| ea88b3b | Niklas Neubrand | 18 July 2024, 08:33:01 UTC | Update README.md Update Links to DREAM challenges. The domain changed. | 18 July 2024, 08:33:01 UTC |
| 3f56245 | Niklas Neubrand | 01 July 2024, 08:14:57 UTC | Revert "Avoid crash of arSimuData" This reverts commit e5171fc089f1f1b95e46820216bec566d51d836e. | 01 July 2024, 08:14:57 UTC |
| e5171fc | Niklas Neubrand | 01 July 2024, 07:42:46 UTC | Avoid crash of arSimuData arSimu throws warning instead of error for arCalcRes | 01 July 2024, 07:42:46 UTC |
| 4275344 | Niklas Neubrand | 01 July 2024, 07:29:06 UTC | Fix in export functions SBML: init parameters were not assigned correctly PEtab: log trafo of observables was not correct | 01 July 2024, 07:29:06 UTC |
| 1b910bb | ckreutz | 18 June 2024, 06:50:41 UTC | Merge branch 'master' of https://github.com/Data2Dynamics/d2d | 18 June 2024, 06:50:41 UTC |
| c6b7912 | ckreutz | 18 June 2024, 06:50:17 UTC | yLabels were not correctly assigned | 18 June 2024, 06:50:17 UTC |
| 5230673 | Niklas Neubrand | 14 June 2024, 11:26:25 UTC | Merge branch 'master' of https://github.com/Data2Dynamics/d2d | 14 June 2024, 11:26:25 UTC |
| 1ccdba4 | Niklas Neubrand | 14 June 2024, 11:26:03 UTC | Fix Bug in arLoadData My previous commit introduced a bug. Now the approach is more conservative, i.e. the new code (readtable) is only used if the old code (xlsread) did not work. | 14 June 2024, 11:26:03 UTC |
| c69bbfc | ckreutz | 12 June 2024, 20:19:47 UTC | Handling NaN | 12 June 2024, 20:19:47 UTC |
| 699fb39 | ckreutz | 12 June 2024, 20:16:02 UTC | Better font size of title | 12 June 2024, 20:16:02 UTC |
| e709131 | ckreutz | 12 June 2024, 20:15:19 UTC | Plotting uncertainty as region | 12 June 2024, 20:15:19 UTC |
| c2f636a | ckreutz | 12 June 2024, 20:14:45 UTC | Better debugging of residuals | 12 June 2024, 20:14:45 UTC |
| fe98101 | ckreutz | 12 June 2024, 20:13:22 UTC | New D2D URL in Report | 12 June 2024, 20:13:22 UTC |
| cd27269 | ckreutz | 12 June 2024, 20:12:48 UTC | New D2D URL in Report | 12 June 2024, 20:12:48 UTC |
| 498afee | ckreutz | 12 June 2024, 20:12:19 UTC | Bug fix | 12 June 2024, 20:12:19 UTC |
| aaf26fb | Niklas Neubrand | 12 June 2024, 10:21:31 UTC | increased compatibility | 12 June 2024, 10:21:31 UTC |
| 9d46c52 | Niklas Neubrand | 12 June 2024, 10:06:22 UTC | Improved PEtab support * re-written export function (before the conditions were not represented correctly) * some small logical fixes to sbml export * fixes to PEtab import | 12 June 2024, 10:06:22 UTC |
| a655fda | Niklas Neubrand | 12 June 2024, 09:47:53 UTC | Fix the path | 12 June 2024, 09:47:53 UTC |
| 21c83ec | Niklas Neubrand | 12 June 2024, 09:30:22 UTC | Fix to matlab path arInit deletes rtf package from matlab path. Have to add it again in some situations. | 12 June 2024, 09:30:22 UTC |
| 281fb6a | Niklas Neubrand | 12 June 2024, 08:04:47 UTC | arLoadData more robust replace deprecated matlab function xlsread by more robust readtable | 12 June 2024, 08:04:47 UTC |
