| cdb27a7 | Ali Sinan Saglam | 16 May 2019, 17:55:00 UTC | Working on new branch to add bng version checking and a simple mechanism for auto-updates to BNG | 16 May 2019, 17:55:00 UTC |
| ab0bf4c | Ali Sinan Saglam | 16 May 2019, 17:52:31 UTC | Made BioNetGen folder version agnostic to make it easier to keep it updated and not to hardcode the version number. Also in preparation for future changes to determine version number from the BNG distribution and automated BNG update checking. | 16 May 2019, 17:52:31 UTC |
| f48644e | Ali Sinan Saglam | 16 May 2019, 17:51:43 UTC | Updated BNGParser | 16 May 2019, 17:51:43 UTC |
| bd828c6 | Ali Sinan Saglam | 16 April 2019, 18:09:32 UTC | Fixes a bug where if you selected recover workspace, you can't get switch workspace dialog again because a variable doesn't get reset | 16 April 2019, 18:09:32 UTC |
| 9e7f88e | Ali Sinan Saglam | 16 April 2019, 18:06:56 UTC | This try wasn't throwing an IOException, leading to a compiler error | 16 April 2019, 18:06:56 UTC |
| 54a27a5 | Ali Sinan Saglam | 15 April 2019, 17:48:02 UTC | Updated README with installation instructions Moved build process into a separate file, added links to release page as well as direct links to the released builds | 15 April 2019, 17:48:02 UTC |
| df83509 | Ali Sinan Saglam | 15 April 2019, 17:40:02 UTC | Moving txt files around away from main folder, updating README with installtion instructions | 15 April 2019, 17:40:02 UTC |
| 284bdf1 | Ali Sinan Saglam | 18 January 2019, 20:47:15 UTC | Commented out another debug statement, need to pipe these into logging pipeline | 18 January 2019, 20:47:15 UTC |
| b00b7d2 | Ali Sinan Saglam | 17 January 2019, 22:01:29 UTC | Added a null check for when visualization fails | 17 January 2019, 22:01:29 UTC |
| ce5187d | Ali Sinan Saglam | 17 January 2019, 21:13:39 UTC | Removed unnecessary call to a predicate, removed hanging debugging output to the console | 17 January 2019, 21:13:39 UTC |
| e4df726 | Ali Sinan Saglam | 16 January 2019, 16:31:37 UTC | Unhooking the TextHover for 2.3.0 release | 16 January 2019, 16:31:37 UTC |
| 07df96b | Ali Sinan Saglam | 16 January 2019, 16:21:42 UTC | Merge pull request #212 from ASinanSaglam/master Bug fixes, gif to png conversion and text to contact map highlighting | 16 January 2019, 16:21:42 UTC |
| 302fd72 | Ali Sinan Saglam | 16 January 2019, 15:53:49 UTC | Added a check for null in list of rules associated with an edge. This skirts a null ptr error that comes up when an edge without a list of rules is left clicked. | 16 January 2019, 15:53:49 UTC |
| b1e7f55 | Ali Sinan Saglam | 16 January 2019, 15:21:49 UTC | Added text selection highlighing interaction with contact map. Final fix on gif to png conversion | 16 January 2019, 15:21:49 UTC |
| 79cca79 | Ali Sinan Saglam | 16 January 2019, 15:02:58 UTC | Changed java files to use the new png files rather than the old gif icons | 16 January 2019, 15:02:58 UTC |
| 4bdc940 | Ali Sinan Saglam | 16 January 2019, 15:00:10 UTC | Changed view icons to png files from gif, requirement for new Eclipse versions | 16 January 2019, 15:00:10 UTC |
| 95d7a26 | Jim Faeder | 11 January 2019, 22:45:20 UTC | Merge pull request #211 from ASinanSaglam/master Several bug fixes and version uptick | 11 January 2019, 22:45:20 UTC |
| 70f7a21 | Ali Sinan Saglam | 07 January 2019, 16:10:23 UTC | Made text hover a lot more intelligent by parsing the text before passing to eval | 07 January 2019, 16:10:23 UTC |
| 563352c | Ali Sinan Saglam | 03 January 2019, 17:09:28 UTC | First attempt at adding text hovers | 03 January 2019, 17:09:28 UTC |
| 97abab6 | Ali Sinan Saglam | 03 January 2019, 17:03:00 UTC | Adding text hovering to BNGL editor config | 03 January 2019, 17:03:00 UTC |
| de9b3d3 | Ali Sinan Saglam | 04 December 2018, 20:36:34 UTC | Updated some eclipse specific files | 04 December 2018, 20:36:34 UTC |
