--- Release notes CatReNet V0_9_3 (Tue, 9 Apr 2024): --- - added support for display labels --- Release notes CatReNet V0_9_2 (Wed, 3 Apr 2024): --- - added features - bug features - extended author list - added prokaryotic example --- Release notes CatReNet V0_9_1 (Fri, 15 Mar 2024): --- - renamed to CatReNet --- Release notes CatlyNet V0_9_0 (Sun, 3 Mar 2024): --- - renamed to BioRAF --- Release notes CatlyNet V0_8_15 (Sun, 28 Jan 2024): --- - more work on allowing multiple target molecules in min-RAF generating target elements algorithm - updated JavaFX and cleaned up some dependencies --- Release notes CatlyNet V0_8_14 (Fri, 26 Jan 2024): --- - allow multiple target molecules in min-RAF generating target elements algorithm --- Release notes CatlyNet V0_8_13 (Thu, 30 Nov 2023): --- CRITICAL UPDATE - the previous installer installs a program that fails to launch --- Release notes CatlyNet V0_8_12 (Sun, 1 Oct 2023): --- - added licenses --- Release notes CatlyNet V0_8_11 (Fri, 29 Sep 2023): --- - fixed bugs in PDF and SVG export --- Release notes CatlyNet V0_8_10 (Thu, 7 Sep 2023): --- - added options to plain text output of distances --- Release notes CatlyNet V0_8_9 (Thu, 24 Aug 2023): --- -fixed bug that caused interactive changes to food set or reactions to be ignored sometimes --- Release notes CatlyNet V0_8_8 (Wed, 23 Aug 2023): --- CatlyNet: -fixed bug that caused objects to appear in wrong order in SVG and PDF export files --- Release notes CatlyNet V0_8_7 (Mon, 21 Aug 2023): --- - fixed bugs in network coloring dialog - replaced Poisson by Binomial in polymer model --- Release notes CatlyNet V0_8_6 (Wed, 16 Aug 2023): --- - fixed minor fatal bug in polymer model tool output --- Release notes CatlyNet V0_8_5 (Mon, 14 Aug 2023): --- - added command-line program for generating instances of the polymer model --- Release notes CatlyNet V0_8_4 (Thu, 10 Aug 2023): --- - fixed bug that prevented of importing of data when there are multiple possible parsers and one failed --- Release notes CatlyNet V0_8_3 (Thu, 10 Aug 2023): --- - implemented first version of polymer model generator - fixed some bugs --- Release notes CatlyNet V0_8_2 (Wed, 9 Aug 2023): --- - fixed several bugs associated with exporting text and files - added text input field for use with --- Release notes CatlyNet V0_8_1 (Wed, 9 Aug 2023): --- - fixed bug that caused *No Empty* message - turned off notifications by default --- Release notes CatlyNet V0_8_0 (Tue, 8 Aug 2023): --- - fixed recent bug that caused program to choke on networks with colors --- Release notes CatlyNet V0_7_3 (Mon, 7 Aug 2023): --- - fixed several bugs --- Release notes CatlyNet V0_7_2 (Mon, 7 Aug 2023): --- - added Min RAF-Generating Given Element Algorithm - more work on online description - (Internal update: removed swing dependencies) --- Release notes CatlyNet V0_7_1 (Wed, 2 Aug 2023): --- - minor bug fixes --- Release notes CatlyNet V0_7_0 (Wed, 2 Aug 2023): --- - improved user interface - moved from ant build to maven build --- Release notes CatlyNet V0_6_3 (Sat, 22 Jul 2023): --- - reorganized menus and renamed graph to network - fixed bug associated with computing network --- Release notes CatlyNet V0_6_2 (Fri, 21 Jul 2023): --- - reorganized menus and renamed graph to network - fixed bug associated with computing network --- Release notes CatlyNet V0_6_1 (Tue, 11 Jul 2023): --- - added some tool-bar items - updated the icon - migrated code from jloda to jloda2 --- Release notes CatlyNet V0_5_4 (Tue, 11 Jul 2023): --- - added View->List menu that contains items for listing food, reactions, reactants, products, catalysts and inhibitors --- Release notes CatlyNet V0_5_3 (Tue, 4 Jul 2023): --- - Removed Strongly Autocatalytic Max RAF calculation - Removed Partially Autocatalytic Max RAF calculation - Added Strictly Autocatalytic Max RAF calculation - this produces the Max RAF of all reactions that require at least one non-food-set item as catalyst - added wrap button for input food and reactions