| 4c697ee | Helge Hass | 29 July 2015, 07:45:33 UTC | new C code version | 29 July 2015, 07:45:33 UTC |
| 478a95a | Helge Hass | 29 July 2015, 07:33:45 UTC | Integration of KLU sparse solver in d2d integration. Many thanks to Joep for debugging! Set ar.config.useSparseJac = 1; to use it, significant integration time benefits for large and sparse systems! | 29 July 2015, 07:33:45 UTC |
| 380fe55 | Helge Hass | 29 July 2015, 07:29:00 UTC | new SUNDIALS release with interfaces to sparse solver KLU | 29 July 2015, 07:29:00 UTC |
| 6f135d8 | Helge Hass | 29 July 2015, 07:27:07 UTC | small fixes in prediction bands | 29 July 2015, 07:27:07 UTC |
| 493b0c4 | Andreas Raue | 28 July 2015, 15:57:06 UTC | improved functionality | 28 July 2015, 15:57:06 UTC |
| 0a8f746 | Clemens Kreutz | 27 July 2015, 14:32:10 UTC | arLoadPars('ResultFolder_WithoutPath') is now feasible. | 27 July 2015, 14:32:10 UTC |
| 3e92cf3 | Joep Vanlier | 22 July 2015, 13:50:13 UTC | [Fix] Added support for 0x1 cells (Commit by Clemens Blank) | 22 July 2015, 13:50:13 UTC |
| ac83aea | Helge Hass | 22 July 2015, 11:57:00 UTC | new Example folder (ABC toy model) with computation of prediction bands. Added lines for prediction bands to swameye (commented out as default). | 22 July 2015, 11:57:00 UTC |
| cb9baf9 | Helge Hass | 22 July 2015, 11:55:16 UTC | small improvements for prediction bands | 22 July 2015, 11:55:16 UTC |
| 8d4c499 | Joep Vanlier | 21 July 2015, 17:25:25 UTC | [Update] Can now search for which datasets contain data for a specific state or derived variable using arFindCondition and arFindData | 21 July 2015, 17:25:25 UTC |
| eb126f5 | Joep Vanlier | 21 July 2015, 12:15:58 UTC | [Minor] edit to avoid func/variable conflict warning | 21 July 2015, 12:15:58 UTC |
| 616d551 | Joep Vanlier | 21 July 2015, 12:06:16 UTC | [Minor] bugfix | 21 July 2015, 12:06:16 UTC |
| 38e441d | Joep Vanlier | 21 July 2015, 11:40:53 UTC | merge | 21 July 2015, 11:40:53 UTC |
| 8cdfc8a | Joep Vanlier | 21 July 2015, 11:40:24 UTC | [New] 'arInteractivity on' for interactive plot functionality (only ple for now). Also updated the derived variables subs. | 21 July 2015, 11:40:24 UTC |
| 988c548 | Clemens Kreutz | 15 July 2015, 08:48:53 UTC | Minior extended functionality: arLoad(ar.config.savepath) and arPLETrajectories('parameter_name') now feasible | 15 July 2015, 08:48:53 UTC |
| caec7df | Helge Hass | 14 July 2015, 16:29:10 UTC | minor updates on prediction bands. No automatic plotting, path is added by arCheck and precise integration is default now. | 14 July 2015, 16:29:10 UTC |
| aa0599f | Clemens Kreutz | 12 July 2015, 16:38:12 UTC | arSave('current') in help comment | 12 July 2015, 16:38:12 UTC |
| 02dfcd0 | Joep Vanlier | 08 July 2015, 15:31:37 UTC | Merge | 08 July 2015, 15:31:37 UTC |
| 92c42df | Joep Vanlier | 08 July 2015, 15:31:16 UTC | [New] Function to make new conditions, unique to a specific data ID. Purpose is to be able teo specify events for specific datasets without the worry of overlapping conditions. | 08 July 2015, 15:31:16 UTC |