| 207bc58 | Ali Sinan Saglam | 04 December 2018, 20:34:42 UTC | Ticked up BNG version in the bundling scripts | 04 December 2018, 20:34:42 UTC |
| e05f67b | Ali Sinan Saglam | 04 December 2018, 20:31:28 UTC | Tick up the RB version | 04 December 2018, 20:31:28 UTC |
| 03709fc | Ali Sinan Saglam | 29 November 2018, 19:10:55 UTC | Updated internal BioNetGen version | 29 November 2018, 19:10:55 UTC |
| fdfbf74 | Ali Sinan Saglam | 29 November 2018, 18:31:06 UTC | Fixed syntax error in reg exp | 29 November 2018, 18:31:06 UTC |
| 3b5a0d3 | Ali Sinan Saglam | 28 November 2018, 19:57:15 UTC | Fixes #205 by checking if the BNG console is still alive and booting up a new one if it is. BNG console dies in case of this particular syntax error which will also need to be fixed | 28 November 2018, 19:57:15 UTC |
| aefbf40 | Ali Sinan Saglam | 21 November 2018, 17:29:36 UTC | Fixed wrong method call | 21 November 2018, 17:29:36 UTC |
| 4f965cc | Ali Sinan Saglam | 21 November 2018, 17:23:28 UTC | Fixed to match only line continuation characters at the end of the line | 21 November 2018, 17:23:28 UTC |
| 30823a3 | Ali Sinan Saglam | 20 November 2018, 15:43:07 UTC | Fixes issue #200 | 20 November 2018, 15:43:07 UTC |
| 5a8bdde | Jim Faeder | 05 July 2018, 15:46:33 UTC | Update README.md | 05 July 2018, 15:46:33 UTC |
| 9b0fc88 | Jim Faeder | 05 July 2018, 15:45:33 UTC | Update README.md | 05 July 2018, 15:45:33 UTC |
| 86125ab | Jim Faeder | 05 July 2018, 15:42:55 UTC | Create README.md | 05 July 2018, 15:42:55 UTC |
| 106789e | Jim Faeder | 05 July 2018, 15:39:33 UTC | Update README.md | 05 July 2018, 15:39:33 UTC |
| 4b799f2 | jrfaeder | 05 July 2018, 15:35:05 UTC | Added GetStarted | 05 July 2018, 15:35:05 UTC |
| 9be379f | jrfaeder | 05 July 2018, 15:26:33 UTC | Resized first image. | 05 July 2018, 15:26:33 UTC |
| cd6f93e | Jim Faeder | 05 July 2018, 15:18:49 UTC | Update README.md | 05 July 2018, 15:18:49 UTC |
| 8dc224b | Jim Faeder | 05 July 2018, 15:16:00 UTC | Update README.md | 05 July 2018, 15:16:00 UTC |
| f2e5694 | Jim Faeder | 05 July 2018, 15:15:46 UTC | Update README.md | 05 July 2018, 15:15:46 UTC |
| 7f081ce | Jim Faeder | 05 July 2018, 15:13:47 UTC | Update README.md | 05 July 2018, 15:13:47 UTC |
| ed2454d | Jim Faeder | 05 July 2018, 15:11:28 UTC | Create README.md | 05 July 2018, 15:11:28 UTC |
| 408bf45 | jrfaeder | 05 July 2018, 15:07:42 UTC | Added HOWTO section. | 05 July 2018, 15:07:42 UTC |
| dfdfae9 | Jacob Czech | 03 July 2018, 16:45:25 UTC | Remove old google code scripts. Google code went down in like 2016. I don't think we need these anymore. | 03 July 2018, 16:45:25 UTC |
| d0cfdc5 | Jacob Czech | 03 July 2018, 16:42:56 UTC | Comment out the win32 build for now. | 03 July 2018, 16:42:56 UTC |
| 6918546 | Jacob Czech | 03 July 2018, 16:27:53 UTC | Add packaging instructions to README. According to Rob's notes, this is a bit of a hack, but it seems to mostly work for Linux at least. | 03 July 2018, 16:27:53 UTC |
| e2eda6d | Jacob Czech | 03 July 2018, 15:20:35 UTC | Fix icon section in README. | 03 July 2018, 15:20:35 UTC |
| 170e660 | Jacob Czech | 03 July 2018, 15:04:14 UTC | More formatting of the README. | 03 July 2018, 15:04:14 UTC |
| 462d733 | Jacob Czech | 03 July 2018, 15:03:00 UTC | Make debugging installation script a little easier. Using "set -o verbose" echos every command to the terminal, which makes debugging a shell script so much less painful. | 03 July 2018, 15:03:00 UTC |
| 9bf5627 | Jacob Czech | 03 July 2018, 14:32:34 UTC | Fix README formatting problem. The lines intended to be commands line literals were not indented enough. | 03 July 2018, 14:32:34 UTC |
