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Dizzy Version History

CompBio Group, Institute for Systems Biology

This document contains the version history for the Dizzy software product.

Version Date Comments Built with ISBJava version number:
1.11.4 2006/09/28
  • Fixed an output formatting bug that resulted in localized numbers being output, which in Germany means that a comma is used as the symbol for the decimal place. This was causing problems for Matlab interpreting the "matlab output" file format, in Germany. Thanks to Steffen Waldherr (Univ. Stuttgart) for pointing out this bug, and for providing a bug fix.
  • Fixed a bug that caused an exception when Dizzy was run on certain Windows platforms with an unusual file type in the classpath. Thanks to Patrick Grant for reporting this bug.
  • Fixed a bug in the Gibson-Bruck simulator, that was preventing reactions whose propensities are an explicit function of time, from having their next "firing time" updated after each iteration of the algorithm. Thanks to Dominique Chu (University of Kent, UK) for reporting this bug.
1.11.3 2006/04/18
  • Fixed a bug in the SBML import feature, where a model containing a species concentration rule would result in an error message. Thanks to Nguyen Van Tam (JMI, New Delhi) for pointing out this bug.
  • Fixed a bug in the Gibson-Bruck simulator, that was affecting the rare case of a stochastic model in which a reaction propensity is an explicit function of time. Thanks to Dominique Chu (University of Kent, UK) for reporting this bug.
1.11.2 2006/01/26
  • Included the latest version of the Systems Biology Workbench (SBW) library, which will allow Dizzy to interoperate with SBW version 2.5.0.
1.11.1 2005/08/11
  • Fixed a bug in the editor pane, where a NullPointerException was occurring when the user attempted to run "Tools->Simulate" on a model that did not have a filename associated with it yet.
1.11.0 2005/07/08
  • Added a "command-language" model exporter, which will export the model to Chemical Model Definition Language (CMDL) Format.
  • Fixed a bug where the file browser for "export model" was not set to the current working directory. Exporting a model also now resets the current working directory, for consistency with other file operations in the application.
1.10.0 2005/07/01
  • Modified the Systems Biology Workbench (SBW) interface so that the Dizzy simulation launcher is now an "Analysis Service". This means that the Dizzy simulation service shows up in the "SBW" menu in JDesigner and other SBW-enabled tools.
  • The "About Dizzy" menu item now displays the copyright notice.
  • Updated the version of the external SBW library (SBWCore.jar) to version 2.3.0.
1.9.3 2005/06/19
  • Added a work-around for a bug in the Systems Biology Workbench (SBW) interface, that could potentially cause the simulation service to fail to register with the SBW Broker on non-Windows systems. Thanks to Frank Bergmann for supplying the patch.
  • Added a new method to the SBW interface, that allows a CMDL model to be passed to Dizzy via SBW. Using this feature requires knowing how to programmatically call the SBW. File inclusion via the #include directive is not allowed, when passing model text to Dizzy via the SBW interface (for security reasons).
1.9.2 2005/06/15
  • Fixed problem with build script, where it was impossible to do any ant tasks, even those tasks that do not require InstallAnywhere, on a system that does not have the InstallAnywhere JAR file installed into the Ant lib directory.
  • Fixed a bug where the "File->Close" menu item was not being enabled after the user loads a zero-length file into the edit buffer.
  • Fixing missing sample file "Michaelis.cmdl". Removed unneeded sample file "sample-model-sbml.xml".
  • Fixed a problem where the RegisterSBWSimulators launcher was failing with an exception, when the installed version of the Systems Biology Workbench (SBW) is 2.0.0 or greater. Now, Dizzy works correctly with SBW version 2.2.1 or newer. This has the side effect that the version of Dizzy distributed through the graphical installer will not work with 1.X.X versions of the SBW. However, see the user manual for information about how to make Dizzy compatible with 1.X.X versions of SBW. Thanks to Stanley Ng and Ole Schulz-Trieglaf for reporting this problem.
1.9.1 2005/04/05
  • Fixed a NullPointerException that was occurring when a model contained a species whose initial population value exceeded the maximum allowed for stochastic simulations. This exception would occur the second time the user attempted to initiate a stochastic simulation. The correct behavior is for the simulator to give the same error message each time the user attempts to run a stochastic simulation with the (flawed) model. Thanks to Vincent Rouilly for submitting the bug report.
