incorrect rounding) that appeared in various parts of the user interface (and on axis tick labels)
    due a faulty number formatting library. Numbers everywhere are now correctly rounded. Note that the Parameters panel, 
    the Graph Table and exported data tables were not using this faulty library, and have always been correctly rounded.
  Made input boxes larger so that you can see the entire number in the Sliders and Monte Carlo dialogs.
  Parameter sets can now be renamed when you edit a parameter set.
  The Find dialog no longer has to be dismissed twice.
  Dialogs which could only be dismissed using the OK and Cancel buttons are now dismissable using the dismiss button in the titlebar.

Chemical Reactions module:
  Fixed the flaky initial conditions input boxes. Fixed the bug where chemical reaction icons would move around or reorder themselves when you saved or loaded a model. Fixed a bug that prevented editing chemical reactions after converting a flowchart model to a normal model.

macOS on Apple Silicon/arm64/M1:
  Fixed a spurious divide-by-zero floating point error for the auto-stepsize and stiff solvers.

See the 10.3.2 notes as well if you are upgrading from the last official release (10.2.8).

Version 10.3.2 2021-10-15

Model evaluation:
  Added a popup warning for floating-point errors of the types Invalid Operation, Overflow, and Divide by Zero.

Flowchart: 
  Text labels of copied and pasted flowchart elements will now have the same font style, background opacity and relative position as the originals.
  Reduced the speed of flowchart expansion and contraction when dragging flowchart elements to a more controlable speed.
  Reduced the flowchart scrollbar scrolling speed.
  Undo/redo disabled on flowcharts and globals until they work correctly.
  Fixed unique name generation bug for copied and pasted flowchart elements for flowcharts with submodels.
  Got rid of annoying error message when you erase a flowchart element name. Simply revert the name change.

Sliders:
  If the model has defined sliders, open the sliders panel when opening the model.
  Pop-out sliders window. To save graph space, sliders can be detached into a separate window. Use Parameters -> Detach/Reattach sliders to pop the sliders into a single external window, or to anchor them back in the graph windows. 

Graph:
  Allow selection of multiple variables to add or remove from the current graph in the Choose Variables dialog.
  Graph -> New Graph and Graph -> Duplicate Graph will show sliders if the sliders are visible on the originals.
  Graph -> New Graph and Graph -> Duplicate Graph will preserve axes preferences, such as log versus linear scale.
  Scrollbars added to the movable notes (such as Parameters) on graphs.

Datasets panel:
  The datasets panel now has a nicer table, and shows 2D datasets.
  You can now export datasets using the datasets panel.
  If a dataset is renamed or discarded, mark the model as modified to make sure the changes will get saved.
  Users will be warned and prevented from importing datasets with non-monotonic axes.

Loading and saving files:
  Fixed a bug that sometimes disabled the shortcuts for File->Save and File->Save As.
  When shutting down and offering to save unsaved models, use Save instead of Save As when possible.
  If the last opened file doesn't exist, don't make a big fuss on startup if the last opened file does not exist.
  Bug fix which prevents files with chemical reactions from writing bad model files. If you delete a chemical reaction image from Equations or Globals, when you save the file, it will reappear. To delete a chemical reaction, click on it, and delete it using the chemical reactions dialog.
  Bug fix for reading models which contain info from the Parameters -> Sensitivity dialog.

Parameter sets:
  Parameter set names can now contain spaces. For example, "Regimen 1" and "Regimine 2".

Preferences:
  Preferences tabs will now show scrollbars if the window is too small to contain all of the options.
  Added a preference to suppress floating-point error. Use with caution, as it can hide problems with your models.
  Added a preference to the Graph tab which determines if sliders are docked to graphs or in a separate window by default.
  Added a preference to use wide plot lines by default on new models.

Version 10.2.8 2021-05-07

Bug fix release: Fixed a bug in versions 10.2.6 and 10.2.7 that made it impossible to see the graph table for parameter plots. Changed the Apple M1 version to default to not stopping on floating point exceptions, because some non-exceptional models are triggering floating point exceptions and stopping early.
For Windows 7, we have included BerkeleyMadonna.bat in the installation directory. The .exe still does not work on Windows 7, but double-clicking BerkeleyMadonna.bat will launch Berkeley Madonna, if you need to run it on an older Windows OS.

Version 10.2.7 2021-03-19

Bug fix release for the netflow() built-in function when operating on array expressions. In versions 10.0.0 through 10.2.6, the expression netflow(a) works for variable a, but netflow(a[i]) will cause a compilation error for array a. This release restores the behavior seen in versions 8 and 9.