| 601053c | Jacob Czech | 03 July 2018, 01:05:43 UTC | Update version number in installation script. Also, use "set -e" to catch errors in s_build_BNGParser.sh. Some other minor tweaks. | 03 July 2018, 01:05:43 UTC |
| 17d11ed | Jacob Czech | 03 July 2018, 01:05:23 UTC | Clean up README | 03 July 2018, 01:05:23 UTC |
| 8224401 | Jacob Czech | 02 July 2018, 23:30:03 UTC | Fix markdown formatting. | 02 July 2018, 23:30:03 UTC |
| c854afe | Jacob Czech | 02 July 2018, 23:29:47 UTC | Clean up installation script. | 02 July 2018, 23:29:47 UTC |
| 262c8f5 | jrfaeder | 22 November 2017, 20:55:17 UTC | Update README.md | 22 November 2017, 20:55:17 UTC |
| 1591d2d | jrfaeder | 22 November 2017, 20:54:30 UTC | Update README.md | 22 November 2017, 20:54:30 UTC |
| 654303e | jrfaeder | 22 November 2017, 20:54:00 UTC | Update README.md | 22 November 2017, 20:54:00 UTC |
| 8c96abb | jrfaeder | 22 November 2017, 20:51:00 UTC | Update README.md | 22 November 2017, 20:51:00 UTC |
| 68bb886 | Robert Clark | 03 August 2017, 18:39:58 UTC | A touch-up to ensure that Java can be included in the future. | 03 August 2017, 18:39:58 UTC |
| 7394b0f | Robert Clark | 31 July 2017, 14:55:58 UTC | More notes about version numbers | 31 July 2017, 14:55:58 UTC |
| 3637385 | Robert Clark | 31 July 2017, 03:52:09 UTC | Increment version number | 31 July 2017, 03:52:09 UTC |
| 5a089b8 | Robert Clark | 17 July 2017, 03:14:59 UTC | One last change | 17 July 2017, 03:14:59 UTC |
| fbbf1db | Robert Clark | 17 July 2017, 02:53:43 UTC | Make distinction between bngdir_external and bngdir_internal | 17 July 2017, 02:53:43 UTC |
| 1220f71 | Robert Clark | 05 June 2017, 18:05:02 UTC | Increase the required Java level to 1.8. Increase the required Java level to 1.8. | 05 June 2017, 18:05:02 UTC |
| c8f00a1 | Robert Clark | 24 May 2017, 19:25:16 UTC | Minor changes to .ini file for RuleBender Minor changes to .ini file for RuleBender | 24 May 2017, 19:25:16 UTC |
| d96c7bd | Robert Clark | 24 May 2017, 15:41:01 UTC | Add reminder about changes needed. Add reminder about changes needed. | 24 May 2017, 15:41:01 UTC |
| 4b56994 | Robert Clark | 26 April 2017, 18:44:49 UTC | Make timeout threashold adjustable for Contact Map creation. | 26 April 2017, 18:44:49 UTC |
| 7af80a0 | Robert Clark | 20 April 2017, 22:00:39 UTC | Add new java instructions for Win32 and Win64 | 20 April 2017, 22:00:39 UTC |
| 382d95c | Robert Clark | 20 April 2017, 18:07:02 UTC | Small change to file permissions | 20 April 2017, 18:07:02 UTC |
| 5164e6d | Robert Clark | 20 April 2017, 17:58:04 UTC | A first stab at embedding Java into the distribution package | 20 April 2017, 17:58:04 UTC |
| 5d0e784 | Robert Clark | 20 April 2017, 15:53:28 UTC | Point the OSX java virtual machine to dynamic library. Here I followed the recommendation of Marcel Austenfeld in this web page: https://www.eclipse.org/forums/index.php/t/518603/ | 20 April 2017, 15:53:28 UTC |
| da2fb47 | Robert Clark | 19 April 2017, 20:08:31 UTC | First stab at a new Apple installation process. | 19 April 2017, 20:08:31 UTC |
| 872b9a6 | jrfaeder | 19 April 2017, 13:47:22 UTC | Update README.md Fixed typos and made a note about JDK. Is root access really required to get JRE working as needed? | 19 April 2017, 13:47:22 UTC |
| 13b059b | Robert Clark | 17 April 2017, 15:33:18 UTC | Permit multiple occurances of a molecule in a rule. | 17 April 2017, 15:33:18 UTC |
| 800bb01 | Robert Clark | 29 March 2017, 17:51:38 UTC | Fix one spot where spaces might be insterted into project names | 29 March 2017, 17:51:38 UTC |
| 280f304 | Robert Clark | 23 January 2017, 19:59:01 UTC | Add the creation of the BioNetGen distribution packages | 23 January 2017, 19:59:01 UTC |
| bafeddc | Robert Clark | 23 January 2017, 16:48:01 UTC | more changes to packaging | 23 January 2017, 16:48:01 UTC |
| e718d5a | Robert Clark | 23 January 2017, 16:26:17 UTC | One more change to installation script | 23 January 2017, 16:26:17 UTC |
