| 76ffda7 | Helge Hass | 22 December 2014, 11:38:04 UTC | Possibility to scale integration tolerances with dy/dx, thus including the y tolerances of the optimisation in the integration of internal states. Flags are ar.config.atolV and ar.config.atolV_Sens | 22 December 2014, 11:38:04 UTC |
| 66f4e02 | Andreas Raue | 19 December 2014, 21:04:37 UTC | bug fix | 19 December 2014, 21:04:37 UTC |
| eb407dc | Andreas Raue | 19 December 2014, 18:58:13 UTC | new function arLoadParsSingle and small bug fix | 19 December 2014, 18:58:13 UTC |
| a4ce0f1 | Clemens Kreutz | 19 December 2014, 10:55:52 UTC | Variables ar and pleGlobals are automatically made "global" in the base workspace. | 19 December 2014, 10:55:52 UTC |
| e7935c0 | Andreas Raue | 18 December 2014, 18:34:47 UTC | bug fix | 18 December 2014, 18:34:47 UTC |
| 155eb80 | Bernhard Steiert | 03 December 2014, 06:31:17 UTC | Fixed issue #20 | 03 December 2014, 06:31:17 UTC |
| 49e656d | Bernhard Steiert | 27 November 2014, 15:44:53 UTC | bug fix: pleExtend now can be restarted if any errors occured during the previous run; uncommented try-catch from arPlotMulti | 27 November 2014, 15:44:53 UTC |
| fd47e7e | Andreas Raue | 26 November 2014, 16:40:09 UTC | added new feature, specify additional equations for SS solution | 26 November 2014, 16:40:09 UTC |
| 3ded52a | Andreas Raue | 25 November 2014, 18:54:49 UTC | new feature, set parameters like arSetPars but for all name fullfilling a pattern. | 25 November 2014, 18:54:49 UTC |
| 9737892 | Andreas Raue | 25 November 2014, 16:13:57 UTC | Merge | 25 November 2014, 16:13:57 UTC |
| 0c147fe | Andreas Raue | 25 November 2014, 16:12:18 UTC | bug fix that does not mess up GUI display when suptitle is available | 25 November 2014, 16:12:18 UTC |
| 4f810b7 | Clemens Kreutz | 25 November 2014, 15:42:22 UTC | 1) simulation of specific data sets, 2) yExpStd is also taken from the simulation. | 25 November 2014, 15:42:22 UTC |
| d3b328c | Andreas Raue | 25 November 2014, 15:32:17 UTC | output nicer | 25 November 2014, 15:32:17 UTC |
| 8ef47c6 | Andreas Raue | 25 November 2014, 15:32:04 UTC | small bug fix | 25 November 2014, 15:32:04 UTC |
| 1e89146 | Andreas Raue | 25 November 2014, 15:31:45 UTC | moved suptitle block up to prevent problems with the legend | 25 November 2014, 15:31:45 UTC |
| 57cf5d2 | Clemens Kreutz | 25 November 2014, 10:32:30 UTC | Small bug fix for plotting highlighted data points | 25 November 2014, 10:32:30 UTC |
| fdcfad3 | Clemens Kreutz | 25 November 2014, 10:23:46 UTC | Again: Bug fix for unfitted models (where ar.chi2fit, ar.ndata, ar.nprior is missing) | 25 November 2014, 10:23:46 UTC |
| 51d6def | Clemens Kreutz | 21 November 2014, 10:57:20 UTC | Possibility to highlight data-points by arPlotY. | 21 November 2014, 10:57:20 UTC |
| 3d8ad49 | Clemens Kreutz | 21 November 2014, 10:27:16 UTC | Bug fix for unfitted models (where ar.chi2fit, ar.ndata, ar.nprior is missing) | 21 November 2014, 10:27:16 UTC |
| c6ef977 | Andreas Raue | 19 November 2014, 20:34:21 UTC | another bug fix | 19 November 2014, 20:34:21 UTC |
| cf0d26e | Andreas Raue | 19 November 2014, 20:29:47 UTC | bug fix of suptitle function that messed up display of legends. and legend fix for plot_x_collected feature | 19 November 2014, 20:29:47 UTC |
| d4093ba | Andreas Raue | 18 November 2014, 16:17:37 UTC | bug fix | 18 November 2014, 16:17:37 UTC |
| 7e27525 | Andreas Raue | 18 November 2014, 15:56:10 UTC | corrections and manual merge of earlier submit | 18 November 2014, 15:56:10 UTC |
| 57ab9ec | Andreas Raue | 18 November 2014, 15:44:15 UTC | new feature: if .def file of data set is missing, but .xls or .csv file is there, create a "generic" .def file from a template. | 18 November 2014, 15:44:15 UTC |
| 1a494d1 | Andreas Raue | 18 November 2014, 15:42:59 UTC | bug fix for MASSACTION | 18 November 2014, 15:42:59 UTC |
