#==================================================================== # # $Id: RELEASE_NOTES.txt,v 1.16.2.55 2005/10/12 20:54:18 emeryconrad Exp $ # # Purpose: Oscill8 RELEASE_NOTES file. # # Author: Emery Conrad # #==================================================================== #==================================================================== # release 1.12.1 notes (2005/10/12) #==================================================================== Updates are: * Fixed another GUI run hang issue. * Enabled XP windows sytle (the SEHException has gone away). * Added a tutorial for the chap10_serious.ode model. #==================================================================== # release 1.12.0 notes (2005/10/11) #==================================================================== Updates are: * Added line properties (color, width, style) to plots; right click on legend to set these properties. BTW, "Alt Width" refers to stable points in bifurcation diagrams, so you can have two separate settable thicknesses for bifurcation curves. * Added font size to plot properties. * Added legend visibility toggle and offset from right/top. * Changed "Control-P" print to bmp/png/jpg to create an image identical in size to what is displayed in Oscill8--saved file is now completely WYSIWYG). * Added antialiasing to lines in plots; no more jagged edges. #==================================================================== # release 1.11.0 notes (2005/10/06) #==================================================================== Updates are: * Auto set directory in "New" after file load (last release). * Auto conversion of ODE file to readable form (\n-->\r\n conv). * Fixed \ continuation of lines for DOS/Windows \r\n line end (Bug #1313228). * Added overwrite confirm when you try to create a new workspace that will overwrite an old one. * Added auto backup feature (for data recovery in an emergency). Your workspace directory now has a "backup" directory which contains a sequence of last known good workspaces. In the future, this will only contain a maximum number of files, but for now (in this oscill8 version), there will be an unlimited number of copies here... you may want to purge the older ones if you have disk space problems. * Added ODE/XML/SBML file to valid "File->Open" options... this will pass you off to the workspace creation interface. #==================================================================== # release 1.10.3 notes (2005/10/05) #==================================================================== Updates are: * Fixed error handling for model init (o8core properly exits) (Bug #1313228). * Added o8core log output to GUI log. * Changed the look/feel of log form; need to add convenient highlighting etc. #==================================================================== # release 1.10.2 notes (2005/10/04) #==================================================================== Updates are: * Fixed minor silliness with an extra data point (in very rare cases). * Added parsing and model speed test cases to o8core_tests. #==================================================================== # release 1.10.1 notes (2005/10/04) #==================================================================== Updates are: * Addressed mutiple problems with simulator re: xpp simulation test suite (thanks Nick); only one of the remaining failing tests (arcsin) is a real fail, the rest are unimplemented features. * Fixed error in global flag parser (which was introduced in v1.10.0 when I added a slightly sloppier syntax variant). #==================================================================== # release 1.10.0 notes (2005/09/30) #==================================================================== Updates are: * Fixed @dt parse from ODE file to read floats, not ints. * Added less/greater than functions to valid operators, ONLY WITH PROPERLY PARENTHESISED EXPRESSIONS!! That is, 2+2>2+1=2+(2>2)+1=2+0+1=3, not 0 for false!! Also note that this doesn't include <= and >=. I'll fix this in the future. * Added heav(cond) function. * Added conversion for certain special character sequences, including > and <. * Added a sloppier syntax for global to accomodate XPP users! * Added implicit "t" symbol for time. Now you can include time dependent terms in your ODEs and discrete events! #==================================================================== # release 1.9.32 notes (2005/09/29) #==================================================================== Updates are: * Added data corruption protection; there is now an md5 hash produced for output; if the output changes from its first run, a "Bad Data" message shows up in the plot and you need to rerun to refresh the data. (Rerun currently only works for RunSets, though... I'll enable it for regular runs later). #==================================================================== # release 1.9.31 notes (2005/09/28) #==================================================================== Updates are: * Fixed XY data load to be more robust (you can have seperate columns by spaces, tabs, commas, and a few other characters)! * Added right click to run time series from a time series graph. * Fixed time series run to include the FINAL point. * Fixed -ts:out to give TIME only ONCE!! * Fixed time series run from command line to parse out XPP-style @ options in place of the command line options (you must, however, specify "-ts:format xpp" if you choose to leave out the -ts:output option). #==================================================================== # release 1.9.30 notes (2005/09/28) #==================================================================== Updates are: * updated error message passing between o8core and GUI, now you get some kind of useful message! #==================================================================== # release 1.9.29 notes (2005/09/27) #==================================================================== Updates are: * added some common functions to expression parser. This includes