| 97c516b | Robert Clark | 23 January 2017, 16:00:31 UTC | Make sure that the NFsim source code ge shipped | 23 January 2017, 16:00:31 UTC |
| be22e24 | Robert Clark | 20 January 2017, 23:16:36 UTC | Small fix to packaging script | 20 January 2017, 23:16:36 UTC |
| 3d86efc | Robert Clark | 20 January 2017, 22:44:19 UTC | Update the build script for Win32 and Win64 packaging | 20 January 2017, 22:44:19 UTC |
| 1cd8ee8 | Robert Clark | 12 January 2017, 16:53:21 UTC | Change version number. | 12 January 2017, 16:53:21 UTC |
| a32910f | Robert Clark | 19 December 2016, 16:54:38 UTC | Another change needed for Issue 199 | 19 December 2016, 16:54:38 UTC |
| 68e06af | Robert Clark | 16 December 2016, 19:56:12 UTC | Another small change in packaging script | 16 December 2016, 19:56:12 UTC |
| 0e32c25 | Robert Clark | 16 December 2016, 19:15:16 UTC | Fix up the script that generates the distributions | 16 December 2016, 19:15:16 UTC |
| 868e573 | Robert Clark | 16 December 2016, 18:27:50 UTC | Increment Build Stamp: 2.2 for RuleBender | 16 December 2016, 18:27:50 UTC |
| 38930d6 | Robert Clark | 09 December 2016, 21:08:58 UTC | A fix for Issue 199 See issue 199 for details. | 09 December 2016, 21:08:58 UTC |
| efba5f0 | Robert Clark | 30 September 2016, 15:55:20 UTC | Add an error dialog to draw attention to ill-defined RHS in functions section | 30 September 2016, 15:55:20 UTC |
| 73cb3ba | Robert Clark | 29 June 2016, 20:46:46 UTC | Fix block comment issue on Mac. Buildstamp: 2.1.0.8 | 29 June 2016, 20:46:46 UTC |
| 2bc8955 | Robert Clark | 10 June 2016, 21:19:55 UTC | Increment the build stamp to 2.1.0.7 | 10 June 2016, 21:19:55 UTC |
| 369d73a | Robert Clark | 10 June 2016, 21:16:50 UTC | Fix the accelerated mouse behavior in Mosbie. | 10 June 2016, 21:16:50 UTC |
| 0979c04 | Robert Clark | 06 June 2016, 15:31:51 UTC | Small change to dialogue box that says "Workspace does not exist." | 06 June 2016, 15:31:51 UTC |
| d91b7b8 | Robert Clark | 06 June 2016, 14:25:55 UTC | Increment the build stamp to 2.1.0.6 | 06 June 2016, 14:25:55 UTC |
| 455320a | Robert Clark | 06 June 2016, 14:21:57 UTC | Second of two defects concerning keyboard listeners. | 06 June 2016, 14:21:57 UTC |
| 9f5cd8c | Robert Clark | 03 June 2016, 17:37:37 UTC | First of two defects concerning keyboard listeners. | 03 June 2016, 17:37:37 UTC |
| 6cb5387 | Robert Clark | 26 May 2016, 15:20:43 UTC | Increment version number to 2.1.0.5 | 26 May 2016, 15:20:43 UTC |
| ce67a55 | Robert Clark | 23 May 2016, 19:24:10 UTC | Added comment tying Issue #188 with the ApplicationWorkbenchWindowAdvisor file. The ApplicationWorkbenchWindowAdvisor file is where a change should be made to address issue #188. But I'd like to leave it for a couple of weeks. | 23 May 2016, 19:24:10 UTC |
| 5df2aab | Robert Clark | 20 May 2016, 15:48:32 UTC | Fix default setting for "save workspace location" and "save BioNetGen location" The default setting for both of these variables should be true. They can be set to false by the user, if needed. | 20 May 2016, 15:48:32 UTC |
| 76dcf43 | Robert Clark | 20 May 2016, 15:31:23 UTC | Change "Perl Not Found" message. The message was: Perl must be installed on your system to run RuleBender. The message is now: Perl must be installed on your system to run simulations on RuleBender. | 20 May 2016, 15:31:23 UTC |
| 31a4ad5 | Robert Clark | 17 May 2016, 20:05:29 UTC | Need to set the m_selectedResource variable as well as fill the text box. | 17 May 2016, 20:05:29 UTC |
| 2e447f7 | Robert Clark | 17 May 2016, 17:28:13 UTC | Small changes to the packaging process | 17 May 2016, 17:28:13 UTC |
| ae375be | Robert Clark | 17 May 2016, 16:37:00 UTC | Automatically put .bngl file name into Simulation textArea. | 17 May 2016, 16:37:00 UTC |
