| bc2a82d | Joep Vanlier | 26 March 2015, 10:37:47 UTC | Fix: qEvent remaining uninitialized when useEvents was set to zero Fix: conditions with no dynamic parameters do no longer fail simulation New feature: Added steady state equilibration with sensitivity propagation (see new examples). New feature: Added dynamic events (see new examples). | 26 March 2015, 10:37:47 UTC |
| 0d88a54 | Clemens Kreutz | 24 March 2015, 12:28:25 UTC | Reducing error messages for new Plots | 24 March 2015, 12:28:25 UTC |
| cf82812 | Clemens Kreutz | 24 March 2015, 12:26:14 UTC | ar.model.data.p is overwritten by pold to enable repeated calls of arCompileAll | 24 March 2015, 12:26:14 UTC |
| e20896c | Clemens Kreutz | 24 March 2015, 09:07:45 UTC | Minor improvements | 24 March 2015, 09:07:45 UTC |
| 085b4ae | Clemens Kreutz | 24 March 2015, 08:49:27 UTC | Minor bug fix occuring during plotting if y_ssa consists only of NaNs | 24 March 2015, 08:49:27 UTC |
| 81770db | Clemens Kreutz | 24 March 2015, 08:47:36 UTC | arLoad changes ar.config.savepath if the folder has been renamed externally | 24 March 2015, 08:47:36 UTC |
| 6086a79 | Bernhard Steiert | 23 March 2015, 12:09:18 UTC | Minor | 23 March 2015, 12:09:18 UTC |
| f99d839 | Andreas Raue | 20 March 2015, 13:45:17 UTC | Merge | 20 March 2015, 13:45:17 UTC |
| f78a968 | Andreas Raue | 20 March 2015, 13:44:28 UTC | Big fix in new c code that caused error when compiling on Windows | 20 March 2015, 13:44:28 UTC |
| d05f2f3 | Joep Vanlier | 20 March 2015, 13:33:16 UTC | modx_B should be zero by default | 20 March 2015, 13:33:16 UTC |
| cb1f3e9 | Andreas Raue | 20 March 2015, 13:22:16 UTC | some smaller improvements in output | 20 March 2015, 13:22:16 UTC |
| ba4f3fd | Joep Vanlier | 20 March 2015, 13:00:53 UTC | Part 1 of a big update. Refactored event system. Concentrations/internal sensitivity equation state can now be accessed from outside at event points. t=inf is interpreted as meaning equilibruim simulation. Part two will be the MATLAB end of things, such that these new functionalities can be accessed by the user. | 20 March 2015, 13:00:53 UTC |
| 59c1488 | Joep Vanlier | 17 March 2015, 11:16:35 UTC | Added more error checking. | 17 March 2015, 11:16:35 UTC |
| 2d389cb | Joep Vanlier | 16 March 2015, 16:47:19 UTC | Added check for ERRORS section if OBSERVABLES section was specified in a model def file. | 16 March 2015, 16:47:19 UTC |
| 97e346b | Joep Vanlier | 16 March 2015, 16:01:13 UTC | Added check for DERIVED section | 16 March 2015, 16:01:13 UTC |
| df622c1 | Joep Vanlier | 16 March 2015, 15:35:59 UTC | Removed comment | 16 March 2015, 15:35:59 UTC |
| 8a5b01d | Joep Vanlier | 16 March 2015, 15:36:36 UTC | Merged in jan-glx/d2d-software (pull request #2) Improved input checking slightly. | 16 March 2015, 15:36:36 UTC |
| 3950979 | Joep Vanlier | 13 March 2015, 18:05:15 UTC | small edit in new functionality | 13 March 2015, 18:05:15 UTC |
| 2a135a1 | Joep Vanlier | 13 March 2015, 17:15:57 UTC | merge | 13 March 2015, 17:15:57 UTC |
| b6cd605 | Joep Vanlier | 13 March 2015, 17:13:39 UTC | Added sensitivities of step functions; smooth step functions and Gaussian bolus input functions as well as a few examples. | 13 March 2015, 17:13:39 UTC |
| 0c18c1a | Clemens Kreutz | 13 March 2015, 14:55:22 UTC | Replacement of space characters in xls data column headers. | 13 March 2015, 14:55:22 UTC |
| 304e62d | Andreas Raue | 13 March 2015, 01:57:25 UTC | final version that was submitted | 13 March 2015, 01:57:25 UTC |
| 93b35c5 | Clemens Kreutz | 10 March 2015, 14:51:04 UTC | ple: the contribution from ALL priors is calculated and plotted. Up to now, only the contribution of the PLE-parameter was considered. | 10 March 2015, 14:51:04 UTC |