| 4ebed0c | Andreas Raue | 18 November 2014, 15:42:29 UTC | created option for non-log dose response plots: ar.model.plot.doseresponselog10axis and new plot collected option ar.config.plot_x_collected, for showing X curves in one subplot (please note, this will not work well for plots where several condition are shown together) | 18 November 2014, 15:42:29 UTC |
| 8f16ea4 | Andreas Raue | 18 November 2014, 15:39:30 UTC | check if new parameters are in the bounds | 18 November 2014, 15:39:30 UTC |
| d76a7cb | Andreas Raue | 18 November 2014, 15:39:06 UTC | prevent error for large scales | 18 November 2014, 15:39:06 UTC |
| 57c75e2 | Andreas Raue | 18 November 2014, 15:38:39 UTC | added sorting of data | 18 November 2014, 15:38:39 UTC |
| 600c5ab | Clemens Kreutz | 13 November 2014, 14:38:59 UTC | Enhanced functionality for loading and saving: Large structs are compressed; chi2, npara etc is shown if available in _only; arSave('foldername'), arLoad(3) feasible. | 13 November 2014, 14:38:59 UTC |
| 712c460 | Clemens Kreutz | 13 November 2014, 10:42:12 UTC | suptitle.m from fileExchange | 13 November 2014, 10:42:12 UTC |
| 7ce46bd | Clemens Kreutz | 13 November 2014, 10:27:08 UTC | Merge | 13 November 2014, 10:27:08 UTC |
| 6cf9732 | Clemens Kreutz | 13 November 2014, 10:18:23 UTC | Closed branch default | 13 November 2014, 10:18:23 UTC |
| 26e7dbb | Clemens Kreutz | 13 November 2014, 08:41:35 UTC | New functionality of arPlotX.m: After klicking into a subplot, annotation of the displayed data is obtained by the command get(gca,'UserData') | 13 November 2014, 08:41:35 UTC |
| 83aa29c | Clemens Kreutz | 13 November 2014, 08:40:34 UTC | New functionality of arPlotY.m: After klicking into a subplot, annotation of the displayed data is obtained by the command get(gca,'UserData') | 13 November 2014, 08:40:34 UTC |
| 4eeff1b | Andreas Raue | 11 November 2014, 19:42:05 UTC | Removed the '-silent' flag, as it throws error for Windows systems. | 11 November 2014, 19:42:05 UTC |
| 069d8ac | Andreas Raue | 11 November 2014, 19:41:20 UTC | This reverts Revision: 337 I found that the naming gets inconsistent if the folder addition is removed. Sorry, Max... | 11 November 2014, 19:41:20 UTC |
| f1d6fcc | Andreas Raue | 11 November 2014, 19:39:57 UTC | added curvature constraints | 11 November 2014, 19:39:57 UTC |
| 3051701 | Clemens Kreutz | 06 November 2014, 18:26:47 UTC | Added functionality to arPrint.m: A subset of parameters can be selected by indices or regular expressions. | 06 November 2014, 18:26:47 UTC |
| d6ebc8e | Bernhard Steiert | 06 November 2014, 13:18:53 UTC | added function to adjust optimization tolerances to model size | 06 November 2014, 13:18:53 UTC |
| 1181870 | Andreas Raue | 03 November 2014, 21:51:24 UTC | removed dependency on model.fxeq that is not used any more | 03 November 2014, 21:51:24 UTC |
| d5eb04c | Andreas Raue | 03 November 2014, 21:49:12 UTC | some small tool functions that are nice to have... | 03 November 2014, 21:49:12 UTC |
| 1e9fd87 | Andreas Raue | 21 October 2014, 13:11:16 UTC | Small change in PlotY and new function that runs systems commands on cluster | 21 October 2014, 13:11:16 UTC |
| 0d5194d | Max Schelker | 20 October 2014, 09:13:41 UTC | Merge | 20 October 2014, 09:13:41 UTC |
| 1f6b9f6 | Max Schelker | 20 October 2014, 09:13:31 UTC | minor | 20 October 2014, 09:13:31 UTC |
| 39712fb | Max Schelker | 20 October 2014, 08:55:38 UTC | apply patch by ilia_kats for arReport on linux machines | 20 October 2014, 08:55:38 UTC |
| eda34af | Bernhard Steiert | 18 October 2014, 14:42:38 UTC | Set mex(...) to silent and removed 'BufSize' for MATLAB 2014b | 18 October 2014, 14:42:38 UTC |
| 6058d9b | Max Schelker | 14 October 2014, 10:26:39 UTC | minor | 14 October 2014, 10:26:39 UTC |