| 47c2488 | Clemens Kreutz | 08 July 2015, 13:39:00 UTC | Minor improvements. | 08 July 2015, 13:39:00 UTC |
| b5ceb6c | Joep Vanlier | 07 July 2015, 15:28:39 UTC | [New] DERIVED variables can now reference other DERIVED variables. Note: only explicit equations are supported. No x = f(x) stuff. | 07 July 2015, 15:28:39 UTC |
| 614a599 | Joep Vanlier | 01 July 2015, 12:12:36 UTC | merge | 01 July 2015, 12:12:36 UTC |
| f856c69 | Joep Vanlier | 01 July 2015, 12:11:42 UTC | merge | 01 July 2015, 12:11:42 UTC |
| 4625566 | Joep Vanlier | 01 July 2015, 12:11:20 UTC | [Minor] File to facilitate interaction with python (commit from Clemens Blank) | 01 July 2015, 12:11:20 UTC |
| ddd855e | Helge Hass | 01 July 2015, 09:08:03 UTC | Framework for integration of confidence bands, located in folder PPL. Changes in arLink provide functionality to add a data point by hand. Changes in arGetData and plotting files to plot the integrated confidence bands via the LB/UB variables. Black stars for the confidence band thresholds of the validation profile likelihood approach of C. Kreutz. | 01 July 2015, 09:08:03 UTC |
| 435a431 | Andreas Raue | 29 June 2015, 22:35:45 UTC | final accepted paper | 29 June 2015, 22:35:45 UTC |
| 362b59b | Joep Vanlier | 23 June 2015, 09:06:13 UTC | merge | 23 June 2015, 09:06:13 UTC |
| 87d0ad9 | Joep Vanlier | 23 June 2015, 09:05:46 UTC | [minor] Have to set global parameters before starting subsequent profiles or they will have no effect in the multiple profile case. | 23 June 2015, 09:05:46 UTC |
| 8a43795 | Max Schelker | 22 June 2015, 19:55:34 UTC | corrects small typo | 22 June 2015, 19:55:34 UTC |
| fd0e721 | Bernhard Steiert | 22 June 2015, 14:38:48 UTC | Small fix related to issue #30 | 22 June 2015, 14:38:48 UTC |
| 94d03d5 | JoepVanlier | 21 June 2015, 23:23:49 UTC | [minor] Update arGet.m: Support for multiple conditions and passing custom ar struct (Clemens Blank) | 21 June 2015, 23:23:49 UTC |
| 63539b9 | Joep Vanlier | 18 June 2015, 16:40:34 UTC | Merge | 18 June 2015, 16:40:34 UTC |
| 3517dbc | Joep Vanlier | 18 June 2015, 16:37:32 UTC | [minor] bugfix in arReport | 18 June 2015, 16:37:32 UTC |
| acb06af | Andreas Raue | 17 June 2015, 13:24:58 UTC | added backups for cluster runs | 17 June 2015, 13:24:58 UTC |
| 77c3bf1 | Joep Vanlier | 17 June 2015, 11:06:58 UTC | Minor bugfix in logging functionality of arAddEvent | 17 June 2015, 11:06:58 UTC |
| 174ff32 | Joep Vanlier | 12 June 2015, 13:31:00 UTC | fixed bug in arFit: missing default parameter when no arguments were passed | 12 June 2015, 13:31:00 UTC |
| affe795 | Joep Vanlier | 12 June 2015, 12:06:21 UTC | Added event support to arExport and removed dependence on completely stored ar struct. | 12 June 2015, 12:06:21 UTC |
| 36af01e | Joep Vanlier | 12 June 2015, 11:16:18 UTC | Added event logging (for saving purposes) and bugfix arFindInputs regarding condition variables | 12 June 2015, 11:16:18 UTC |