  • Improved the error message shown by the simulation launcher, when the user attempts to launch a stochastic simulation and when one of the species has an initial population value that exceeds the maximum allowed for stochastic simulations. The error message now gives the offending species name and the initial population value.
  • Fixed a bug whereby a SBML model with UTF-8 character encoding (and actually using special UTF-8 characters) loaded into the editor pane, and then subsequently passed to the "simulate..." or the "export model" menu item, would cause a SAXParserException on the Macintosh OSX platform. Thanks to Vincent Rouilly for submitting this bug report.
  • Fixed a bug in the simulation launcher where the "secs remaining" text field would show too many significant digits when the number of estimated seconds remaining is very large.
  • Fixed a potential problem with the editor pane, such that when the user selected "save as" or "save", the file was being written with the platform's default character encoding. This meant that (in the case of SBML models) the encoding specified in the XML header was being ignored, and (in the case of CMDL models) the model would not be written in the UTF-8 encoding on platforms whose default encoding is not UTF-8. This means that on certain platforms, the "save" or "save as" functions would end up writing a file that does not conform to published character encoding specifications for SBML and CMDL.
  • Fixed a bug in in the "View..." -> "human-readable" menu item feature, where the comma-and-newline separator string was not being printed in every case that it should have. This led to improperly formatted output for the "human-readable" view/export feature.
  • Fixed a bug in the simulation engine that was causing incorrect results when simulating certain SBML models that have "substance" units of "mole". Thanks to Vincent Rouilly for submitting the bug report. This bug does not affect the results of SBML models with "substance" units of "item" or CMDL models.
  • Fixed a bug in the editor pane that was causing the editor to fail to "forget" the model parser type, when the edit buffer is cleared using the "File" -> "Close" menu item.
  • Modified the stochastic simulators to check all dynamical symbols to see if any species value exceeds the maximum allowed for stochastic simulations (approximately 9.0771993e+15), each time a "result time point" is sampled (by default, 100 time points spaced at equal intervals during the simulation). This ensures that the stochastic simulators will continuously check to see if any species values exceed the maximum allowed species value, throughout the course of the simulation. This fixes a potential problem with a simulation such as
    X = 1.0e+15;
    -> X, 1.0;
    which will eventually fail in a stochastic simulator, due numeric precision limitations of floating-point addition.
  • Improved the wording of some error messages in the simulation launcher window, the editor pane, and for various menu functions.
  • Fixed bug in the runmodel program where the command-line simulation launcher was not obtaining the defualt relative and absolute error tolerances for the simulator, so the user would get an error if both tolerances were not explicitly specified on the command-line.
  • Modified the "Tools -> View... > cytoscape" feature so that the NetX start-up dialog box does not appear at application start-up. The dialog box asks you where you want to store your NetX cache. After this modification, the dialog box should only appear the first time you actually use this feature.
1.9.0 2005/02/04
  • Added a new section "Simulators" to the User Manual, describing the different simulators that are available in Dizzy
  • Fixed a potential problem with the sample programs for creating Dizzy models using the ISBJava API, where the reserved symbol mapper was not being set for the model. This was leading to confusion when people attempted to reference reserved symbols in expressions, which was causing an exception to be thrown. This is just a documentation change.
  • Fixed a NullPointerException that occurs when the model editor buffer has no filename defined for it (i.e., when the buffer has not yet been saved to a file), and when there is a parser error in processing the model definition text. Improved some parser error messages to make them more human-comprehensible.
  • Fixed a bug in the editor code where the "save as" operation was failing to update the "current directory" that is used for preprocessor file inclusion.
  • Fixed a bug in the CMDL parser which was causing an exception to be thrown, when a model contained a loop definition in which either the start or stop value was a mathematical expression containing parentheses.
  • Added support for a min() and max() function, to the mathematical expression-processing engine. Mathematical expressions in the CMDL can now use these two functions, as functions of two arguments, such as
    Thanks to Adam Duguid, for submitting the source code patch.
  • Fixed confusing error messages in the Runge-Kutta simulator with fixed step-size, for the case when the relative error tolerance is exceeded.
  • Modified the simulation launcher screen and the command-line simulation launcher program to permit disabling the error checking in the fixed-stepsize Runge-Kutta simulator (ODE-RK5-fixed). In the simulation launcher screen, the error checking is disabled by deleting the relative and/or absolute error tolerance parameters in the corresponding text entry boxes. In the simulation launcher command-line program, the error checking is disabled by passing an argument modifier "null" after the corresponding command-line argument, such as
    -relativeTolerance null
    Each of the error types can be disabled separately, or they can be disabled together.