| 842ef24 | Max Schelker | 10 October 2014, 13:06:04 UTC | added function for renaming workspaces while keeping the time stamp | 10 October 2014, 13:06:04 UTC |
| 11fc4b1 | Max Schelker | 10 October 2014, 13:05:00 UTC | minor fix of rev 337 | 10 October 2014, 13:05:00 UTC |
| 1eb7042 | Max Schelker | 10 October 2014, 12:08:23 UTC | added better naming for data files in subfolders | 10 October 2014, 12:08:23 UTC |
| 8dd1917 | Lorenz Adlung | 03 October 2014, 06:48:01 UTC | Minor typo corrections in arReport and arPresentation | 03 October 2014, 06:48:01 UTC |
| d1a2bc7 | Andreas Raue | 12 September 2014, 19:15:11 UTC | small change and new cluster function | 12 September 2014, 19:15:11 UTC |
| 533c72a | Andreas Raue | 18 August 2014, 14:05:41 UTC | some small changes | 18 August 2014, 14:05:41 UTC |
| 75519ad | Max Schelker | 08 August 2014, 10:47:02 UTC | added function to remove saved Workspaces through fileChooser | 08 August 2014, 10:47:02 UTC |
| 6745067 | Max Schelker | 08 August 2014, 08:43:50 UTC | small fix for bug occuring when trying to calculate ple of fixed parameters. | 08 August 2014, 08:43:50 UTC |
| e9d80fe | Andreas Raue | 06 August 2014, 02:42:26 UTC | small bug fixes, in particular initial update of arNavigator GUI | 06 August 2014, 02:42:26 UTC |
| 26385f6 | Bernhard Steiert | 04 August 2014, 13:16:41 UTC | Small fixes | 04 August 2014, 13:16:41 UTC |
| 454dc26 | Andreas Raue | 31 July 2014, 14:40:51 UTC | small change, mean to median | 31 July 2014, 14:40:51 UTC |
| 20fbcd8 | Lorenz Adlung | 16 July 2014, 15:13:18 UTC | merge fits after separately saved LHSs with randomseed | 16 July 2014, 15:13:18 UTC |
| f1b92d8 | Lorenz Adlung | 16 July 2014, 14:28:31 UTC | Should resolve Issue #16 | 16 July 2014, 14:28:31 UTC |
| 995a503 | Bernhard Steiert | 15 July 2014, 15:59:28 UTC | small fix | 15 July 2014, 15:59:28 UTC |
| 10ac367 | Andreas Raue | 15 July 2014, 15:26:03 UTC | small bug fix | 15 July 2014, 15:26:03 UTC |
| d14cbd1 | Bernhard Steiert | 15 July 2014, 15:11:50 UTC | Throw error if STATE name is reserved by MATLAB | 15 July 2014, 15:11:50 UTC |
| 255c2f1 | Andreas Raue | 15 July 2014, 15:09:16 UTC | merge | 15 July 2014, 15:09:16 UTC |
| 9eb25a5 | Andreas Raue | 14 July 2014, 13:01:19 UTC | New function to compile model on Cluster, still experimental | 14 July 2014, 13:01:19 UTC |
| 58de37a | Andreas Raue | 14 July 2014, 13:00:20 UTC | New plot function that compares parameter values across saved workspaces | 14 July 2014, 13:00:20 UTC |
| 185199e | Andreas Raue | 14 July 2014, 12:59:20 UTC | removed unused function | 14 July 2014, 12:59:20 UTC |
| 0a56801 | Andreas Raue | 14 July 2014, 12:57:30 UTC | completely revised stochastic simulations (SSA). Now all the code is included and compiled in the main mex file arSimuCalc.c, arSSACalc.c is not used any more. No additional compiling is required. arSSA is still used (like arSimu for deterministic simulations) to call a stochastic simulation. All setting are in arInit. | 14 July 2014, 12:57:30 UTC |
| 2c675a1 | Andreas Raue | 14 July 2014, 12:53:42 UTC | Bug fix for dose response in multiple conditions | 14 July 2014, 12:53:42 UTC |
| 4414bfc | Andreas Raue | 14 July 2014, 12:00:47 UTC | Changes in the way tic-toc runtime is captured | 14 July 2014, 12:00:47 UTC |
| eccdf18 | Andreas Raue | 14 July 2014, 11:59:51 UTC | Changes in Cluster function, I am still trying to optimize the usage of these functions | 14 July 2014, 11:59:51 UTC |
| 7eaa923 | Andreas Raue | 14 July 2014, 11:58:37 UTC | Some clean up and organization in arInit Minor improvement in arLoadData | 14 July 2014, 11:58:37 UTC |
| e863a84 | Max Schelker | 19 June 2014, 09:01:17 UTC | fixed warnings in sundials c-code | 19 June 2014, 09:01:17 UTC |
| d05b2e9 | Max Schelker | 11 June 2014, 11:45:10 UTC | fixed minor bug in project creator script | 11 June 2014, 11:45:10 UTC |