| 352ec22 | Niklas Neubrand | 14 May 2024, 12:52:27 UTC | Bug fix PEtab Condition Import assigment of condition specific initial values for states is more robust now | 14 May 2024, 12:52:27 UTC |
| 3b48edb | Niklas Neubrand | 13 May 2024, 10:34:12 UTC | arInit can now only modify the ar struct Wrapping the main code of arInit in a function. This fixes a bug when calling arInit in a loop (arInit no longer overwrites index "i" and other variuables). | 13 May 2024, 10:34:12 UTC |
| 1a320e6 | Niklas Neubrand | 13 May 2024, 10:12:58 UTC | PEtab_test: save results to file | 13 May 2024, 10:12:58 UTC |
| db496fb | Niklas Neubrand | 13 May 2024, 10:02:37 UTC | Fixed failed PEtab_Tests | 13 May 2024, 10:02:37 UTC |
| 5c09b16 | Niklas Neubrand | 07 May 2024, 13:02:31 UTC | arImportPEtab more convenient Automatically run "arInit" if d2d not initialized or if model already loaded | 07 May 2024, 13:02:31 UTC |
| 9c1c07a | Niklas Neubrand | 02 May 2024, 12:03:23 UTC | Improved PEtab/SBML compatibility * arExportPEtab now also generates *.yaml file * arImportPEtab can now automatically import from the PEtab folder * arParseSBML: bug fix | 02 May 2024, 12:03:23 UTC |
| 3d9b7b2 | Niklas Neubrand | 30 April 2024, 11:38:27 UTC | Revert Changes to arCompile | 30 April 2024, 11:38:27 UTC |
| d72b88d | Niklas Neubrand | 30 April 2024, 11:27:53 UTC | Merge branch 'master' of github.com:Data2Dynamics/d2d | 30 April 2024, 11:27:53 UTC |
| a122c8a | Niklas Neubrand | 30 April 2024, 11:27:36 UTC | Collection of bug fixes * Made arCompileAllSetups robust against 'clear' commands in Setup.m file * Made arSimuData more robust against ODE integration problems * Fixed indices in arExportSBML_FullModel * Included pwd in list_files_recursive | 30 April 2024, 11:27:36 UTC |
| db161d1 | niklasneubrand | 30 April 2024, 11:22:50 UTC | Merge branch 'master' of github.com:Data2Dynamics/d2d | 30 April 2024, 11:22:50 UTC |
| 28e5208 | niklasneubrand | 30 April 2024, 11:22:09 UTC | Bug fixes in arCompile not sure if these are individual problems, or if other preople also have this | 30 April 2024, 11:22:09 UTC |
| 1a82e5b | Niklas Neubrand | 30 April 2024, 11:04:47 UTC | Minor fixes regarding console output | 30 April 2024, 11:04:47 UTC |
| ceb53e3 | Andreas Raue | 16 April 2024, 15:07:56 UTC | Update README.md | 16 April 2024, 15:07:56 UTC |
| d647481 | Timo Rachel | 31 January 2024, 15:08:24 UTC | Merge branch 'master' of github.com:Data2Dynamics/d2d | 31 January 2024, 15:08:24 UTC |
| 8ee14b7 | Timo Rachel | 31 January 2024, 15:08:01 UTC | updates on arLRT and arWaterfallPlot | 31 January 2024, 15:08:01 UTC |
| d558983 | Franz-Georg Wieland | 17 January 2024, 09:21:29 UTC | Option to hide windows in ple calculation Use flag hideWindows to hide calculation of ple and waitbar. Use flag ar.config.noWaitBarWindow to move waitbar to command line output in general. Use flag ar.config.noWaitBar to hide waitbar completely. | 17 January 2024, 09:21:29 UTC |