exp, log, log10, ln, sin/cos/tan, asin/acos/atan, sinh/cosh,tanh, abs. Use this some care... to keep speed high, I don't check arguments to make sure they are valid (e.g, acos(2)=#-1.IND or something ugly). * added user definable functions to ODE spec. That is user, can define MyFunc(x,y)=x^2+y and then use it in their ODE def. Beware not to use valid parameters/state variables for the names of the arguments to these functions... * added capability to run a TimeSeries from the command line w/o needing to write your own .o8r file. The relevant pars are -ts:out, -ts:format, -ts:t_end, -ts:n_points, -ts:rtol, and -ts:atol. Enjoy (you can output to xpp, o8p, columnar etc). #==================================================================== # release 1.9.28 notes (2005/09/22) #==================================================================== Updates are: * linux updates; core is now compiling on linux. * fixed new zero range crash in plotting. * added BP (branch point) label to plottable labels. #==================================================================== # release 1.9.27 notes (2005/09/12) #==================================================================== Updates are: * Graphs are now sexier! Tic marks and ranges are intellegently set and labels are nice round (minimal number of sig digits) viewable numbers. * Adjusted point tolerance (easier to get alt-click continuation options). * Renamed labels for LP bif points (SN and CF are distinguished). * Fixed check boxes for active column in model data display. * Fixed "close-to-zero" label snafu... #==================================================================== # release 1.9.26 notes (2005/09/08) #==================================================================== Updates are: * Fixed bug #1284230 (graphs not representative of what AUTO returned; problems was overflow errors in reading doubles since AUTO was outputting 1e-320 type doubles; created thresholding for output of double from AUTO). * Fixed bug #1242323, the disappearing notes issue. * Fixed annoying auto zoom bug on startup (after open and a double click, the zoom lines would be there. Now though you have to have the focus on the plot (double click in the plot) to do zooming). * Fixed bug #1284229, deleting a subrun of an instance of a runset will not crash anymore... it is prohibited for the time-being. #==================================================================== # release 1.9.25 notes (2005/09/07) #==================================================================== Updates are: * Fixed Export/Add XY data to do ONLY first active curve. The Export Raw Data will export all curve data in a plot, but cannot be loaded right now. #==================================================================== # release 1.9.24 notes (2005/09/07) #==================================================================== Updates are: * Fixed limit cycle continuation; period, min and max amplitude are returned and can be plotted seperately. * Adjusted tolerance for right click on plot. #==================================================================== # release 1.9.23 notes (2005/09/01) #==================================================================== Updates are: * updated temperature compensation tools and period calculations. * Added activation energy quantities (eps_e, eps_s) and data type (type) to the settable quantities in model data (used for temperature comp and sv->par for bifurcation analysis). * Replaced model data save and read with o8mi save/read instead of spaced-seperated columnar data. * changed default sample period/min/max parameters to be more generally applicable. * completed adding in full minpack dist and some tests. ready to test bifurcation optimization with levenberg-marquardt code, probably need to add some sort of constraint mechanism to minpack for this to work well. * fixed bug that caused a crash when you delete the very last node in the history tree! * fixed multiple open crash. #==================================================================== # release 1.9.22 notes (2005/08/18) #==================================================================== Updates are: * fixed one more error in the CVode code... a very minor bug in most cases, but catastrophic in many of my test models (especially those including discrete events)! #==================================================================== # release 1.9.21 notes (2005/08/05) #==================================================================== Updates are: * Fixed divide by zero error when a user forgets to input some information and the expected number of outputs from a run is zero. #==================================================================== # release 1.9.20 notes (2005/08/04) #==================================================================== Updates are: * Compatible with JDesigner2.0.23+. * Multiple loads possible from JDesigner (different models etc). * Cleaned up plot wipe on new model load. #==================================================================== # release 1.9.19 notes (2005/08/03) #==================================================================== Updates are: * Enhanced error handling for SBW interface to report propagated errors from SBW. * Fixed installer to run the sbwregister command for oscill8 and o8core. * Added index, label, type to export of raw data from a graphic. * NOTE: until the next release of SBW (which will include the new XPP translator service), you can get the necessary modules from http://public.kgi.edu/~rrao/XPP. #==================================================================== # release 1.9.18 notes (2005/08/02) #==================================================================== Updates are: * Starting Oscill8 from SBW menu in JDesigner (v1.96x) works now (doesn't properly work from JDesigner2--I'll talk to Herbert Sauro about this). #==================================================================== # release 1.9.17 notes (2005/08/01) #==================================================================== Updates