1.8.2 2004/11/18
  • Decreased the application start-up time by 45%, by making the search for plug-in components more efficient.
  • Created a "View" sub-menu of "Tools", containing the aliases of all model viewers. Moved the "View in Cytoscape" and "View in Human-Readable Format" menu items to this new sub-menu.
  • Created a "Export" sub-menu of "Tools", containing the aliases of all the model exporters. The aliases that used to appear in a dialog box when the "Export..." menu item was selected, now appear in the "Export" sub-menu.
  • Added a "line counter" feature to the main model editor window. The line number of the current cursor position in the editor buffer is displayed, and updated whenever you move the cursor in the editor window. Thanks to Earl Solis, for suggesting this useful feature.
  • Added new sample model definition file, Michaelis.cmdl, to the "samples" directory.
1.8.1 2004/11/12
  • Please note that there have been some changes in the ISBJava API in this release. For more information, please refer to the description of changes in version 2.0.0 in the ISBJava Version History.
  • Fixed a bug in the simulation results table window, which was causing the table window to not be resizable.
  • Modified the simulation engine to better handle formatting of not-a-number (NaN) and infinity values, in simulation results.
  • Modified the runmodel program so that it will notify the user if the simulator is not capable of computing steady-state fluctuations, if the -computeFluctuations flag is passed on the command-line.
  • Fixed a bug in the CMDL parser which caused an exception when one attempts to simulate a model containing a macro reference embedded within another macro definition.
  • Fixed a bug in the editor pane. When the user would close the file loaded in the editor pane and then attempt to open a new file, the user would be needlessly prompted as to whether to save the changes in the editor buffer, to a file.
  • Modified the CMDL to enable the parsing of floating-point numeric literals expressed in scientific notation, such as 1.0e-7 and 2.7e+14.
  • Fixed a bug where ISO-8859-1 characters greater than 127 in the CMDL model definition file were causing exceptions when the model was processed, on Red Hat Linux. CMDL files are now always processed using UTF-8 encoding. This will ensure that CMDL model processing is consistent across different locales. Files opened using the "include" directive will be processed in the same character set as the parent file.
  • Fixed a potential bug where SBML files were being read in the default locale encoding for text files, and not in the encoding specified in the XML file header.
  • Fixed a bug (reported by Alex Kowald) in the org.systemsbiology.chem.ModelBuilderCommandLanguage in which an exception is thrown, if a quoted string is embedded within a deferred-evaluation mathematical expression. This prevents referencing a symbol name that contains an integer (e.g., an index) obtained from a mathematical expression, within the context of a deferred-evaluation mathematical expression. This bug potentially affects models in which the loop construct is used, in conjunction with reaction definitions with complex (deferred-evaluation) kinetic rate expressions.
  • Slight change to the help browser, so that it will not take up all the screen, when the screen size is very large. The initial size of the help browser window is now capped at 800x600 (but can be modified by the user), and will never exceed 80% of the screen size in either dimension.
1.8.0 2004/10/11
  • Fixed a bug in the build file that was preventing the source code from being included in the ISBJava source distribution archives.
  • Modified the chemical model definition language to disallow user definition of a symbol that begins with an underscore character. This ensures that user-defined symbols will not conflict with the names of automatically defined symbols (such as automatically defined chemical reaction names).
  • Modified the simulation launcher window so that internal symbols are never displayed in the listbox of symbols, and in the text output of the command-line simulation launcher.
  • Fixed a bug in the repressilator.xml sample file; the listOfUnitDefinitions section was omitted, which was causing the initial species populations to be interpreted in terms of moles (the default), rather than molecules.
  • From this release forward, Dizzy will be compiled with optimization enabled, before a new version is released.
  • Modified the CMDL (chemical model definition language) so that the log() command has been changed to the ln() command. This was done for consistency with standard computer science notation, in which ln() represents the natural logarithm, and log() represents the logarithm base 10.
  • Added a new text field "number of history bins" to the simulation launcher. This allows the user to control the number of bins for storing the past values of a species that participates in a delayed or multi-step reaction. This field is only displayed if the model contains a multi-step or delayed reaction.
  • Added a new command-line option "-numHistoryBins" to the command-line simulation runner, "runmodel". This option enables the specification of the number of bins that are to be used to store the past values of a species that participates in a delayed or multi-step reaction. This value, if specified, is only used by the simulation launcher if the model actually contains a delayed or multi-step reaction.