| e9dbb68 | Timo Rachel | 08 January 2024, 16:23:00 UTC | typos and minot changes | 08 January 2024, 16:23:00 UTC |
| 0ec58a9 | ckreutz | 12 December 2023, 14:20:27 UTC | Updates transient function | 12 December 2023, 14:20:27 UTC |
| 65434b3 | ckreutz | 12 December 2023, 14:17:49 UTC | Modification arCreateDataStruct | 12 December 2023, 14:17:49 UTC |
| 0f83333 | ckreutz | 06 December 2023, 13:29:52 UTC | Additional example for RTF, dose-dependency | 06 December 2023, 13:29:52 UTC |
| 95499dd | nneubr | 15 November 2023, 13:23:17 UTC | improved logical structure and readability of nCVRestart loop | 15 November 2023, 13:23:17 UTC |
| a5b5acf | nneubr | 14 November 2023, 13:26:09 UTC | Improved concole output | 14 November 2023, 13:26:09 UTC |
| 4173e95 | nneubr | 14 November 2023, 12:21:46 UTC | console output easier to understand | 14 November 2023, 12:21:46 UTC |
| 0b7e762 | Timo Rachel | 04 September 2023, 20:00:47 UTC | Merge branch 'master' of github.com:Data2Dynamics/d2d | 04 September 2023, 20:00:47 UTC |
| e288d1c | Timo Rachel | 04 September 2023, 20:00:35 UTC | update pleAsssessIdentifibility | 04 September 2023, 20:00:35 UTC |
| 93cd15a | niklasneubrand | 17 August 2023, 09:34:56 UTC | Improved arCopybenchmarkModels to handle chars, strings and cells | 17 August 2023, 09:34:56 UTC |
| d21bfdf | niklasneubrand | 14 August 2023, 07:15:20 UTC | Merge branch 'master' of github.com:Data2Dynamics/d2d | 14 August 2023, 07:15:20 UTC |
| e8dc2c7 | niklasneubrand | 14 August 2023, 07:14:35 UTC | Extension and cleanup of arCopyBenchmarkModels | 14 August 2023, 07:14:35 UTC |
| 3c44785 | niklasneubrand | 14 August 2023, 07:05:24 UTC | Bugfix in compilation mode 'core'. Now Results are saved. | 14 August 2023, 07:05:24 UTC |
| 74cfa0c | Timo Rachel | 11 August 2023, 11:00:07 UTC | bugfix arSimuData and update pleAssessIdentifibility.m | 11 August 2023, 11:00:07 UTC |
| 2562d3f | Timo Rachel | 08 August 2023, 19:39:51 UTC | Merge branch 'master' of github.com:Data2Dynamics/d2d | 08 August 2023, 19:39:51 UTC |
| 92b75a9 | Timo Rachel | 08 August 2023, 19:39:36 UTC | new function pleAssessIdentifibility and grad_tresh in PLEInit changed | 08 August 2023, 19:39:36 UTC |
| c63b3c8 | Timo Rachel | 08 August 2023, 19:38:56 UTC | new function pleAssessIdentifibility and grad_tresh in PLEInit changed | 08 August 2023, 19:38:56 UTC |
| 5d943c7 | niklasneubrand | 04 August 2023, 13:26:02 UTC | Merge branch 'master' of github.com:Data2Dynamics/d2d | 04 August 2023, 13:26:02 UTC |
| 8a4625a | niklasneubrand | 04 August 2023, 13:24:22 UTC | Minor fix to avoid -Wdiscardedqualifier warning at model compilation | 04 August 2023, 13:24:22 UTC |
| 88d645e | Timo Rachel | 01 August 2023, 13:44:19 UTC | Merge branch 'master' of github.com:Data2Dynamics/d2d | 01 August 2023, 13:44:19 UTC |
| 348c3d0 | nneubr | 01 August 2023, 13:20:20 UTC | removed L1 trdog | 01 August 2023, 13:20:20 UTC |
| 6ae70f4 | Timo Rachel | 31 July 2023, 14:17:07 UTC | Merge branch 'master' of https://github.com/Data2Dynamics/d2d | 31 July 2023, 14:17:07 UTC |