Version 10.2.6 2021-03-08

This release brings back the boundary value solver, the optimizer and sensitivity analysis.
Boundary Value Problems: Use the boundary value solver in the Parameters menu to solve for parameters which optimize a set of boundary conditions. For example, if variable v(t) depends on parameter p, you can optimize p such that v takes on a specified value V at time t = T: v(T) = V. Added back the Kroeg capillary boundary value problem model in Help -> Examples.
Sensitivity Analysis: Sensitivity analysis on variable v, with respect to parameter p, displays (v(p*1.001) - v(p))/0.001 if p is nonzero, (v(0.001)-v(0))/0.001 if p is zero. We are planning on several additions, including adding two-sided analysis, as well as allowing the user to change the size of the variation. We suggest toggling on the graph legend after a sensitivity analysis run.
Batch Runs changes: 1) The (None) parameter choice now works. Use this option when your model contains random number generators and you do not need to systematically vary any model parameters. 2) The Batch Runs dialog now remembers the previous batch run settings, and will save these settings when you save your models. Added the patch clamp Monte Carlo simulation using the Batch Runs dialog to Help -> Examples.
Monte Carlo additions and bug fixes: 1) Histograms used to be cumulative over all MC runs. Now they reset each run. 2) If the model changed after an MC run, then subsequent runs could modify the wrong parameters. 3) The list of available and selected parameters in the dialog now update when the model changes. 4) MC parameters now reliably revert to their starting value when the MC run finishes. 5) You can now specify if you want separate runs or the mean or mean +/- s.d., like for batch runs. 6) Increased the width of distribution parameter fields so the full number should be visible.
Copying data from tables now also copies the column header containing the variable name. This works even when copying parts of a table.
Parameter panel: You can now select multiple parameters in the parameter panel and reset them all with a single click of the Reset button.
Fixed a bug which prevented the copying of graphs using Edit -> Copy Image.
Fixed several bugs which only appear when the TIME variable is renamed. These bugs interfered with curve fitting and the optimizer.
Curve fit settings are now are saved both within the current session, and when you save a model. When you reopen the curve fit dialog, your previous settings will be restored.
Phase plane plots: Bug fix: Previously, when the x axis variable was changed from the independent variable (usually TIME) to some other variable, the first column of the graph table displayed the name of the x axis variable, but contained the independent variable (TIME) data. Now when you change the x axis variable, the graph table displays the independent variable, the x axis variable, and all y axes variables.
For Apple Silicon / M1 macs only: BerkeleyMadonna-10.2.6-SetupM1Mac.dmg runs natively on M1 macs. This version has not been fully tested, but appears to work well, and is faster than running the x86 version (BerkeleyMadonna-10.2.6-SetupMac.dmg) under Rosetta. If you run the M1 version and encounter any issues, please let us know.

Version 10.1.3 2020-08-30

Version 10.1.3 fixes a major compiler bug with the STEP function: expressions of the form a + step(h,t) (but not step(h,t) + a) are calculated incorrectly in version 10.0.0 through 10.1.2. This version restores the correct behavior, as seen in versions 8 and 9.
Changed the startup process on macOS to better assist users with installing Apple's xcode command line tools, including adding links to our technical FAQ. Also improved the error message related to compilation failures due to lack of the command line tools.
Added text editing shortcuts commands for bold, italics and underline: Ctrl-B, Ctrl-I, and Ctrl-U on Windows, Command-B, Command-I, and Command-U on macOS.

Version 10.1.2 2020-07-15

Version 10.1.2 for Windows and macOS. First official version 10 release. Runs models 2-5 times faster than version 9 and has access to significantly more RAM. Does not require you to install java. See the version 10.1.1 notes below for some of changes since version 9.2.1.
We have added a new builtin function to the language: arctan2(y, x). Unlike arctan(y/x), arctan2(y,x) can distinguish between the 2nd and 4th quadrants, and similarly, between the first and third quadrents of the plane.
We will be adding many features to version 10 in the coming months, and look forward to your feedback.

Version 9.2.2 2020-07-15

We will continue to backport most feature changes from version 10 to version 9 for customers who are running on legacy Windows and macOS operating systems. These changes exclude any speed, memory and feature immprovements to the computational engine, and any changes to the old java versions required by version 9. Thus you may need to read changes for previous version 10 releases to see all the changes in the current version 9 release.

Version 10.1.1 2020-07-06

Version 10.1.1 for macOS.
First 64 bit test release! Contains a new model evalutaion engine. Model execution is roughly 4-5 times faster. Models can now use significanly more memory than the 1 GB limit for the 32 bit version 9.
Users will no longer have to install java.
On macOS, Apple's Xcode command line tools are required. When version 10 is run, if the command line tools are not present, the user will be prompted to allow the Xcode command line tools to be installed from the App Store. While it should not be necessary, you can install them manually by running 'xcode-select --install' from the command line. This process may take a few minutes.
Updated version of the User's Guide is included.
Bug fix: In beta version 10.0, models with graph statements worked, and models with dataset functions worked, but models with both language features failed. This has been fixed.
Added pop-up error messages for the compiler errors TOLERANCE < 0 and DTMAX < DTMIN.
Histograms: Better x axis ranges and tick labels. Added a right margin.
Fixed syntax highlighting region for compiler errors when the model contains multi-byte characters.
Added a popup for curve fits to indicate that the fit is ongoing. Future updates will add more information to the popup.
Added a quit button to the progress indicators for normal and batch runs.
Bug fix: If after a curve fit, the user closes the note containg the RMS deviation, a new note will appear after the next curve fit. At the moment, there is still no way to recover a closed curve fit RMS deviation note.
The datasets panel now shows 2D datasets in a spreadsheet, similar to 1D dataset.

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 circumstances. 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.