Version History & Change Log:

Ingeneue Version 0.93b by KJK (January 2008)

Changed: Source code documentation updates & fixes.
Changed: Startup screen size to scale to monitor.
Added: Updated GPL to source headers.

Ingeneue Version 0.93a by KJK (December 2007)

Changed: Ingeneue help converted to HTML 4.0 transitional from XHTML for compatibility with Java html viewer on Mac.
Updated: Turing network.
Other code tweaks, changes, & optimizations.

Ingeneue Version 0.93 by KJK (December 2007)

Added: Turing network model.
Added: Documenation for Initial conditions in similar style to the documentation for affectors.
Added: Documentation for stoppers.
Added: Can view Initial conditions and stoppers documentation in Ingeneue.
Added: New Ingeneue logo.
Added: startup batch file for windows & command shell script for mac.
Fixed: Camgraph panel too small to accomodate contents.
Fixed: Save as under file menu did not allow creation of new files.
Fixed: Help window too small to accomodate contents.
Changed: Manual converted to HTML and accessible from within Ingeneue.
Changed: Tutorials 1, 2, 3 converted to HTML and accessible from within Ingeneue.
Changed: Updated Ingeneue help system.
Changed: Ingeneue now reports warning when an invalid color is specified in net file.
Changed: Ingeneue now reports warning when width or height = 0 (due to not being set in net file).
Changed: Ingeneue now prints warning and raises exception when numsides is invalid instead of raising a cryptic nullPointerException.
Changed: Ingeneue now reports warning when height != 1 and numsides = 2 (for line of cells).
Changed: Tutorials & Manual updated for current version of Ingeneue.
Other code tweaks, changes, & optimizations.

Ingeneue Version 0.92 by KJK (November 2007)

Fixed: Changing integration stop times under Run->Options did not work.
Fixed: Time graphs save dialogue box did not allow creation of new files.
Fixed: Help should be displayed at startup.
Fixed: Ingeneue manual missing.
Fixed: CrossCorrelation save dialogue box did not allow creation of new files.
Fixed: CrossCorrelation did not write any output to file.
Fixed: Documentation for some affectors had errors.
Changed: By default, time plot has auto resize and overwrite turned on.
Changed: Reorganized models into networks directory.
Changed: Time counter updates every integration step now. Fixes counter not updaing when Step pressed.
Changed: Moved switch tutorial files to switch networks directory.
Removed: Debug classes.
Removed: Error console was unused and took up screen space.
Removed: Clusterpack and associated features, as they are for internal use and broke a few things.
Removed: Unneeded files in the authors/ouput/testing folders.
Added: COPYING.txt that contains latest GPL.
Added: Some new affectors.
Added: Neurogenic model paper files now bundled with Ingeneue.
Other code tweaks, changes, & optimizations.

Ingeneue Version 0.91 by EM, GMO and BJM (July 2005)

Added: Clusterpack package for exploration of randomly wired gene networks.
Changed: Iterator viewer updated to allow saving of images and more options.
Other code tweaks & optimizations.

Ingeneue Version 0.9e (Quagmire!) by WJS

ParameterSet Instantiation: Now when you click on a parameter set in the IteratorViewer, the values for that parameter set will be loaded into the model.
User Configuration File: There is now a file called configure.xml which contains user configuration information. It will eventually save the entire state of the program on close so that it may be restored when the program is started again. For now it saves the name of any model and iterator that were loaded when the program was last closed and reloads them on restart. This has saved me a lot of time when it comes to testing.
Significant correctness added: NetworkViewer now "properly" displays Enhacer Affectors.

Ingeneue Version 0.9d (Furious George) by WJS

TimeGraph: The TimeGraph now allows the collection of data sets from multiple integrator runs in a way that's both elegant and baffeling.
SimpleViewer modes: The ParameterViewer, CellViewer and TimeGraph now have a simple display mode. Clicking on the imshrinken button (the (-)) on Apples will invoke this mode. Clicking on the imbiggun button (+) will restore the normal mode. Some other viewers may evenetually be endowed with this fine gift.
IteratorViewer: More changes and addittions to the IteratorViewer including integration of CamGraph.
CamGraph: The CamGraph has been re-written to allow for easier integration with the IteratorViewer. It will now display new, sucessful parameter sets as they are discovered.
ParameterViewer: The viewer was not displaying the correct parameter values when being actuveky updated in iteration mode.
NetworkViewer: The NewtworkViewer painting code has been changed to allow faster accurate painting of node colors in active display mode. Apple arrow painting bug worked around.
Significant Correctness added.

Ingeneue Version 0.9c (Tree Frog) by WJS

InteratorViewer:The IteratorViewer is a new utility for managing iterator runs and their outputs. It may be used to start, top and reset the iterator. You may also change the outputfile and store all the results (ParameterSets associated with final ModelStates) so that you can thumb through them after a long run. You can have results displayed in various viewers (CellViewer, NodeStateViewer, ParameterViewer and CAMGraph) as the iterator is running.
Consoles and Errors: The output and Error Consoles are still there but have been turned off by default since they're kinda' sucky.
Significant correctness added.

Ingeneue Version 0.9b (Happy Seal) by WJS

TimeGraph: I've added a TimeGraph utility that allows one to look at simple line graphs of the normailzed node values. Use TimeGraph to collect run data from one or more integrator runs and then add line graphs by choosing the cell and node. There are many wonderful options guaranteed to delight any user.
Correctness: Significant corectness has been added to the codebase.

Ingeneue Version 0.9a (Lava Lamp) by WJS

General: I've created a single main GUI JFrame with a JDesktop. All other components are or will eventually appear within the JDesktop frame. I find this makes the program easier to work with when you have many windows open and other applications are open as well. I'm also persuing the general philosophy of making sure the GUI components are well separated from the newtwork objects. This makes it easy to have multiple instances of viewers and will eventually make it easy to have the interface attached to multiple remote processes running on the cluster.
There is now one general main menu for opening and closing files and invoking viewers, editors, etc. Individual viewers/editors have their own menubars as needed.
In general all viewers communicate through the GUI with the model so that all values are updated as they are changed. Changes to the network made within a viewer/editor are also propogated properly to other components.
Error messages. I'm just beginning the process of introducing popup error messages as needed.
CellSurfaceViewer: This has been completely re-written. It's faster now and seems pretty stable. I've also added a number of display options including linear, threshold, log, exp and pseudocolor. You can also remove and add nodes and reposition them easily and resize the whole display.
Network Viewer: This has been completely re-written. I paid close attention to making sure that lines and arrow draw well. It also has a built in auto-arrange function and the display can be set to auto-resize when the whole panel is resized (though this does cause some hinkyness). Both the NodeInspector and AffectorInspector are built in to the NetworkViewer. It is also possible to change some visual properties of the network such as highlit color for selected nodes and affectors.
Node Viewer:The Node Viewer allows the value of all nodes in each cell to be viewed and changed. Click on the cell in the cell surface view on top to select the cell.
ParameterViewer: This has been completely re-written. Its values will update to show the current parameters when an iterator is running.
Output/Error Console: Output and Error consoles have been added to aid OSX users. All standard output messages are re-directed to the Ouput Console and errors thrown by the JRE will go to the Error Console. Either can be closed and the messages will return the starndard console if there is one open (as with Linux and Windows). The console behavior is still a bit hinky, but I'll improve them soon.
Model State Editor: The Model State Editor is a work in progress. It will eventually allow you to quickly define model states by using a Photoshop-like interface to build stripes, gradients etc. on a display of the cell surface. The constructed model states will be used to construct initial conditions or build stoppers.