are: * Bug #1219436, delete key in tree view is now fixed. * Export XY data now exports all active curves of 1st plot index. * Delete node now reselects active node after delete (to get the plots properly displayed). * Oscill8Directory is no longer dependent on environment variables, rather uses the Assembly location. * Added in new SBML --> ODE translation via SBW (using the edu.kgi.XPPTranslator module). * Oscill8 GUI is now a SBW module, usable via the SBW menu in tools like JDesigner etc (via plugin Analyzer interface). So, you can now create a model in JDesigner and then go directly to Oscill8 via a menu item. * Discrete Events are now fully implemented after a minor fix to CVODE root finder. #==================================================================== # release 1.9.16 notes (2005/06/16) #==================================================================== Updates are: * Switched to BSD license... no more license changes, promise! * Added plots to twiddler and fixed instance reruns. #==================================================================== # release 1.9.15 notes (2005/06/13) #==================================================================== Updates are: * Release SamplePeriodMinMax run type in GUI. This calculates the period, minimum and maximum (for all state variables) in some range of a particular parameter. #==================================================================== # release 1.9.14 notes (2005/06/12) #==================================================================== Updates are: * Twiddler fixes, disabled a few dangerous features for demo! * Added example ode files to setup installer; discontinued examples installer. #==================================================================== # release 1.9.13 notes (2005/06/12) #==================================================================== Updates are: * Added in twiddler interface. Doesn't yet contain embedded graphs grid (thumbnails) for runs, but is working! #==================================================================== # release 1.9.11 notes (2005/06/10) # (compilation of 1.9.1-1.9.11 notes) #==================================================================== Updates are: * (RFE #1171955) Run manager implemented, still needs work but is usable. * (RFE #1171953) Combine plot feature is implemented (drag and drop from run tree to plot area). * (Bug #1187379) Fixed BP line thickness off by one point * (Bug #1170165) Fixed edge interpolation (nice and linear now) * (Bug *1200896) Barf on no pars fixed (several releases ago!) * Several bugs have been fixed in the last several releases, including #1186030, #1182517, #1182498, #1172673, #1172672, #1171257, #1167895. * Added save to bmp and print features; run context menu has nice print summary feature which encapsulates the graph and other info for a run. * Many updates to matching... added relative matching, match classes now allows multiple identical p-value matches, takes best. * Fixed Cntl+S to bmp to 640,480 size for niceness. * Added zoom lines. * Fixed nit/nit1 infinite loop in AUTO. * Added scale, n_breaths, qtol etc to matching code. This algorithm ROCKS! * Added SBW StartGUI service, JDesigner can use it. * Added multi match_map, take lowest fitness. Many fixes and updates to matching code. * Added -c/--coreport command line option so user can run mutiple oscill8/o8core copies on a single machine. * Matching is working nicely in core. ##################################################################### # # PREVIOUS RELEASES # ##################################################################### #==================================================================== # release 1.1.6 notes (2005/05/17) #==================================================================== Updates are: * Updated period/min/max. * Changed default multiplication factor on parameter init from 1000.0 to 10.0... let's be conservative and then the user can increase to his/her needs. Also, in possvs case, parmin=0. * Fixed silly expected outputs error (was waiting when no outputs were coming!) * Added -o/--overwrite command line arg; default is now NOT to overwrite. There is still a dialog that asks for confirmation. #==================================================================== # release 1.1.5 notes (2005/05/14) #==================================================================== Updates are: * Fixed Newton a bit... * Made overwrite confirm more reasonable! (Verification is a checkbox with a button, defaults to NO). * Added -p/--possvs and -d/--directory options to command line start; -p means positive state variables, -d is the place into which we put the new workspace (with it's own directory... so -d is the cache directory, which gets a workspace directory by the name of your file). The special case of "-d ." is equivalent to "-d wscache". * Added in experimental period/min/max calculation algorithm. * Began integration of new dataset/plotset philosophy into the core; the full transition will take quite a while, but from here on out, this will be the new medium for data passing in Oscill8 (since it's convenient, flexibile and connected to actual visualization). * Fixed several little bugs here and there! #==================================================================== # release 1.1.4 notes (2005/05/12) #==================================================================== Updates are: * Cleaned up workspace creation from the GUI. Although you can run things from the command line, I wanted to make the GUI version simpler for the user. * Updated user docs to include mention of new command-line creation methods as well as SBML capability. #==================================================================== # release 1.1.3 notes (2005/05/11) #==================================================================== Updates are: * Completed migration to CDDL (no GPL or other licensed code is now included with Oscill8). Newton calculation is done based on LAPACK/BLAS/MINPACK code