panes --- Release notes CatlyNet V0_5_2 (Mon, 3 Jul 2023): --- - Added Strongly Autocatalytic Max RAF calculation - Added Partially Autocatalytic Max RAF calculation --- Release notes CatlyNet V0_4_1_beta (Mon, 20 Mar 2023): --- - now supports reactions that do not mention a catalyst. - for reactions that do not mention a catalyst, a special food item $ is inserted into the food set and is then used to formally catalyze the reaction. Other reactions may mention $ also, and they will then always be catalyzed - The previous dependency graph is now called association graph - Added calculation of actual dependency graph, putting an edge from r to s if r is essential for s - The dependency graph algorithm is currently too slow for CRS that contain many reactions --- Release notes CatlyNet V0_5_1 (Tue, 7 Feb 2023): --- -- fixed update URL --- Release notes CatlyNet V0_5_0 (Sat, 17 Sep 2022): --- - added command line program to MacOS and Linux distributions, run catlynet/tools/catlynet-tool to see all command line options - updated JDK - minor improvements --- Release notes CatlyNet V0_4_0_beta (Sat, 12 Feb 2022): --- - supports MacOS M1 chip - improved dark mode --- Release notes CatlyNet V0_3_1_beta (Fri, 18 Dec 2020): --- - fixed bug that prevented *formnat nodes and edges* dialog from reopening after closed. --- Release notes CatlyNet V0_3_0_beta (Thu, 17 Dec 2020): --- CatlyNet: - added Edit->Preferences->Format Nodes and Edges dialog for setting shapes, colors, size and line width --- Release notes CatlyNet /V0_2_10_beta (Wed, 17 Jun 2020): --- - fixed bugs that caused some food nodes not to fire when using *multicopy food nodes* in visualization and animation - reduced the level of clustering of molecules in animation --- Release notes CatlyNet /V0_2_9_beta (Mon, 15 Jun 2020): --- - now use circles to represent molecules and squares to represent reactions, as this is what most papers on RAF theory do (if you want me to implement a switch to allow one to change the shapes used to represent different entities, then please let me know) - minor bug fixes --- Release notes CatlyNet /V0_2_8_beta (Wed, 20 May 2020): --- - don’t create tab for empty reaction system - added colors and text/circle options for animation --- Release notes CatlyNet /V0_2_7_alpha (Wed, 13 May 2020): --- - If Windows version doesn’t start after this update, please completely uninstall and then reinstall - Updated to openjdk14/jdk-14.0.1+7 and OpenJFX 14 - Added computation of CoreRAF - Reuse -compute importance- setting when opening new window --- Release notes CatlyNet /V0_2_6_alpha (Wed, 22 Apr 2020): --- - Fixed bug in parser that for some reaction formats caused incorrect number of reactions in MaxCAF, MaxRAF and other calculations - Simplified internal representation of catalysts --- Release notes CatlyNet /V0_2_5_alpha (Sun, 19 Apr 2020): --- - Reimplemented core code so as to not require use of dummy reactions --- Release notes CatlyNet /V0_2_4_alpha (Sun, 19 Apr 2020): --- - Reimplemented core code so as to not require use of dummy reactions --- Release notes CatlyNet /V0_2_3_alpha (Sat, 18 Apr 2020): --- - If windows version doesn’t start after update, please completely uninstall and then reinstall - Updated to Liberica JDK 13.0.2+9 and OpenJFX 14 - added new Export List of Reactions menu item to allow export of specified reactions to a new file --- Release notes CatlyNet /V0_2_2_alpha (Fri, 17 Apr 2020): --- - labeled this an alpha release because some major bugs are still appearing - fixed bug in processing of complex catalyst expressions that caused errors in the MaxCAF calculation. - modified animation to prevent overfilling - added calculation of all trivial CAFs and all trivial RAFs - fixed bug in activation of Find tool bar - implemented select from previous window menu item --- Release notes CatlyNet /V0_2_1_beta (Mon, 13 Apr 2020): --- - Updated to Liberica JDK 13.0.2+9 - JDK now also bundled on linux platform - Fixed bugs in quit command on linux and windows --- Release notes CatlyNet /V0_2_0_beta (Thu, 9 Apr 2020): --- - implemented algorithm removing trivial RAFs --- Release notes CatlyNet /V0_1_8_beta (Wed, 8 Apr 2020): --- - fixed bugs and added improvements in graph construction and node selection - implemented first version of heuristic for removing trivial RAFs --- Release notes CatlyNet /V0_1_7_beta (Sun, 5 Apr 2020): --- - reimplemented Min Irr RAF heuristic - implemented quotient RAF algorithm - modified Export menu items so as to ask whether exported reaction system should be opened in a new window - fixed a bug in code that determined with original food molecules are mentioned in a computed reaction system --- Release notes CatlyNet /V0_1_6_beta (Tue, 31 Mar 2020): --- - add experimental version of heuristic for finding a minimum irreducible RAF --- Release notes CatlyNet /V0_1_5_beta (Fri, 27 Mar 2020): --- - add experimental version of *greedily grow maxCAF to maxRAF* algorithm, requires testing --- Release notes CatlyNet /V0_1_4_beta (Wed, 18 Mar 2020): --- - fixed bug in *check for updates* menu item that caused program to hang --- Release notes CatlyNet /V0_1_3_beta (Mon, 9 Mar 2020): --- - fixed bug in construction of dependency graphs - added export selected nodes feature - added select connected component feature - minor bug fixes --- Release notes CatlyNet /V0_1_2_beta (Fri, 21 Feb 2020): --- - bug fixes --- Release notes CatlyNet /V0_1_1_beta (Fri, 21 Feb 2020): --- - fixed bug in graph construction for catalysts with conjunctions --- Release notes CatlyNet /V0_1_0_beta (Fri, 21 Feb 2020): --- - Implemented visualization of *dependency graph* visualization. There are two ways to define dependency between two reactions R1 and R2: 1) R2 requires a product from R1 as an input reactant or input catalyst (or inhibitor), or 2) R2 requires a product from R1 as an input reactant. Both are implemented, (1) is called a Dependency Graph and (2) a Reactant Dependency Graph. - Double-clicking on a node will select all adjacent nodes and edges - Triple-clicking on a node will select the connected component containing the node - Dragging a selected node will now also drag all other selected nodes --- Release notes CatlyNet /V0_0_25_beta (Thu, 20 Feb 2020): --- - added option for exporting RAF, CAF etc - added option for hiding catalysts (to simplify graph) - added option for representing food by multiple nodes (to simplify graph) - implemented copy menu item for graph --- Release notes CatlyNet /V0_0_24_beta (Mon, 17 Feb 2020): --- - fixed bug that prevented parsing of reactions when molecule names consist of numbers. - now, molecules can have coefficients as long as all molecules have non-number names - if molecule names are numbers, then coefficients are not allowed - fixed some problems associated with visualization of graph --- Release notes CatlyNet /V0_0_23_alpha (Thu, 6 Feb 2020): --- - Fixed major bug that caused incorrect RAF to be computed - Can now process (and ignore, for now) coefficients for reactants and products - Worked on GUI --- Release notes CatlyNet /V0_0_22_alpha (Wed, 29 Jan 2020): --- - added support for arbitrary boolean expressions for catalysts involving and (ampersand), or (comma) and brackets (but no negation) - fixed numerous bugs involving open windows - computation of importance now optional - faster graph layout (parallelized algorithm) - graph labels now optional --- Release notes CatlyNet /V0_0_21_alpha (Mon, 13 Jan 2020): --- - fixed bug that sometimes prevented program from shutting down on quit --- Release notes CatlyNet /V0_0_20_alpha: --- - changed hosting URL - minor fixes --- Release notes CatlyNet /V0_0_19_alpha: --- - added a heuristic for computing a canonical uninhibited RAF --- Release notes CatlyNet /V0_0_0_alpha: --- - Very first version of CatlyNet - This is bare bones, doesn't support *and* conditions on catalysts - Doesn't support multiple file formats - Doesn't provide visualization - Does do maxCAF, maxRAF and maxPseudoRAF calculation