| 4015c95 | Andreas Raue | 11 June 2015, 19:38:58 UTC | Merge | 11 June 2015, 19:38:58 UTC |
| 3709332 | Andreas Raue | 11 June 2015, 19:38:26 UTC | added parfor_progress to cluster functions | 11 June 2015, 19:38:26 UTC |
| 12a118e | Joep Vanlier | 11 June 2015, 16:11:55 UTC | Added packaging file for D2D model distribution (useful if you make Examples). | 11 June 2015, 16:11:55 UTC |
| 9a60409 | Wolfgang Mader | 11 June 2015, 09:24:09 UTC | Use fabs() instead of abs() in x_calc() Fix the compiler warning caused by the rescaling routine in x_calc() by using the floating point version of abs(), fabs(). In contrast to C++, in C, abs() returns an integer such that a floating point argument is truncated to the next integer. math.h provides fabs() for floating point arguments. Signed-off-by: Wolfgang Mader <Wolfgang.Mader@fdm.uni-freiburg.de> | 11 June 2015, 09:24:09 UTC |
| 894bd45 | Andreas Raue | 10 June 2015, 14:30:03 UTC | small improvements in output | 10 June 2015, 14:30:03 UTC |
| b11e5ac | Bernhard Steiert | 10 June 2015, 14:24:45 UTC | Fix issue #30 | 10 June 2015, 14:24:45 UTC |
| 7e00952 | Joep Vanlier | 09 June 2015, 12:09:42 UTC | Wrote a lightweight function for quickly reversibly changing parameters without having to resort to arLoad/arSavePars. | 09 June 2015, 12:09:42 UTC |
| 75bdda5 | Andreas Raue | 08 June 2015, 14:36:41 UTC | Improved cluster functions | 08 June 2015, 14:36:41 UTC |
| 259ec81 | Andreas Raue | 03 June 2015, 18:48:23 UTC | minor bug fixes | 03 June 2015, 18:48:23 UTC |
| d638ba5 | Lorenz Adlung | 03 June 2015, 13:22:26 UTC | Example Beer et al. Molecular Biosystems 2014 | 03 June 2015, 13:22:26 UTC |
| bbeeb41 | Andreas Raue | 03 June 2015, 13:10:04 UTC | Merge | 03 June 2015, 13:10:04 UTC |
| 1c67da8 | Andreas Raue | 03 June 2015, 13:07:37 UTC | Some updates for cluster functions for R2015a | 03 June 2015, 13:07:37 UTC |
| 56b3151 | Clemens Kreutz | 03 June 2015, 09:46:37 UTC | Assessing ODE tolerances and integration problems: Some improvements and better documentation. | 03 June 2015, 09:46:37 UTC |
| a5889b0 | JoepVanlier | 01 June 2015, 12:24:44 UTC | Added filter to arPrint for parameters close to their bounds. | 01 June 2015, 12:24:44 UTC |
| 745892d | JoepVanlier | 01 June 2015, 12:10:32 UTC | Merge | 01 June 2015, 12:10:32 UTC |
| 7a17ccb | JoepVanlier | 01 June 2015, 12:10:03 UTC | Added lower and upper bound filter to arPrint | 01 June 2015, 12:10:03 UTC |
| 81b4e8b | Andreas Raue | 29 May 2015, 01:00:14 UTC | manuscript files form revision | 29 May 2015, 01:00:14 UTC |
| 82f13b8 | Joep Vanlier | 28 May 2015, 11:44:13 UTC | arFindData.m | 28 May 2015, 11:44:13 UTC |
| f88776f | Joep Vanlier | 28 May 2015, 11:37:33 UTC | arFindData: Compare by numeric value rather than do a string compare. | 28 May 2015, 11:37:33 UTC |
| 6118ef9 | Joep Vanlier | 28 May 2015, 09:43:19 UTC | Undid two changes I should not have pushed. Added them to the ignore list now, sorry. | 28 May 2015, 09:43:19 UTC |