| 24d3206 | Helge Hass | 16 May 2014, 08:03:24 UTC | Export Data from arFramework to csv file compatible with Daniel's R framework | 16 May 2014, 08:03:24 UTC |
| 1a49d59 | Max Schelker | 22 April 2014, 13:15:27 UTC | bug fix for fmincon and SBML-importer | 22 April 2014, 13:15:27 UTC |
| 1056fd8 | Andreas Raue | 21 April 2014, 17:10:46 UTC | code clean up | 21 April 2014, 17:10:46 UTC |
| c2a4adf | Andreas Raue | 21 April 2014, 15:50:14 UTC | updated cluster function for R2014a compatibility | 21 April 2014, 15:50:14 UTC |
| d48afdb | Andreas Raue | 21 April 2014, 15:49:19 UTC | fixed example setup scripts for new notation | 21 April 2014, 15:49:19 UTC |
| e1a27c8 | Andreas Raue | 21 April 2014, 14:46:14 UTC | Important! Simplified in arLoadModel and arLoadData function calls. Will throw errors if code is not adapted to new usage. Please follow the new notation and update your code accordingly. | 21 April 2014, 14:46:14 UTC |
| d963dcb | Andreas Raue | 21 April 2014, 14:42:58 UTC | some code maintenances to improve future cluster compatibility | 21 April 2014, 14:42:58 UTC |
| 9c11674 | Andreas Raue | 21 April 2014, 14:42:12 UTC | added pool size to function call | 21 April 2014, 14:42:12 UTC |
| 8c701fa | Andreas Raue | 12 April 2014, 01:00:29 UTC | small bug fix | 12 April 2014, 01:00:29 UTC |
| e6be772 | Christian Tönsing | 01 April 2014, 16:23:02 UTC | fix for issue#15: arReport does now work also with model definition files without model-wide OBSERVABLES | 01 April 2014, 16:23:02 UTC |
| 1f82ab6 | Helge Hass | 31 March 2014, 15:45:20 UTC | additional txt file output of observables to work with transformation software of Benjamin Merkt | 31 March 2014, 15:45:20 UTC |
| 3d86860 | Andreas Raue | 27 March 2014, 17:52:21 UTC | Some minor changes, modofications and corrections | 27 March 2014, 17:52:21 UTC |
| 103e94c | Max Schelker | 14 March 2014, 11:24:00 UTC | bug in arNavigator fixed | 14 March 2014, 11:24:00 UTC |
| d4b33c6 | Max Schelker | 14 March 2014, 09:46:45 UTC | added button "FitSingle" in arNavigator | 14 March 2014, 09:46:45 UTC |
| 5f30005 | Max Schelker | 14 March 2014, 09:36:52 UTC | bug fix for arNavigator. show current list of experiments in popupmenu1 (instead of some old one by Andreas ;-)) | 14 March 2014, 09:36:52 UTC |
| fdf4fe5 | Andreas Raue | 06 March 2014, 18:07:03 UTC | bug fix in arTuner cause by introdiction of arNavigator | 06 March 2014, 18:07:03 UTC |
| 7b2ba17 | Andreas Raue | 05 March 2014, 19:48:17 UTC | Introducing a new gui, arNavigator. It makes it easy to go through all data sets and adjust observable parameters quickly. | 05 March 2014, 19:48:17 UTC |
| bafbf70 | Andreas Raue | 02 March 2014, 03:09:04 UTC | fixed bug in plot function | 02 March 2014, 03:09:04 UTC |
| e836a50 | Andreas Raue | 26 February 2014, 16:33:55 UTC | small improvement in multi plots function | 26 February 2014, 16:33:55 UTC |
| 6ac875d | Andreas Raue | 26 February 2014, 16:33:24 UTC | some small improves / fixes | 26 February 2014, 16:33:24 UTC |
| ff4babc | Andreas Raue | 21 February 2014, 22:57:03 UTC | bug fix in arLoadData and Cluster version of arMCMC | 21 February 2014, 22:57:03 UTC |
| f2beda0 | Andreas Raue | 19 February 2014, 19:00:04 UTC | several minor changes | 19 February 2014, 19:00:04 UTC |
| 297952f | Andreas Raue | 10 February 2014, 14:07:41 UTC | improvement of the save/load function. parameters will be save in a separate and smaller file now was well: workspace_pars_only.mat This make transfer of fitting results from/to server easier and speed up arLoadPars. | 10 February 2014, 14:07:41 UTC |
| 7a49415 | Andreas Raue | 08 February 2014, 02:51:39 UTC | bug fix in new report function | 08 February 2014, 02:51:39 UTC |
| d89ea32 | Andreas Raue | 08 February 2014, 01:40:52 UTC | a bunch of minor changes | 08 February 2014, 01:40:52 UTC |