now. #==================================================================== # release 1.1.2 notes (2005/05/11) #==================================================================== Updates are: * Changed license to CDDL, began removing dependencies on GSL. With the next release, there will never again be ANY strictly-licensed code used by Oscill8!! * Fixed barf on @ symbol in XPPAUT ODE files (thought I had done that before, but NO!) * Fixed another error in the parser that was getting incorrect operator precedence for / vs. * in certain cases. #==================================================================== # release 1.1.1 notes (2005/05/09) #==================================================================== Updates are: * Fixed continuation parameters being properly passed to two parameter continuation. * Added SBML/XML and ODE start (without having to explicitly create the workspace--a workspace gets created in the local workspace cache). * Added command-line start with .o8w, .ode, and .sbml/.xml files as input (which utilizes the auto-creation of workspaces). * JigCell SBML->ODE conversion added. JigCell install dir is hard-coded right now to the default JigCell install dir. NOTE: Oscill8's model parser doesn't yet accept functional expressions so not all SBML files will work!! This feature is forthcoming. [REQUIRES JigCell version >= 5.0.1] * Added PATH update to registy/code section of windows exe installer. * Removed annoying "Not implemented yet" messages. #==================================================================== # release 1.1.0 (2005/05/02) #==================================================================== This is the first "official" release! Most of the basic functionality is now included. Bifurcation searching, matching, and robust limit cycle continuation has been put off to release 1.2 (expected June/July 2005). Known Issues: * There are still quirks in the basic interaction with the GUI, (for example in the implementation of the run history; crude and slow behavior will result for analyses with many runs and lots of datashow the poor). * Limit cycle continuation is broken for most large models. ##################################################################### # PRE v1.1 ##################################################################### #==================================================================== # release 1.0.28 notes (2005/05/01) #==================================================================== Updates are: * Fixed int/string issue with labels. #==================================================================== # release 1.0.27 notes (2005/04/30) #==================================================================== Updates are: * Added 1pbd biospice analyzer. * Fixed biospice analyzers and plotter interaction. #==================================================================== # release 1.0.26 notes (2005/04/29) #==================================================================== Updates are: * Started adding in biospice analyzers, first version for simulator, plotter coming along. * Refactor of start up, o8gui changed to dll assembly, new gui runs under the oscill8 name. * Stand-alone plotter created. #==================================================================== # release 1.0.25 notes (2005/04/26) #==================================================================== Updates are: * Fixed silly ws close on creation! * Fixed logger flush on exit. #==================================================================== # release 1.0.24 notes (2005/04/24) #==================================================================== Updates are: * Added log plot feature. * Reorganized workspace a bit. * Added splash screen. * Added "About" dialog under Help menu (lists version). * Added o8gui.log output for debugging (into installation directory... could cause problems for user who don't own their machine and aren't allowed to write there... fix later!!) * Completed most documentation for v1.1. #==================================================================== # release 1.0.23.1 notes (2005/04/20) #==================================================================== Updates are: * Fixed infinity scale problem. * Fixed notes panel again ;-< #==================================================================== # release 1.0.23 notes (2005/04/20) #==================================================================== Updates are: * Fixed DrawLines crash when NaN shows up in data set (temporary patch, better handled by message from o8core). * Fixed non-disappearing note panel upon workspace close. * Fixed strange max/min behavior for negative parameters. * Added steady state tolerance into ODE solver parameters (when finding stable steady state). #==================================================================== # release 1.0.22 notes (2005/04/18) #==================================================================== Updates are: * Added in ODE and AUTO numerical parameters. * Rearranged the run configuration. #==================================================================== # release 1.0.21 notes (2005/04/18) #==================================================================== Updates are: * Fixed min/max auto set on workspace creation to notice a parameter setting of zero and make special bounds for it. * Added save/read model data from files. * Added help link (external browser .html help). * Fixed big ugly bug in expression parser when parenthesizing for operators (didn't previously parenthesize subexpression properly!!) #==================================================================== # release 1.0.20 notes (2005/04/08) #==================================================================== Updates are: * Fixed rename so that triggers the rename! * Added "global" discrete event identifier (state vars/pars can reset based on state) * Added save XY data from a plot option. * Added load XY data from a file to a plot option. * Fixed model constructor to barf on unbound/undefined symbols. * Fixed velocity --> velocity symbol bind * Fixed ode_clean.pl tool to properly address arguments in functions (we mangle the arguments now... WARNING, don't use double underscores in your parameter or variable names because we use __*__ to mangle the names) #==================================================================== # release 1.0.19 notes (2005/04/04) #==================================================================== Updates are: * Abort O8AUTO calculation for invalid pivots... we'll debug this later! * Changed default AUTO dsmin to 1e-6 (from 1e-11), default calcs were taking to long! * Fixed GUI spin waiting in progress form during run (silly me, silly, silly). * Added flag for chemical systems (positive svs, par vals) vs. arbitrary systems (where sv and par can be negative) and altered core to not just deal with chemical systems. There is a new checkbox when you are creating a workspace that sets this flag. * Fixed min/max to be 0.01 and 100x base value (for x, it's more like 0, and 1000*x) * Default mode for 1P/2P now is to plot only first relavant curve on the Y axis! * Fixed initial notes check (when it wasn't showing). * Fixed crash awareness due to AUTO anomolies (division by zero etc). * Fixed many little GUI issues (run notes check box etc). #==================================================================== # release 1.0.18 notes (2005/03/26) #==================================================================== Updates are: * Added plot properties saving!! * Added run generation to run tree context menu. * Notes feature is active now (available from the View menu or the run tree context menu). * Added model data view to run tree context menu. * Added title to plot properties. * Removed examples from exe installer. There is a seperate examples installer now. * NOTE: Backup you workspace file (.o8w) prior to running this version. If you had a previous workspace that you'd like to open with this version, you MUST visit each run manually (by clicking in the run history view) in order for all the correct new properties to be created... if you don't you run the risk of corrupting the workspace file!! #==================================================================== # release 1.0.17 notes (2005/03/24) #==================================================================== Updates are: * Added plot legend; each curve toggles. * Added "move to top" feature for run tree (rename also works). * Added hotkeys: In the run tree, you can use "" to delete run, "r" to rename run, "m" to move to top, "" moves you to the plot area. In the plot area, you now have several new hotkeys: "x" sets xmax to xmin+(xmax-xmin)/2, "X" sets xmax to xmin+2*(xmax-xmin), "y" sets ymax to ymin+(ymax-ymin)/2, "Y" sets ymax to ymin+2*(ymax-ymin). Holding "" at the same time as x,X,y,Y makes similar changes to xmin (moves half way towards/twice as far to/from xmax or ymax. * Fixed bug in O8AUTO that only allowed a certain number of output bytes per line in text version of solutions (which caused a hang). #==================================================================== # release 1.0.16 notes (2005/03/23) #==================================================================== Updates are: * Added two parameter continuation (BEWARE OF AUTO!) * A few small updates to graphing and zooming. #==================================================================== # release 1.0.15 notes (2005/03/22) #==================================================================== Updates are: * Fixed NaN graph problem * Added Delete feature to run tree history (Rename is in process) * Cleaned 3rd party CVODE and AUTO libraries to not do silly things like exit and to tap into the Oscill8 logging facility. * Fixed little bug that caused crashed for ODE files with no velocity terms. * o8core is now a process which you don't see pop up; it runs in the background and is open/closed for every new workspace (for now). * o8core logging is now done to "o8core.log" in the workspace directory. #==================================================================== # release 1.0.14 notes (2005/03/21) #==================================================================== Many updates, including: * Everything is now packaged into a simple installer .exe for windows (using Inno Setup). It behaves like a proper install; you can uninstall later using the Add/Remove Programs feature of windows. * I've upgraded the run tree implementation. * GUI code has been thoroughly documented and cleaned up quite a bit. * New run information panel below the run tree view. * Improved interaction between o8gui and o8core. A few more features and we'll be ready for v1.1. NOTE: For those of you who installed a version prior to this, you'll need to remove the directory you unzipped to (and for good measure you might as well remove the OSCILL8_DIR environment variable and the "C:\oscill8\bin" from the "Path" variable). The new installer does all this automatically. #==================================================================== # release 1.0.11 notes (2005/03/18) #==================================================================== I forgot to disable a few features in the 1.0.10 pre-release, so they are now disabled. #==================================================================== # release 1.0.10 notes (2005/03/17) #==================================================================== This is an initial alpha release. To install, simply unzip the package to a simple location, like C:\. The zip file contains a directory "oscill8" with all the necessary files in it. Add an environment variable "OSCILL8_DIR" with the value "C:\oscill8", then add "c:/oscill8/bin" to your "Path" variable. You will need to have the .NET 1.1 redistributable installed in order for this software to run. WARNING: This is JUST an initial version; it is not yet tested rigorously. We will be releasing v1.1 on 2005/04/01, which will have user documentation and an automated installation. USE THIS RELEASE AT YOUR OWN RISK!! Have a great day! Emery Conrad