| b4d40d6 | Clemens Kreutz | 10 March 2015, 10:34:11 UTC | 2 further References | 10 March 2015, 10:34:11 UTC |
| 7cfca2f | Andreas Raue | 10 March 2015, 00:20:41 UTC | implemented comment from Jan H | 10 March 2015, 00:20:41 UTC |
| b67c2a3 | Andreas Raue | 09 March 2015, 23:42:39 UTC | added more references | 09 March 2015, 23:42:39 UTC |
| 9769136 | Lorenz Adlung | 07 March 2015, 07:01:52 UTC | publications_using_d2d.bib edited online with Bitbucket: three references added | 07 March 2015, 07:01:52 UTC |
| 2370a9f | Andreas Raue | 07 March 2015, 01:09:05 UTC | New function that plots how parameters change along a fit sequence. can be use to visualize and parameter matrix | 07 March 2015, 01:09:05 UTC |
| 8efec9a | Andreas Raue | 07 March 2015, 01:02:29 UTC | added default value of new c code feature (solver restarts) in arrant and small code clean up in the other file | 07 March 2015, 01:02:29 UTC |
| 41d65e8 | Andreas Raue | 07 March 2015, 00:56:43 UTC | bibtex containing all references where the software has been used. Please add any missing publications!!! | 07 March 2015, 00:56:43 UTC |
| 927569f | Andreas Raue | 07 March 2015, 00:45:01 UTC | included Tim H.'s corrections | 07 March 2015, 00:45:01 UTC |
| 22cb9f7 | Lorenz Adlung | 06 March 2015, 15:37:26 UTC | d2dpaper.tex edited online with Bitbucket Funding updated (Thanks to Marcel!!) | 06 March 2015, 15:37:26 UTC |
| ce4570b | Max Schelker | 06 March 2015, 14:09:53 UTC | minor fix for latex plots (tikz) | 06 March 2015, 14:09:53 UTC |
| 74b630d | Andreas Raue | 06 March 2015, 00:23:43 UTC | included Jens corrections | 06 March 2015, 00:23:43 UTC |
| d72d4c2 | Andreas Raue | 06 March 2015, 00:17:07 UTC | Increase C version code, after Joep's submits today to prevent compatibility problems | 06 March 2015, 00:17:07 UTC |
| c957462 | Max Schelker | 05 March 2015, 14:59:14 UTC | minor | 05 March 2015, 14:59:14 UTC |
| ce501ee | Max Schelker | 05 March 2015, 14:09:51 UTC | minor | 05 March 2015, 14:09:51 UTC |
| 6ea74e4 | Joep Vanlier | 05 March 2015, 13:10:08 UTC | Merge | 05 March 2015, 13:10:08 UTC |
| df5750a | Joep Vanlier | 05 March 2015, 13:01:46 UTC | Added events for dealing with step inputs. See /Examples/Event_Test for more information. | 05 March 2015, 13:01:46 UTC |
| a5a1678 | Andreas Raue | 05 March 2015, 02:42:45 UTC | cover letter | 05 March 2015, 02:42:45 UTC |
| 71e2a83 | Andreas Raue | 05 March 2015, 01:11:25 UTC | final version to be submitted to all coauthors | 05 March 2015, 01:11:25 UTC |
| d46ec7a | Andreas Raue | 04 March 2015, 14:15:53 UTC | added additional supplementary files | 04 March 2015, 14:15:53 UTC |
| 6871078 | Andreas Raue | 02 March 2015, 14:46:58 UTC | improvements in arNetworkGraphCompartments function | 02 March 2015, 14:46:58 UTC |
| f244b75 | Andreas Raue | 02 March 2015, 00:48:13 UTC | compressed main text to fit on two pages again, by removing some acknowledgement that, because of the extended author list, are now redundant and some extensive affiliations. removed user guide section from supplement, we agreed on having this as a separate supplementary file | 02 March 2015, 00:48:13 UTC |
| 6e8159b | Max Schelker | 01 March 2015, 18:05:00 UTC | added new version of the figure to main text | 01 March 2015, 18:05:00 UTC |
| d0aeab8 | Lorenz Adlung | 01 March 2015, 09:15:24 UTC | d2dpaper_supplement.tex edited online with Bitbucket, minor typos | 01 March 2015, 09:15:24 UTC |
| dbcce9a | Clemens Kreutz | 27 February 2015, 14:57:33 UTC | Small change d2d paper | 27 February 2015, 14:57:33 UTC |
| 3980c8f | Lorenz Adlung | 27 February 2015, 11:16:08 UTC | d2dpaper.tex edited online with Bitbucket, minor typos | 27 February 2015, 11:16:08 UTC |