  • Removed the parameter "min num steps" from the simulation launcher; it has been replaced with the "(step size fractional)" parameter. This parameter specifies the initial step size (as a fraction of the total time of the simulation) in the case of a deterministic/ODE simulator, and it specifies the minimum number ratio of the reaction time to the leap time, in the case of the Tau-Leap simulators.
  • Added the option testOnly to the simulation launcher program runmodel. This option instructs the simulation launcher to process the model definition file, validate the simulation parameters, and then exit. It can be used to test a model and simulation parameters for correctness, without having to execute a simulation.
  • Improved the efficiency of the delayed reaction solver, by halving the amount of history information that needed to be stored regarding each delayed reaction channel.
  • Modified the command-line simulation launcher program runmodel to print out the average number of iterations per second, during the last status statistics-collecting interval.
  • Fixed a serious inefficiency in the simulation engine, for the case of models containing custom kinetic rate law expressions. The inefficiency was in the part of the engine that clears the cache of previously computed expression values. The cache was cleared for all non-dynamic symbols, including those symbols (usually a majority) that are not custom expressions (i.e., symbols that are bare numbers). Modified the simulation engine so that only non-dynamic symbols which are in fact, expressions, have their value caches cleared.
  • Changed the "print" output type, to "table". The "table" output format now displays the simulation results in a resizable table with individually resizable column widths. Changed the "file" output type to "store".
  • For the "table" and "store" output formats, floating-point values are rounded to the correct number of significant digits, based on the relative and absolute error tolerances specified for the simulator.
  • Modified the "plot" output format, so that the model name, simulator alias, and date/time are now displayed in a label that is outside the plot image. When the plot image is saved, the labels will not be saved with it, which is generally preferable because the desired label format and font will differ based on the end application for the plot.
  • Added a list of past simulations to the simulation launcher window. This list can be used to go back and generate a plot, or tabulator view, for the results of a previously run simulation. The results of a previously run simulation may be saved to a file as well.
  • The windows for simulation results plots and tabular views, are now tiled in a cascading pattern together, rather than tiled independently.
  • Fixed a potential bug whereby the user was allowed to specify a relative error tolerance of greater than 1.0.
  • Modified the command-line simulation runner runmodel, so that it prints out simulation results with a number of significant digits that is consistent with the specified absolute and relative error tolerances.
1.7.0 2004/06/08
  • Modified Dizzy to correctly implement the importing and simulation of an SBML model for which the unit of "substance" is "mole". This fixes incorrect simulation behavior when an SBML model with the default substance unit ("mole") is imported.
  • Fixed a bug that was causing an exception to be thrown in the simulation launcher, when Dizzy is deployed using Java Web Start.
  • Modified the simulation framework to model multi-step reactions differently than delayed reactions. Multi-step reactions are now simulated using the Gamma Distribution as described by Gibson and Bruck in their Journal of Physical Chemistry A paper (2000), while delayed reactions are simulated using delay differential equations or (in the case of a stochastic simulation) a time delayed stochastic process.
  • Modified the SBML model export feature so that it correctly preserves the units for "substance" that were originally specified for the model. This avoids a potential problem if a user imports a model from SBML, and then exports the model back to SBML.
  • Decreased the maximum initial step size for the Dormand-Prince 5/4 ODE solver, for the case of a model with a delayed or multistep reaction.
  • Fixed a bug whereby the "tauleap-complex" simulator was giving an exception, when simulating a model imported from SBML, that has local reaction parameters.
1.6.4 2004/04/05
  • Fixed an inefficiency in the Gibson-Bruck simulator, where reaction rates for reactions with custom reaction rate expressions, were being recomputed after every iteration. Now, a dependency tree is built of the reaction's rate expression. The reaction rate is then recomputed only when one of the dynamical elements it is dependent upon, has changed.
  • Split the Tau-Leap simulator into two separate simulators, taulea-complex and tauleap-simple. This allows for using different algorithms for calculating the leap time, for complex and simple models.
  • Made some speed improvements to the stochastic simulators, in the method where the species populations are updated as a result of a reaction event.
  • Fixed a problem with the delayed reaction solver where the delay was artificially long in some cases.
  • Modified the RegisterSBWSimulators program so that it prints out a message indicating that the simulators have been registered with the SBW Broker.
  • Added a new program LaunchSBWSimulators that both registers and launches the SBW interface to the simulators.
