Added some useful additional features

Some useful features added to iridium:

1. Added biomodels search capability
2. X-axis now reflects the selected x axis item in time course
3. Added a new syntax that can be used inside an antimony comment to specify how the simulation experiment was done
4. Exports SED-ML of a given experiment
5. Exports a Combine archive of model and simulation experiment
6. Added a help panel in the output section for antimony syntax and the new metadata syntax.
7. Cosmetic: scroll bar appears in time course simulation if window height is reduced
8. Added recent files in File menu
9. Now has proper Save and Save As functionality
10. Saves window position, size and panel positions to preference file so that the same configuration can be restored in a new session.
11. Fixed font rendering of markdown help files.

Bug fixes and a couple of enhancements

This version has the follows changes:

1. Added select all and unselect all buttons to parameter scan panel
2. Save icon should now work
3. New button now asks first before nuking the model
4. Cursor changes to caret shape when it moves into editor region
5. Add to top check box in slider panel now works
6. Loaded data files now follow the panel currently being used
7. Changed the color palette, removed light colors

There is a Windows version with this release in the form of a zip file. To use it, unzip the file anywhere on your Windows computer and run the IridiumSimulator.exe

The Mac version is the dmg file.

Bug fixes

Bug fixes:

1. Data is now control led by the user, so that data will persist between panel switches
2. Slider are now added to the bottom by default, but it is configurable
3. New slider vales can be copied to the antimony model as replacement or by appending
4. Bug in copying x and y log axis properties between panel and plot control
5. Panels have a default plot style which is linear axis and 0 to 1 limits
6. First time parameter scan is chosen, the time series variable selection is copied over to the observable
7. Finally fixes x axis label for dose scan

Fixes to various bugs

Fixes the following issues:

1. Rearranged parameter scan controls
2. Observable box now has more room.
3. Models don't have to be loaded to run a parameter scan
4. Time End now matches sample time if sample time exceeded Time End
5. Slider changes in time course simulation no longer delete any overlaid data.
6. Save button in toolbar wasn't responding ("Hittest" was off)
7. Clear plot when a new model is loaded or example selected.
8. Scan wasn't honoring the non-species observables
9. All markers now have filled color, not just data that matches a simulation column name
10. Newly added slider now adds to the top of the slider list.

Updates to roadrunner, editor, access to solver parameters, and bug fixes

This release has new new major changes:

1. New text editor for the model
2. Integrating the latest version of the lib roadrunner simulator (2.9.2)
3. Access to code and kinsol tuning parameters
4. Some cosmetic fixes to the interface

Changes to plotting and slider functions

Version 0.980

1. Fixes memo control snapping to the top line when splitter is changed (That was a tough one)
2. Added boundary species to the list of scannable parameters
3. added boundary species to slider list
4. XMin, etc edit box correctly dimmed when using autoscaling
5. Slider values now stay put when switching frames.
6. Save to pdf has been moved to the right click graph popup menu to save space
7. The color of the loaded data points will try to match the simulation color if the column labels match
8. Lucian suggested I allow overlays of multiple loaded data files, there is a check box to enable, by default its off.

Update to graphing options, fix one access violation

This is a minor update but added new options to the graphing style, the graph editor is no longer modal so it can be left open, no need to close it to go back to running simulations. Updated antimony support to latest version 3.1.3. Access violation fixed where closing the 3d plot via the main app caused the 3d plot to be freed twice. Source code on repository is now also current, old version source code from last year deprecated.

Fix log axes when data contains zero plus a few new features

This release fixes the plot issue when a user tries to log an axis and the data contains a zero (silently ignored as other plotting app do).

New features:

1. Right-click on graph to save png image to clipboard
2. Added additional variables to plot in time course (default was as before)
3. Updated steady state panel to plot 3d plots of sensitivities
4. Added python export script that allows user to preserve time course or parameter scan experiment

Opening uncertified apps required the following steps (especially for Tahoe OS)

1. Run app, it complains, you must click DONE
2. Within on hour, go to System Settings -> Privacy & Security
3. Scroll down to the security section and find the message saying the app was blocked
4. Click the Open Anyway, enter your password
5. Either the app opens at this point, if not, go to the app location and open it there
6. In theory you won't have to do this again

Bad styling and odd crash on Mac osx fixed

This is an interim release that fixes two annoying issues:

1. Poor styling and styling error on start up
2. Odd bug in the model editor when deleting a character cased a total crash (took a while to track this down)

Both should be fixed in this release. The other bugs from today will be looked at tomorrow.

See Release notes for details

Changes to this version:

1. Syntax highlighting and line number removed due to instability, will return to this later
2. Fixed sliders getting the wrong numbers
3. Fixed bug in csv reading where the last row wasn't followed by the new line (failed to read last number)
4. Slider parameter list updated when new parameter is introduced to model
5. Better number formatting for x axis labels
6. Improved UI experience when entering min and max axes values
7. Rearranged parameter scan panel, now resembles more the original panel in iridium I
8. Slider have much better granularity when using cursor keys to move them
9. A couple of crashes identified and fixed.