| b77510b | Clemens Kreutz | 27 February 2015, 11:05:14 UTC | ple.m now also accepts parameter names, cells of names and regular expressions. | 27 February 2015, 11:05:14 UTC |
| cfbd928 | Max Schelker | 27 February 2015, 09:48:42 UTC | corrected typos in supplement and main text. removed temp files (do not need to be in repo!) | 27 February 2015, 09:48:42 UTC |
| a1d87f2 | Andreas Raue | 27 February 2015, 03:25:53 UTC | major changes also on the supplementary text | 27 February 2015, 03:25:53 UTC |
| 4f6b490 | Andreas Raue | 27 February 2015, 02:37:34 UTC | I think we are almost there for the main text... | 27 February 2015, 02:37:34 UTC |
| 162a71a | Andreas Raue | 27 February 2015, 00:44:58 UTC | Backout changeset c660c354257f1f83632a8d04db31d48a311b7f87 | 27 February 2015, 00:44:58 UTC |
| 0349af7 | Andreas Raue | 27 February 2015, 00:21:35 UTC | added line breaks for better support of BitBucket | 27 February 2015, 00:21:35 UTC |
| 62d2fa9 | Max Schelker | 26 February 2015, 15:49:13 UTC | added funding to main text and another proposition for the figure | 26 February 2015, 15:49:13 UTC |
| f18481d | Clemens Kreutz | 26 February 2015, 15:44:12 UTC | Paper Supplement: Ein paar Änderungen in Andreas' Teil. | 26 February 2015, 15:44:12 UTC |
| b10252a | Clemens Kreutz | 26 February 2015, 14:46:51 UTC | Paper überarbeitet und gekürzt | 26 February 2015, 14:46:51 UTC |
| dc0a74b | Andreas Raue | 26 February 2015, 14:03:06 UTC | small fixes | 26 February 2015, 14:03:06 UTC |
| 32abf0f | Andreas Raue | 26 February 2015, 04:32:58 UTC | updated word count | 26 February 2015, 04:32:58 UTC |
| fc80d87 | Andreas Raue | 26 February 2015, 02:55:34 UTC | added reference in the main text to the user guide for the raia example as well as the respective section in the supplement. | 26 February 2015, 02:55:34 UTC |
| fd3b4eb | Andreas Raue | 26 February 2015, 02:42:50 UTC | included revisions from Berni and Max | 26 February 2015, 02:42:50 UTC |
| 445bc91 | Andreas Raue | 25 February 2015, 16:23:10 UTC | added generic figure for pathway generated by Graphviz | 25 February 2015, 16:23:10 UTC |
| 5a0d267 | Andreas Raue | 25 February 2015, 16:20:33 UTC | added Clemens and Birgit as authors | 25 February 2015, 16:20:33 UTC |
| d90f044 | Max Schelker | 25 February 2015, 16:09:22 UTC | added ylabels to figure | 25 February 2015, 16:09:22 UTC |
| d6a2d9d | Max Schelker | 25 February 2015, 15:58:42 UTC | updated figure for Application Note | 25 February 2015, 15:58:42 UTC |
| 3fa0dff | Max Schelker | 25 February 2015, 12:03:08 UTC | minor changes for cross platform compatibility | 25 February 2015, 12:03:08 UTC |
| 7d5702b | Max Schelker | 25 February 2015, 11:33:17 UTC | added first draft of figure for the application note. Cleaned up temporary latex files | 25 February 2015, 11:33:17 UTC |
| a58524b | Andreas Raue | 25 February 2015, 00:22:35 UTC | uploaded latex files for application note | 25 February 2015, 00:22:35 UTC |
| bb35523 | Andreas Raue | 24 February 2015, 19:44:38 UTC | minor | 24 February 2015, 19:44:38 UTC |
| 2bd322c | Andreas Raue | 24 February 2015, 19:39:17 UTC | bug fix in new plot function | 24 February 2015, 19:39:17 UTC |
| 77810b0 | Andreas Raue | 24 February 2015, 19:38:57 UTC | Few changes that make the example look nicer | 24 February 2015, 19:38:57 UTC |
| 91d643f | Andreas Raue | 24 February 2015, 17:09:42 UTC | bug fix in cluster function that lead to loss or results in some cases | 24 February 2015, 17:09:42 UTC |
| 927f9f6 | Andreas Raue | 24 February 2015, 17:08:51 UTC | improved model code for Raia example | 24 February 2015, 17:08:51 UTC |
| 9a71c9f | Andreas Raue | 24 February 2015, 17:08:21 UTC | bug fix in new plot functions | 24 February 2015, 17:08:21 UTC |