| b1600f0 | Timo Rachel | 31 July 2023, 13:58:28 UTC | add example to pleSelectOptimum and redo ple for ple.allowbetteroptimum==2 in ple.m if better optimum found | 31 July 2023, 13:58:28 UTC |
| 9a7f501 | ckreutz | 12 June 2023, 11:38:06 UTC | Merge branch 'master' of https://github.com/Data2Dynamics/d2d | 12 June 2023, 11:38:06 UTC |
| e285fe9 | ckreutz | 12 June 2023, 11:37:59 UTC | Trying to get a message, if y is NaN in C code. However, did not work, see comment in code | 12 June 2023, 11:37:59 UTC |
| ffd54c1 | simonbeyer1 | 02 June 2023, 17:28:44 UTC | Update arHelpInputs | 02 June 2023, 17:28:44 UTC |
| 4f25808 | simonbeyer1 | 02 June 2023, 17:26:16 UTC | Periodic stepfunction added | 02 June 2023, 17:26:16 UTC |
| 6d225da | ckreutz | 02 June 2023, 09:01:26 UTC | A new/second function for waterfall plots, i.e. for plotting the result of multistart optimization | 02 June 2023, 09:01:26 UTC |
| 7e5d47a | srv-kreutz | 26 May 2023, 08:31:57 UTC | exp added as keyword | 26 May 2023, 08:31:57 UTC |
| 2869927 | ckreutz | 11 May 2023, 09:40:13 UTC | ODE model template now has Input symtax as comment | 11 May 2023, 09:40:13 UTC |
| ea9dcf2 | ckreutz | 02 May 2023, 11:50:52 UTC | Try to solve the Potential XSS vulnerability in jQuery issue | 02 May 2023, 11:50:52 UTC |
| ef60aa5 | ckreutz | 11 April 2023, 07:15:52 UTC | Path to ProjectTemplate added (for arCreateProject.m) | 11 April 2023, 07:15:52 UTC |
| 53050db | ckreutz | 06 April 2023, 16:10:50 UTC | Bugs and improvement occured during 2nd MSB modelling workshop | 06 April 2023, 16:10:50 UTC |
| 10a50ef | fgwieland | 28 March 2023, 13:15:30 UTC | arLoadData: Optional specification of delimiter for csv observable files | 28 March 2023, 13:15:30 UTC |
| f299621 | fgwieland | 28 March 2023, 13:14:57 UTC | Fix: Bugfixes in arDebugResidual and arGetMerit arGetMerit: Corrected string printing for merit Subfunctions/arDebugResidual: Corrected loop range for NaN sensitivities | 28 March 2023, 13:14:57 UTC |
| 8a5c5b0 | ckreutz | 27 March 2023, 12:01:37 UTC | arLoad now supports sorting according to chi2 and according to checkstr (for finding duplicates) | 27 March 2023, 12:01:37 UTC |
| 0998855 | ckreutz | 13 March 2023, 14:08:59 UTC | Allow unlog, printing [ ... ] around CI | 13 March 2023, 14:08:59 UTC |
| 62eff19 | ckreutz | 13 March 2023, 13:44:08 UTC | Printing a subset of parameters, LB and UB directly after MLE | 13 March 2023, 13:44:08 UTC |
| b3fbbf9 | ckreutz | 24 February 2023, 09:29:20 UTC | arCreateProjekt with templates e.g. for TransientFunction | 24 February 2023, 09:29:20 UTC |
| 28a28b1 | ckreutz | 21 February 2023, 19:29:36 UTC | arCreateProject is now feasible with different model templates | 21 February 2023, 19:29:36 UTC |
| 86436b4 | M. Heinrich | 20 February 2023, 11:25:27 UTC | Changes in StrucID, implementation of parameter scatter, bug fix with example | 20 February 2023, 11:25:27 UTC |
| b68041d | srv-kreutz | 31 January 2023, 15:22:38 UTC | Renaming after resolving bad merge | 31 January 2023, 15:22:38 UTC |