| 5e0b27a | Joep Vanlier | 27 May 2015, 18:20:09 UTC | Error check for arPrintSteadyState | 27 May 2015, 18:20:09 UTC |
| fe0132d | Clemens Kreutz | 27 May 2015, 14:39:58 UTC | Bug fixed, better comments | 27 May 2015, 14:39:58 UTC |
| 96523e7 | Clemens Kreutz | 27 May 2015, 14:32:55 UTC | New function for more conveniently setting the qPlot flags. | 27 May 2015, 14:32:55 UTC |
| 3afef72 | Clemens Kreutz | 27 May 2015, 14:29:40 UTC | New function for selection parameters and/or data to be fitted by name. | 27 May 2015, 14:29:40 UTC |
| d8eb843 | Clemens Kreutz | 27 May 2015, 14:27:40 UTC | New function which can be used like feval. It ensures that the original ar is reset if an error occurs in an analysis. | 27 May 2015, 14:27:40 UTC |
| db77414 | Clemens Kreutz | 22 May 2015, 13:36:30 UTC | New function for finding a parameter which is responsible for integration errors. | 22 May 2015, 13:36:30 UTC |
| 2375267 | Andreas Raue | 22 May 2015, 00:12:13 UTC | manuscript change for revision 1 | 22 May 2015, 00:12:13 UTC |
| 81b689c | Clemens Kreutz | 21 May 2015, 15:01:02 UTC | Recompiling a model with force=false/true is now feasible. | 21 May 2015, 15:01:02 UTC |
| 32b202d | Clemens Kreutz | 21 May 2015, 15:00:00 UTC | Better output and bug fix for chi-square test. | 21 May 2015, 15:00:00 UTC |
| 6987957 | Clemens Kreutz | 21 May 2015, 14:59:10 UTC | New option for LHS: If integration was not feasible, the fit is restarted with a new initial guess. | 21 May 2015, 14:59:10 UTC |
| 59a6350 | Clemens Kreutz | 21 May 2015, 14:47:19 UTC | Bug fix if no arguments are supplied. | 21 May 2015, 14:47:19 UTC |
| 371df04 | Clemens Kreutz | 21 May 2015, 14:46:44 UTC | arNetworkGraph: Warning message for windows. | 21 May 2015, 14:46:44 UTC |
| e5cf3f6 | JoepVanlier | 19 May 2015, 16:50:14 UTC | Added hill function to function replacement list | 19 May 2015, 16:50:14 UTC |
| f5ad727 | JoepVanlier | 19 May 2015, 13:56:13 UTC | Better error message | 19 May 2015, 13:56:13 UTC |
| d0a33df | JoepVanlier | 19 May 2015, 13:37:10 UTC | Added proper error handling for equilibration steps | 19 May 2015, 13:37:10 UTC |
| 64cc2d7 | JoepVanlier | 19 May 2015, 09:16:42 UTC | Edited arFindInputs to work with condition inputs rather than data inputs. Also updated the event example. | 19 May 2015, 09:16:42 UTC |
| 09d7f32 | JoepVanlier | 18 May 2015, 16:27:05 UTC | arGet function (added by Clemens Blank), used to extract data structures from the ar struct | 18 May 2015, 16:27:05 UTC |
| 397d6b3 | JoepVanlier | 18 May 2015, 16:19:54 UTC | Removed OSX Desktop Services Store files | 18 May 2015, 16:19:54 UTC |
| 283af28 | JoepVanlier | 18 May 2015, 16:11:58 UTC | Added verbose mode to arPrintSteadyState and added a sanity check to arSteadyState. | 18 May 2015, 16:11:58 UTC |
| 46cf8a2 | JoepVanlier | 18 May 2015, 15:45:10 UTC | Helper function to print pre-equilibration information | 18 May 2015, 15:45:10 UTC |
