I'm back to active development. A few improvements, most notably (for Tongli Zhang) a command line version of bifurcation search (random walk).
Oscill8 has many new features since the last announcement, including alt-click time series runs from one and two parameter bifurcation diagrams, plotting of aux variables, and better SBW integration (simulator is available in SBW now).
Enjoy the bifurcation analysis, with improved logging and error handling so that you can know what went wrong ;-). See release notes for a full list of new and improved features.
Oscill8 is a dynamical systems analysis package that incorporates CVODE, AUTO and other useful tools. The parser is now basically feature complete (handles almost all ODE files). Enjoy!
Many new features available, including limit cycle continuation, easier XY data support and improved reliability of integrator. Many bug fixes as well.
Oscill8 is now SBW aware and can be run from JDesigner via the SBW menu in both the v1x and v2x lines.
SBW module mode works for JDesigner SBW menu start!
This feature requires installation of SBW (in addition to the XPP converter SBW module exe's from V. Ravi Rao--see Ravi's website for these until they are included in the SBW package).
Oscill8, v1.9.7: Many new features. SBW SBML--> ODE conversion now available, new RunSet feature with parameter twiddler feature, first version of bifurcation matching routines are working from command line (not yet documented).
Many new enhancements, including RunSet collections of runs (which can derive values from other runs with changes in parameter/sv values via algebraic expressions), graph combination by drag & drop, period/min/max sampler is now working as well. Enjoy!
This is the first official release of Oscill8 with many, many new features. Parameter optimization via bifurcation is now implemented in the core, though not yet in the GUI. Print features, zoom features, are now implemented.
Updates from v1.0 include migration to CDDL (from LGPL), removed dependence on GSL, added in minpack for jacobian calculations and later optimization functionality, fixed barf on @ symbol in XPPAUT ODE files, fixed another error in the parser that was getting incorrect operator precedence for / vs. * in certain cases. 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), added JigCell SBML->ODE conversion (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 (for you Nick Allen!)
First official release of Oscill8. Please see http://oscill8.sourceforge.net/doc for details!
this version has several new features, including biospice analyzers and a stand-alone plotter (currently only functionally useful for the biospice analyzers). v1.1 is a day or so from being released.
this release include log scale plotting, a new fancy splash screen, a new log file for the o8gui (for reporting bugs), and a general rearrangement of the interface with user docs
basically complete for v1.1 (release planned for May 2nd).
AUTO/CVODE parameters are now exposed to the user!!
see release notes. there was an ugly mistake in the expression parser that caused certain expression (which were already partially parenthesized) to be mis-evaluated.
Many minor fixes that make life a little more reliable with model input etc. Also, major upgrad to integrator allows for discrete events now (via "global" switch as in XPPAUT).
Many updates, see release notes. Postponed planned April 1st release to get ready for BioSPICE. 1.1 will be release prior to the 15th of April.
Many changes were made and this version is packed with new features; I will probably wait until April 1st (or shortly there after) to release again, and that will be the full v1.1.
Made many many upgrades, getting there!! See release notes for details.
# release 1.0.15 notes (2005/03/22)
o Fixed NaN graph problem
o Added Delete feature to run tree history (Rename is in process)
o Cleaned 3rd party CVODE and AUTO libraries to not do silly things like exit and to tap into the Oscill8 logging facility.
o Fixed little bug that caused crashed for ODE files with no velocity terms.... read more
# release 1.0.14 notes (2005/03/21)
Many updates, including:
o 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.
o I've upgraded the run tree implementation.... read more
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.... read more