1.6.3 2004/03/26
  • Fixed a bug in the SBML model reader, that was reported by Adam Margolin. This bug would cause an error in some cases, where there are more boundary species than dynamical species in a model.
  • Improved the speed of the Gillesipe Tau-Leap simulator, for large models with complex reaction rate expressions.
  • Made some speed improvements to the mathematical expression evaluation engine, which will improve the performance for simulating models with complex rate expressions, as well as the Gillespie Tau-Leap simulator.
1.6.2 2004/03/22
  • Implemented expression value caching for the deterministic simulators. This improves simulation performance for complex models containing nested sub-expressions. Slightly improved the speed of simulations of models containing deferred-evaluation expressions.
  • Modified the stochastic simulators so that if the initial value for a dynamic species is not an integer, the simulator will use the random number generator to select the nearest integer, in a weighted fashion, so that on average the initial value is equal to the floating-point value specified.
  • Fixed a bug in runmodel program, such that the output file format specified on the command-line was being ignored.
  • Fixed a problem with the way that reaction rates were being computed, for the rare corner-case of a fractional non-dynamic (boundary) species population, in the stochastic simulators.
1.6.1 2004/03/12
  • Fixed some instability problems with the Gillespie Tau-Leap stochastic simulator.
  • Made some speed improvements to the Gillespie Tau-Leap stochastic simulator.
1.6.0 2004/03/10
  • Added a new stochastic simulator "gillespie-tauleap", that can obtain an approximate solution of the chemical master equation, according to an accuracy parameter that is specified by the user. This simulator is potentially faster than the "gillespie-direct" simulator, because it can take large jumps in time, that will involve many reaction steps, in one iteration of the simulator.
  • Added a feature whereby the "runmodel" program is capable of computing the steady-state fluctuations of any of the dynamical species in the model, as an optional post-simulation computation. This feature is activated using the optional "-computeFluctuations" command-line argument.
  • Made some speed improvements to the delayed reaction solver, for the case of stochastic simulations.
  • Fixed a bug the chemical model definition language (CMDL) parser, where a symbol defined within an included file, would never appear as a species in the containing model, even if it is included as a participant in a reaction.
  • Fixed a bug in the deterministic ODE solvers, for the case of a model with a delayed reaction with a large time delay, and a large stopTime parameter for the simulation. In such cases, the initial step size could be too large for the delayed reaction solver to handle, which would cause the simulation to fail with an exception.
  • Fixed a problem in the simulation engine, that was causing stochastic simulations with a non-integer initial value for species populations, to become unstable.
1.5.2 2004/02/25
  • Fixed a problem with the translation of CMDL (".dizzy") model descriptions into SBML. Kinetic Laws and other formulas are now correctly output to SBML, with the species symbols in the formulas representing concentrations, rather than substance amounts.
  • Slightly improved performance by some code refactoring in the simulation engine.
  • Fixed a problem whereby formulas in imported SBML models were not being interpreted correctly by the simulator; species symbols were not being interpreted as representing a concentration.
  • Fixed a problem with the script; it was not working, due to changes to the SBML reader in the 1.5.0 release.
1.5.1 2004/02/24
  • Fixed several bugs in the behavior of the progress indicator bar and the "secs remaining" text field, in the simulation launcher frame. The progress indicator and "secs remaining" text field should now behave properly when the "pause", "cancel", and "resume" buttons are used to control the simulation.
  • Modified the simulation launcher frame so that the progress indicator and the "secs remaining" text field are always visible, not just when a simulation is running. This reduces annoying flicker of the user interface controls when a simulation starts and stops.
1.5.0 2004/02/13
  • Added a graphical progress bar and a text field indicating the estimated number of seconds for the simulation to complete, to the simulation launcher window.
  • Added the ability to the runmodel command-line program, to print periodic status reports on the progress of the simulation, to standard error (stderr).
  • Made several changes to the simulation engine and expression-evaluation code, to improve the speed of simulations.
  • Removed redundant step in the implementations of the stochastic simulators (Gillespie and Gibson-Bruck), where the expression value caches were being cleared twice.
  • Fixed a problem in the jfreechart.jar library, which was causing "class definition not found" error messages to be written to the console, upon start-up of the Dizzy application.
1.4.4 2004/02/10
  • Fixed a bug in the deterministic simulators based on the OdeToJava ODE solvers, in which the simulators were failing to delete the temporary file containing the simulation results. This was cluttering up the temporary files directory with old (unneeded) data files.
