/******************************************************************************* * ProMoT * --------------------------------------------------------------------------- * Copyright (c) 1997-2012 ProMoT Development Team * Max Planck Institute Magdeburg, Germany * http://www.mpi-magdeburg.mpg.de/projects/promot * * This is free software; you can redistribute it and/or modify it * under the terms of the GNU General Public License as published * by the Free Software Foundation; either version 2 of the License, or * any later version. * * THIS SOFTWARE IS DISTRIBUTED IN THE HOPE THAT IT WILL BE USEFUL, * BUT WITHOUT ANY WARRANTY; WITHOUT EVEN THE WARRANTY OF * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. * IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF * SUCH DAMAGE. * * You should have received a copy of the GNU General Public License * along with this library; if not, write to the Free Software Foundation, * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. * * --------------------------------------------------------------------------- * $Id$ ******************************************************************************/ ------------------------------------------------------------------- v-0-4-0 ------------------------------------------------------------------- - Initial revision of PROMOT version 4 - PROMOT ported to CVS - Object-oriented language definition of MDL - New version of FrameTalk (weak, strong parts, link-from) ------------------------------------------------------------------- v-0-4-1 ------------------------------------------------------------------- - `Component' renamed to `module' ------------------------------------------------------------------- v-0-4-2 ------------------------------------------------------------------- - mexpr.lisp: CG parser extended to slot paths - In mexprs. variables are no longer represented as objects, but as instances of slot-path. - promot-link introduced. The command option `:links' is no longer mapped to FDL. promot-link is rather used as strong parts. This led to major changes in the generation of link equations. ------------------------------------------------------------------- v-0-4-3 ------------------------------------------------------------------- - mdl.lisp: bug fixed when generating weak parts for mexprs in indices - format-mexpr.lisp: now also generates LaTeX code - First steps to implement module arrays ------------------------------------------------------------------- v-0-4-4 ------------------------------------------------------------------- - First version of implementing terminal arrays: This implementation is not based on FDL slot arrays. It does not allow the splitting of terminal arrays into single terminals, which is a must! ------------------------------------------------------------------- v-0-4-4 ------------------------------------------------------------------- - Fixed bug in sort-dependency-p (model.lisp). - The call to sort-dependency-p was not symmetric. ------------------------------------------------------------------- v-0-4-5 ------------------------------------------------------------------- - Removed sort-dependency-p. - Sorting variables according to their dependencies with LISP `sort' was buggy. - Reason: If a>b and b>c, it cannot be concluded that a>c! - Now: 1) the dependency lists of all variables are agglomerated 2) the total dependency graph is traversed by depth-first search 3) the nodes that are traversed last are printed first + additional alphabetic sorting of `all-direct-variables' in `dependency-list' (roots-mixins.lisp) ------------------------------------------------------------------- v-0-4-6 ------------------------------------------------------------------- - Coupling, propagation of vector terminals now running for - Two-phases, three-phases in kb/test-arrays.mdl - For this: model-name determination completely revised - path-indices-* methods introduced - Module arrays now running, at least for all modules in `test-arrays.mdl' - Terminal arrays now running, at least for all modules in `test-arrays.mdl' - Complete revision of - roots-mixins.lisp: path-indices-* - model.lisp: model-direct-identity-equations - Lots of other changes, bug fixes, I can't remember ------------------------------------------------------------------- v-0-4-7 ------------------------------------------------------------------- - Output of variables with :report attribute Now uses :x-scope, :y-scope, :z-scope in define-process-values ------------------------------------------------------------------- v-0-5-0 ------------------------------------------------------------------- - src/graphics/*: First new version of PROMOT Model Editor that runs with FDL - src/kernel/cg.lisp: Better formatting of CG file (Stefan Schwarzkopf) - images/Makefile created - kb/test-suite created for testing new PROMOT versions - Lots of bug fixes ------------------------------------------------------------------- v-0-5-1, 1998-06-04 ------------------------------------------------------------------- - src/kernel/format-mexpr.lisp: Bug fixed when formatting :cond - src/kernel/roots-mixins.lisp: Real and integer parameters are no longer indexed within indexed modules ------------------------------------------------------------------- v-0-5-2, 1998-06-16 ------------------------------------------------------------------- - src/kernel/cg.lisp: format-cg-commands improved - src/kernel/browser-interface.lisp src/kernel/mdl.lisp src/kernel/utilities.lisp src/graphics/browser.lisp src/graphics/editor.lisp src/graphics/mdl-command-viewer.lisp src/graphics/mdl-command-emacs.lisp: MDL commands are formatted in a pretty way for output to command viewer, EMACS or file - src/kernel/mdl.lisp: interprete Mixins of FDL part slot are now sorted alphabetically to avoid circular class precedence lists - src/kernel/optimize.lisp: NEW - Substitute variables rather than generating coupling equations - Substitution of state variables in mexpressions of help variables does not work in general, because of wrong pattern initialization. e.g., pattern is out of bounds in ba-process.cg ------------------------------------------------------------------- v-0-5-3 ------------------------------------------------------------------- - src/kernel/cg.lisp: bug fixed in format-cg-cmd-obj for process-values ------------------------------------------------------------------- v-0-5-4, 1998-09-25 ------------------------------------------------------------------- - Version as of SFB-412 evaluation - report for funding period 1996-1998 - Presentation of kb/hafke/obertopp and kb/distillation (tmm-process, ba-process) - src/kernel/utilities.lisp: print-class-tree writes class tree to stdout - src/kernel/editor-interface.lisp: set-diva-file-names modifies the keywords :diva-cg-file-name, :diva-fortran-files-subname, :diva-data-file-name and :diva-latex-file-name of a module; write-diva-files writes CG files and calls the CG - src/kernel/mdl.lisp: The keywords :diva-cg-file-name, :diva-fortran-files-subname, :diva-data-file-name and :diva-latex-file-name have been added to define-module - src/kernel/roots-mixins.lisp: The slots for :diva-cg-file-name, :diva-fortran-files-subname, :diva-data-file-name and :diva-latex-file-name have been added to promot-class-mixin; modified method cg-filename to determine the default CG filename of a module - src/graphics/*.lisp: Model output to DIVA added ------------------------------------------------------------------- v-0-5-5, 1998-11-03 ------------------------------------------------------------------- - src/graphics/editor.lisp, model-editor.lisp: added output to EPS file - Martin Ginkel starts working on ProMoT - Help variables are no longer written as indexed CG-help variables in the case of indexed modules. They are rather multiply assigned in equation loops. - Support of ACL 5.0 added. src/kernel/error.lisp and src/kernel/mdl.lisp: without-package-locks added because of use of symbols class and type - Bug fixed in src/kernel/roots-mixins.lisp: path-indices Do not generate indices in model name if a variable (strong part of a module) has been propagated to an indexed terminal. Example: kb/bio/speicher-neu.mdl ------------------------------------------------------------------- v-0-5-5-0 ------------------------------------------------------------------- - Inserted a branch into CVS to keep a clean working version This should be a mostly bugfree release, without new errors from the new GUI development. ------------------------------------------------------------------- v-0-5-6, 1999-01-07 ------------------------------------------------------------------- - Development release - src/kernel/mdl2diva reports errors correctly - src/kernel/optimize.lisp does the job of optimizing linked state-variables to help-variables in most cases. For safety reasons it is optional to do this - The Project for the GUI in Java/JFC with connection via ILU has been started - Volker Padur has joined the team, he develops the Java part ------------------------------------------------------------------- v-0-6-0, 2000-06-20 ------------------------------------------------------------------- - The optimizer is broken due to new structures in the kernel - errors.lisp has been renamed into conditions.lisp because we use conditions now for error reporting - The principle of using FDL has changed. ProMoT implements now it's own superclasses. this should be extended for the interactive editing of classes without using MDL. - The Java GUI has now almost the same functionality as the Clim one - Clim is still possible but I will stop the development on it - Images and scripting is now written to run almost automatical ------------------------------------------------------------------- v-0-6-0-0 ------------------------------------------------------------------- - New stable version instead of v-0-5-5 - Optimizer is ok now - Emacs and Java should work together through the old interface - Still some bugs in the GUI ------------------------------------------------------------------- v-0-7-0, 2004-11-09 ------------------------------------------------------------------- - ------------------------------------------------------------------- v-0-7-1, 2005-05-12 ------------------------------------------------------------------- - ------------------------------------------------------------------- v-0-7-2, 2006-08-16 ------------------------------------------------------------------- - Stable version with new features - SBML support matures - Diana output is fully functional - Support for structural models - Visual exploration