| b7f3706 | srv-kreutz | 31 January 2023, 15:21:51 UTC | Resolve bad merge | 31 January 2023, 15:21:51 UTC |
| 80e95da | fgwieland | 31 January 2023, 09:39:54 UTC | Bugfix in arCompile for large sets of compilation files (Windows) | 31 January 2023, 09:39:54 UTC |
| b9c8673 | srv-kreutz | 24 January 2023, 21:31:36 UTC | Confidence levels now in the title | 24 January 2023, 21:31:36 UTC |
| 2b9b2d3 | srv-kreutz | 17 January 2023, 08:54:17 UTC | Nicer VPL output, profile2CI added | 17 January 2023, 08:54:17 UTC |
| 523b08f | Adrian Hauber | 10 January 2023, 15:41:30 UTC | Regularization with penalization of fold-change differences | 10 January 2023, 15:41:30 UTC |
| b743fdc | JanineEgert | 03 January 2023, 10:38:45 UTC | update transient and realistic functions | 03 January 2023, 10:38:45 UTC |
| fcfff95 | JanineEgert | 03 January 2023, 10:18:00 UTC | PEtab export, add greater equal as spline input | 03 January 2023, 10:18:00 UTC |
| 9b2a64c | JanineEgert | 03 January 2023, 10:14:57 UTC | remove old version of realistic simulation | 03 January 2023, 10:14:57 UTC |
| ee3236d | JanineEgert | 03 January 2023, 10:12:43 UTC | Realistic simulation of measurements | 03 January 2023, 10:12:43 UTC |
| 0a81b2c | JanineEgert | 03 January 2023, 10:08:54 UTC | Transient function template | 03 January 2023, 10:08:54 UTC |
| e89fc74 | JanineEgert | 03 January 2023, 10:08:05 UTC | Update transient functions | 03 January 2023, 10:08:05 UTC |
| f29c56a | clemenskreutz | 12 December 2022, 10:35:20 UTC | Handling different order in ar.fittransient and ar.p | 12 December 2022, 10:35:20 UTC |
| f2e5a2a | clemenskreutz | 12 December 2022, 10:30:53 UTC | Comments in the code and a new color | 12 December 2022, 10:30:53 UTC |
| ba88af5 | clemenskreutz | 12 December 2022, 10:29:02 UTC | Other tex filenames to not overwrite the output of arReport.m | 12 December 2022, 10:29:02 UTC |
| e3c956f | clemenskreutz | 06 December 2022, 13:46:33 UTC | Nicer profile likelihood plots | 06 December 2022, 13:46:33 UTC |
| 3e442b3 | clemenskreutz | 06 December 2022, 13:44:30 UTC | Automatic recompilation | 06 December 2022, 13:44:30 UTC |
| 20557be | clemenskreutz | 11 November 2022, 12:32:27 UTC | Function should work without ar struct | 11 November 2022, 12:32:27 UTC |
| 032adf5 | clemenskreutz | 11 November 2022, 12:27:33 UTC | Merge branch 'master' of https://github.com/Data2Dynamics/d2d | 11 November 2022, 12:27:33 UTC |
| 657d782 | clemenskreutz | 11 November 2022, 12:27:19 UTC | handle missing field ar.setup | 11 November 2022, 12:27:19 UTC |
| a5431c9 | srv-kreutz | 11 November 2022, 12:19:18 UTC | Wrong model and data filenames corrected | 11 November 2022, 12:19:18 UTC |
| 275e7ce | srv-kreutz | 11 November 2022, 12:05:13 UTC | R2021b included in version dependency | 11 November 2022, 12:05:13 UTC |
| 532b3c7 | Lukas Refisch | 16 September 2022, 15:11:43 UTC | some tweaks for logarithm of states | 16 September 2022, 15:11:43 UTC |