  • Added a new launcher runmodel in the bin subdirectory of the Dizzy installation directory. This launcher is designed to launch the command-line interface to Dizzy, without needing any prior user configuration.
  • Simplified the script, to make user configuration easier.
  • Removed the runmodel.bat script, because it is superseded by the runmodel launcher.
1.4.3 2004/02/06
  • Created a new program "SimulationLauncherCommandLine" that runs a simulation in batch mode, saving the results to a file that the user specifies. The "" and "runmodel.bat" scripts now run this batch mode simulation program, instead of the old program that would open a simulation launcher window.
  • Fixed a bug in the command-line parsing for the Dizzy command-line applications "ModelLoaderApp" and "SimulationLauncherCommandLine", causing an error when a very short command-line option is passed to the parser.
  • The Dizzy application now prints out the total number of iterations that occurred in the simulation, to the console window, after the simulation completes.
  • The "ensemble size" and "min number of time steps" simulation parameters are now "long" integer parameters.
  • Fixed a bug in the runmodel.bat batch file.
1.4.1 2004/02/05
  • Fixed a bug where if the user had made a change to the model definition editor buffer, and then selected "Open..." from the "File" menu, the application would disregard the user's answer to the subsequent confirmation dialog box. If the user answered "no" to the prompt for whether to proceed, the application would still open the file and discard the previous edits to the buffer.
  • Modified the simulator engine to prevent huge unnecessary memory allocations when performing a stochastic of a models with an extremely large number of reactions and species. This potentially improves performance in such cases by avoiding the use of large amounts of swap space on the disk drive.
  • Fixed a problem where the application was not properly handling the exceptional case of the system running out of memory during the initialization of a simulator.
  • Modified the simulation launcher so that when the user clicks on the "start" button, the response of the button control is immediate. In cases of very large and complex models and certain simulators (namely, "gibson-bruck"), initialization was taking a long time, which was delaying the response of the button control. Now, initialization of the simulator is performed in the background, just prior to execution of the actual simulation.
  • Modified the simulation launcher to rename the "stop" button to the "pause" button.
  • Changed the way that the deterministic simulators handle delayed (or multi-step) reactions, to improve numerical stability and performance.
  • Modified the "odeToJava-dopr54-adaptive" simulator, so that it is now possible to pause or cancel a running simulation within this simulator.
  • Removed support for the functions gammaln() and rand() in mathematical expressions. The rand() function causes problems with the expression value cachying feature introduced in version 1.4.0, and the gammaln() code is likely encumbered with license issues.
1.4.1 2004/02/02
  • Fixed a bug in the CMDL command language parser, where an exception is thrown if an include directive occurs after a symbol definition.
  • Modified the CMDL command language parser so that it gives a more comprehensible error message if the user attempts to define a symbol name that is reserved for a default model element.
1.4.0 2004/01/30
  • For complex models (many symbols defined as complex expressions), increased the speed of the stochastic simulators by a factor of five. Slightly improved the speed of the simulators for the case of simple models (all elementary reactions, no custom reaction rates).
  • Modified the simulation launcher so that it remembers the directory of the last output file selected, when the output type is "File".
  • Modified the simulation launcher so that the Cancel/Stop/Resume buttons are disabled in the OdeToJava simulators, which do not allow interruption by the simulation launcher.
  • Modified the simulation launcher so that different comma-separated-output (CSV) output file formats are supported, for saving simulation results to a file. Currently there are three options: CSV-excel, CSV-gnuplot, and CSV-matlab. The only difference currently is the choice of character that is used to designate the "comment" line, which is the first line of the output file. This also makes it more clear that the choice of "File" output type, refers to a comma-separated-value file format.
  • Added a new "view model in human-readable format" feature which displays a model description in "human-readable" format, in a dialog box. Added an exporter plug-in so that it is possible to save the model description in the same human-readable format to a file, using the "Export" menu item.
  • Modified the command language parser to fix a hard-to-understand error message that occurs when there is a syntax error inside nested loops.
  • Modified the simulation launcher to permit the user to optionally specify a texual label that is added as a subtitle to the simulation results plot.
  • Fixed a bug in the on-line help search screen where the "jump to next search hit" feature was not working for any searches after the first search.
  • Added a text area to the on-line help search screen, that explains the "jump to the next search hit" feature.
1.3.1 2004/01/27
  • Fixed a bug in the command language parser, which was causing parser errors when a macro definition contains a loop construct.