of models - Graphical editing of variable values ------------------------------------------------------------------- v-0-8-0, 2008-02-22 ------------------------------------------------------------------- - Many extensions in the GUI - Undo for many commands - Automated layout and model documentation - Automated consistency checking ------------------------------------------------------------------- v-0-8-1, 2008-08-15 ------------------------------------------------------------------- - Import of CNA (CellNetAnalyzer) models - Bug fixes in generation of HTML documentation - (Partial) bug fix for renaming of connected slots (see BUGS.txt for limitations) - Modularization support in visual editing - Bug fixes in the variable editor - Support for import and export of layout information in the ProMoT Explorer - Windows version (since September 2008) ------------------------------------------------------------------- v-0-8-2, 2009-08-17, r8738 ------------------------------------------------------------------- - Priorities on check results of checker - Distinguishing between errors and warnings in checker - Some on-the-fly-checks for dynamic modeling - Copy/paste support in editor - De-modularization support (elevation of a modules content to current level) variables and equations (math), places and transitions (events) not elevated - Flipping of nodes in editor for logical models - Refresh-action in editor - Status bar in editor showing status of the editor and checker - Initial support for synthetic biology by scripts generating mdl - Property to mark exportable models - Setting modules to be ignored in export (logical modeling) - Variable for map-number and monotony in logical library and editable in the GUI - Check of corresponding equation-system for a module, visualization of under- and/or overdetermined parts in incidence matrix or visual editor - Improved visual scenario editor in explorer - Improved support for workflow CellNetAnalyzer - Warning for unsaved changes on exit - Command for creation of new models - Reduced clutter in menus and toolbars - Dialogs and control panels reworked for clarity and utility - New ProMoT logo - Documentation updates ------------------------------------------------------------------- v-0-8-3, 2010-08-31, linux: r9285, win: r9303 ------------------------------------------------------------------- New Features - Option for direct loading of libraries for logical and dynamic modeling - Start simulation with Diana from ProMoT GUI - Parametrize model with Diana - Comparison of models and visualization of comparison results - Layout algorithm to visually flatten the model in Visual Explorer - Logical model of EGF receptor signaling added to knowledge base Improvements - Update libraries for logical and dynamic modeling (directions, SBO terms) - Scripts for conversion of models to updated libraries - Refactoring of rename of terminals in Visual Editor - Recalculation of terminal positions after changing canvas size in Visual Editor - Create links of submodules automatically by names in Visual Editor - Set the map number to a selection of nodes (only logical modeling) - Warning of redefinition of classes - Import/export of node/edge attribute files in Visual Explorer - Hierarchy Zoom for edges, Zoom along edge - FishEye Zoom considers edge handle points - Flexible handling of visibility of node/edge labels in Visual Explorer - Extend node size to label text in Visual Explorer - Improved scenario 'Logical Network' - Visualization of submodules with/without terminals - Export network to yEd format - Improved exception handling in ProMoT - Documentation updates Bugfixes - SBML import/export (import events, reversible flag, compartment handling) - Stability issues of Visual Explorer - Correct rendering of edge arrows in Visual Explorer - Update view after attribute file is imported in Visual Explorer ------------------------------------------------------------------- v-0-8-4, 2011-08-21, r9456 ------------------------------------------------------------------- New Features - ACL 8.2 is now used - New global scenario 'Hierarchical Level' for visualization Improvements - New build procedure and ProMoT is now installed under \usr\local\promot instead of \usr\local\diana\promot - Update Piccolo2d to version 1.3.1 - Documentation updates - Extend model statistics report in explorer: Edges with TimeScale > 1, Edges with LogicalExcluded = 1 - reduced-library.mdl: special concentration module with additional variable (conc-sink-var) Bugfixes - Corrected paths of some mdl files in the knowledge base - Corrected 'Create link' dialog (automatic connection of terminals on submodules) ------------------------------------------------------------------- v-0-8-5, 2012-0?-??, r???? ------------------------------------------------------------------- New Features - ACL 9.0 is now used - Support of the Process-Interaction-Model concept by the Process-Interaction-Library and model specialized model converters (export of rule-based models in BNGL from a PIM, conversion of PIMs to site-specific logical models) documented in a new tutorial - Extended Visual Scenarios: add options for layout and exploration schemes Improvements - Menu item, tooltips and shortcuts are added and more consistent Bugfixes - to be announced