| 13d6024 | Clemens Kreutz | 18 May 2015, 11:43:00 UTC | Bug fix. The bug occurred if several d2d projects are in matlab's search path and therefore the path to arClusterCompiledHook.m was wrong. | 18 May 2015, 11:43:00 UTC |
| 31f1e44 | Clemens Kreutz | 18 May 2015, 11:35:23 UTC | Bug fix arCompare | 18 May 2015, 11:35:23 UTC |
| 55cb0ac | Clemens Kreutz | 18 May 2015, 10:41:46 UTC | Bug fix. | 18 May 2015, 10:41:46 UTC |
| 9cf50c2 | Max Schelker | 14 May 2015, 18:15:34 UTC | minor | 14 May 2015, 18:15:34 UTC |
| f4ec212 | Lorenz Adlung | 14 May 2015, 14:32:09 UTC | New Example | 14 May 2015, 14:32:09 UTC |
| 911591c | Lorenz Adlung | 14 May 2015, 14:20:28 UTC | arLoadPars adapted to workspace_pars_only.mat | 14 May 2015, 14:20:28 UTC |
| 5f25484 | Bernhard Steiert | 12 May 2015, 16:16:09 UTC | Small fix in plePlotMulti (thanks Raphael) | 12 May 2015, 16:16:09 UTC |
| fa121c2 | Max Schelker | 08 May 2015, 13:42:35 UTC | Merge | 08 May 2015, 13:42:35 UTC |
| 137f281 | Max Schelker | 08 May 2015, 13:41:02 UTC | added extracting sundials tar in windows. Please check if it still works on unix! | 08 May 2015, 13:41:02 UTC |
| be70ab7 | Andreas Raue | 08 May 2015, 12:56:26 UTC | small changes | 08 May 2015, 12:56:26 UTC |
| 1120b8e | Max Schelker | 07 May 2015, 21:21:08 UTC | added comment | 07 May 2015, 21:21:08 UTC |
| 311b1df | Max Schelker | 07 May 2015, 21:19:27 UTC | copy dll files to working directory if they are not in Windows folder (useful for users on Windows machines without admin privileges) | 07 May 2015, 21:19:27 UTC |
| 358d9ff | Lorenz Adlung | 06 May 2015, 11:46:02 UTC | Should resolve issue #28 arCheck.m edited online with Bitbucket | 06 May 2015, 11:46:02 UTC |
| 89d1934 | Andreas Raue | 04 May 2015, 20:51:42 UTC | added sys/time.h support for Windows, check out arPlotClockTimes to see how different threads and conditions are timed. | 04 May 2015, 20:51:42 UTC |
| b12fcd2 | Andreas Raue | 04 May 2015, 20:12:04 UTC | I improved the way arCompileAll is removing unused parameters from the whole compiled model. It fixes cases where parameter are without effect, a left over from CONDITIONS... Please let me know if you run into any issues with that. | 04 May 2015, 20:12:04 UTC |
| 943a971 | Andreas Raue | 04 May 2015, 20:09:34 UTC | improved new plot functions | 04 May 2015, 20:09:34 UTC |
| d6767a4 | Clemens Kreutz | 30 April 2015, 17:03:31 UTC | Bug fix. | 30 April 2015, 17:03:31 UTC |
| b6aa939 | Max Schelker | 30 April 2015, 16:59:02 UTC | Merge | 30 April 2015, 16:59:02 UTC |
| 94c6bc0 | Max Schelker | 30 April 2015, 16:57:21 UTC | corrected typos | 30 April 2015, 16:57:21 UTC |
| 0ddad5e | Andreas Raue | 30 April 2015, 00:54:41 UTC | small bug fix | 30 April 2015, 00:54:41 UTC |
| 9654a0c | Max Schelker | 29 April 2015, 14:43:43 UTC | fixes bug in arLoadData when having more than one model | 29 April 2015, 14:43:43 UTC |
| e226212 | Andreas Raue | 28 April 2015, 14:09:35 UTC | surpress unneccessary output from archi2 | 28 April 2015, 14:09:35 UTC |