  • Fixed a bug in the command language parser, which was causing parser errors when a loop construct directly precedes a reaction definition statement.
  • Modified the command language parser to allow the value of a symbol to be redefined, as long as the symbol has not been promoted to a Species, Reaction, Parameter, or Compartment at the point where the value of the symbol is redefined. The purpose of this feature is to permit the user to define a template definition with an "output" parameter.
1.3.0 2004/01/26
  • Added a template feature to the Chemical Model Definition Language (CMDL).
  • Improved the efficiency of the first pass of the command-language parser. Improved syntax error detection in the command-language parser.
  • Fixed a bug in the SBML parser where it was not catching the case of a parameter defined without any value (or parameter rule) being provided. This was leading to the application aborting unexpectedly, when a SBML file is loaded containing this type of semantic error.
  • Added support to the SBML reader for reading an SBML model containing a reaction with an intrinsic time delay. The kineticLaw must conform to a strict format rule. The application can now export (to SBML) a model containing a time delay, and read the model back into the simulator.
  • Improved error handling by adding debugging code to the console, in cases of exceptions. The application should no longer abort when an unexpected exception occurs in processing a model.
  • Modified the SBML writer so that it can properly export a model containing a reaction with an intrinsic time delay.
1.2.0 2004/01/13
  • Fixed the problem with the Dizzy installer for the Mac OSX platform, where the installed application launcher would crash with an "unexpected error" dialog box message.
  • Fixed a bug in the layout of the simulation launcher control screen, where the full text of the "select all" button was not being displayed.
  • Fixed a bug in the simulation launcher where the simulation was not being cancelled, in the case where the user selects too many symbols for displaying on a plot.
  • Fixed a bug in the chemical model definition language (CMDL) parser where the application was aborting when the parser encountered a mathematical expression that has invalid syntax.
  • Fixed a bug in the chemical model definition language (CMDL) parser where parsing errors in the model definition file were resulting in the exception class name being unnecessarily included in the message part of the exception.
  • Changed the simulation results plotter so that the vertical axis label is the more generally applicable "value" rather than "populations".
  • Added a new Systems Biology Workbench (SBW) simulation service, for the Gibson-Bruck stochastic simulation algorithm.
  • Modified the "Register SBW Simulators" program so that it registers services for all three supported simulators: Gibson-Bruck, Gillespie, and Deterministic.
  • Implemented a work-around for an InstallAnywhere bug, so that the Dizzy program now launches correctly when installed on a Mac OSX computer.
  • The InstallAnywhere installer for Dizzy now logs error messages to a log file "insDizzy.log".
  • Fixed a bug where the "copy to clipboard" button was failing to be displayed in the simulation results plot window on the Windows platform, in some cases.
  • Fixed a bug where selecting "view in Cytoscape" with a syntactically incorrect model in the editor pane, leads to a NullPointerException.
  • Fixed a bug where models were not displaying correctly within Cytoscape, since version 1.0.0. This is because the Cytoscape SBML reader requires SBML Level 1, version 1.
  • Fixed a bug where the "Save As..." menu item was not being enabled under the correct conditions (it should be enabled whenever the editor buffer is not empty).
  • Fixed a bug where the "Reload model" feature was not working properly.
1.1.1 2004/01/05
  • Modified the delayed reaction solver so that the internal running window average is recalculated from scratch, each time a minimum number of points (default 4000) has been inserted into the queue.
  • Fixed a file-loading bug pertaining to the case where the model builder fails to construct the model from the model definition file.
  • Modified the simulation launcher to dump a stack backtrace to the terminal window if a low-level error condition is detected.
  • Generalized the multi-step reaction solver into a "delayed" reaction solver, to permit phenomenological modelling of reaction processes with an intrinsic time delay.
  • Changed the command language model builder to add language extensions for specifying a multistep or delayed reaction.
  • Fixed bugs in the main editor window and the plot window, where window resizing was not working correctly on the Windows platform.
  • Removed unnecessary label from main editor window, which was taking up space on the screen.
1.1.0 2003/12/22
  • Added a reload menu item, which is used for reloading the model that is currently in the editor window, into the simulation launcher. It replaces the model that is currently loaded into the simulation launcher.
  • Fixed a bug in the simulation launcher, where it would still display a graph even when the simulation was cancelled.
  • Made the simulation plot window dynamically resizable.
  • Made the main editor window dynamically resizable.
  • Added a hook to the simulation launcher so that an external application can dynamically replace the model loaded in the simulation launcher.
  • Added a hook to the simulation launcher so that an external application can detect when a simulation starts or ends.
  • Fixed bug where the Dizzy command language interpreter was rejecting model definition files that ended with whitespace.
  • Added an "append" check-box to the simulation launcher window, which allows for specifying that the output file should be appended to, rather than overwritten.
  • Added a "save as PNG image" button to the simulation results plot window, which is used to save the plot as a PNG image file.
  • Modified the simulation launcher to display all symbols (not just species) in the list-box of symbols that can be displayed in the simulation results.
  • Modified the simulation launcher to allow for an external application to hide the Output Type controls, and added a callback mechanism to return the simulation results to the calling application using a queue data structure.
  • Added support for copying the simulation results plot image to the system clipboard, on operating systems that support image transfer to the clipboard (e.g., Windows).
  • Added full-text search capability for the online application help.
  • The application help frame is now initially centered in the screen.
  • Added a "select all symbols" feature to the simulation launcher.
1.0.0 2003/12/08
  • Added new deterministic (ODE) simulators Dizzy, based on the "odeToJava" library for numerical solution of ODEs. This library includes a Dortmand-Prince 4/5 Runge-Kutta solver with adaptive step-size control, and an implicit/explicit Runge-Kutta solver with adaptive step-size control (for models with a high degree of stiffness).
  • Modified the SBML reader to permit inclusion of "rules" in SBML models
  • Modified the SBML writer to export models in SBML level 1, version 2.
  • Fixed a bug in which the operation does not terminate, when model-building fails after the user selects "Export" from the "Tools" menu.
  • Created separate fields in the SimulationLauncher for specifying the matximum allowed relative and absolute errors
  • Fixed a bug for the case of a parameter defined as a deferred-evaluation expression
0.0.8 2003/11/21
  • Modified the fixed-stepsize deterministic simulator so that it can detect when the simulation error exceeds a certain threshold, and produce a human-comprehensible error message (the message suggests that the step-size be decreased).
  • Modified the "simulation launcher" pane so that it has text-box controls for specifying separate simulator-specific parameters, such as the ensemble size, the minimum number of steps, and the maximum allowed fractional error. Default values are auto-filled in these new fields, depending on the type of simulator selected. The "ensemble size" and "number of steps" are now separate fields.
  • The "plot" output type no longer gives a strange error message when a "NaN" (not-a-number) appears in the simulation output. It now gives a more human-comprehensible error message.
0.0.7 2003/11/07
  • Modified the editor pane so that it "remembers" the directory of the last file that was opened; the default directory for the file chooser for the next "open" command, is set to this directory.
  • Fixed a problem where the ISB and Bolouri Lab logo images were not displaying in the on-line help screen, when the computer is not connected to the network.
  • Removed the table of contents from the HTML User Manual used in the on-line help (the JavaHelp environment provides its own table of contents).
  • Adjusted the default vertical dimension of the editor pane for the model editor, to 40 characters.
0.0.6 2003/10/22
  • In the Dizzy simulation launcher form, made "Plot" the default output mode
  • Redefined how the stochastic simulators compute reaction rates for dimerization reactions, for model interchangability with the ODE simulators.
0.0.5 2003/10/20
  • Fixed a bug in the Gibson-Bruck simulator, for the case of a boundary reactant species.
  • Fixed a bug in the command-language parser, it can now accept tabs as valid whitespace in the model definition file.
  • The SBML import feature can now process model definition files that conform to the SBML Level 1, Version 2 specification.
  • Fixed a bug in which Dizzy would fail to start, in the case where Dizzy was installed in the top-level directory of a Windows (or DOS) drive.
  • Redefined how the stochastic simulators compute reaction rates for dimerization reactions, for model interchangability with the ODE simulators.
0.0.4 2003/08/28 Modified the Cytoscape bridge to use JNLP, so Cytoscape does not have to be bundled with the application 0.0.4
0.0.3 2003/08/26 Added the ability to simulate a multistep chemical reaction as a single composite reaction 0.0.3
0.0.2 2003/08/06 Added the ability to display a model in a Cytoscape window. 0.0.2
0.0.1 2003/08/04 First version of the program. It is an alpha version, intended only for internal use at Institute for Systems Biology. 0.0.1

Last updated: 2006/09/28 21:08:36

Please e-mail comments or corrections regarding this document to: dizzy NOSPAM at NOSPAM