| 04aa6b4 | Andreas Raue | 24 February 2015, 17:07:56 UTC | added png output for windows systems for new plot functions | 24 February 2015, 17:07:56 UTC |
| 30382d3 | Andreas Raue | 24 February 2015, 17:07:29 UTC | improved code | 24 February 2015, 17:07:29 UTC |
| d59250e | Andreas Raue | 16 February 2015, 16:26:30 UTC | bug fix, is work now if no inputs available | 16 February 2015, 16:26:30 UTC |
| 27b402a | Andreas Raue | 16 February 2015, 16:25:45 UTC | bug fix, sets times correctly also if no dynamic variables | 16 February 2015, 16:25:45 UTC |
| 5ab5fef | Andreas Raue | 16 February 2015, 16:24:48 UTC | bug fix, now work also if there is no data loaded | 16 February 2015, 16:24:48 UTC |
| a695999 | Bernhard Steiert | 11 February 2015, 17:12:15 UTC | Small fix for matlab2tikz | 11 February 2015, 17:12:15 UTC |
| 00045bd | Bernhard Steiert | 11 February 2015, 11:08:02 UTC | Updated the ordering of arguments for arSimuData | 11 February 2015, 11:08:02 UTC |
| 69246fa | Andreas Raue | 11 February 2015, 00:09:36 UTC | Merge | 11 February 2015, 00:09:36 UTC |
| e5a6830 | Andreas Raue | 11 February 2015, 00:07:19 UTC | option to not remove the final mex file but clear the intermediate c files | 11 February 2015, 00:07:19 UTC |
| 4107b04 | Andreas Raue | 11 February 2015, 00:06:47 UTC | nice plot | 11 February 2015, 00:06:47 UTC |
| c48ebef | Andreas Raue | 11 February 2015, 00:06:33 UTC | small bug fixes | 11 February 2015, 00:06:33 UTC |
| 3e4f270 | Andreas Raue | 11 February 2015, 00:04:21 UTC | improved function to simulate and save artificial data. The second index argument is not the index of the plot as given by arPlotter, not the index of a singe data set. This has advantages when simulating dose response data. | 11 February 2015, 00:04:21 UTC |
| bd0ff20 | Bernhard Steiert | 09 February 2015, 13:16:05 UTC | Small fixes for fmincon | 09 February 2015, 13:16:05 UTC |
| 44cff38 | Jan Gleixner | 02 February 2015, 12:12:34 UTC | Added input checking: is at least one OBSERVABLE specified? Fixed input checking: is there an ERROR specified for each OBSERVABLE? Hope this helps other noobs. | 02 February 2015, 12:12:34 UTC |
| 6d88f69 | Andreas Raue | 31 January 2015, 02:57:07 UTC | small bug in new function arRandomPars | 31 January 2015, 02:57:07 UTC |
| cc635c3 | Joep Vanlier | 30 January 2015, 10:59:49 UTC | Also checks for xlsx files when extension is specified as xls. | 30 January 2015, 10:59:49 UTC |
| 3f6c847 | Joep Vanlier | 30 January 2015, 10:47:26 UTC | merge after updating arLoadData with xlsx | 30 January 2015, 10:47:26 UTC |
| 3b2f48b | Joep Vanlier | 30 January 2015, 10:41:57 UTC | Added xlsx as supported format. | 30 January 2015, 10:41:57 UTC |
| 3b4ca50 | Clemens Kreutz | 29 January 2015, 09:29:17 UTC | Bug fix arHighlightY.m | 29 January 2015, 09:29:17 UTC |
| 54f5ca4 | Clemens Kreutz | 29 January 2015, 09:27:06 UTC | Extended functionality of arLoadPars.m | 29 January 2015, 09:27:06 UTC |
| 2964811 | Clemens Kreutz | 29 January 2015, 09:25:29 UTC | arPrint: Slightly extended functionality. | 29 January 2015, 09:25:29 UTC |
| bc60584 | Andreas Raue | 28 January 2015, 20:37:42 UTC | I changed the way how legends are created again. There was a bug for dose response data with multiple conditions in that earlier implementation. | 28 January 2015, 20:37:42 UTC |
| 6055389 | Andreas Raue | 28 January 2015, 13:51:05 UTC | Changed LHS sampling functions. I separated the code that generates random samples into a new function arRandomPars It now allows to both use Latin hyper cube sampling (LHS), but also standard random sampling from the specified prior. A more recent analysis by Viktoria Ehret showed that LHS only provides significant benefit for smaller parameter space. Therefore I decided to change the default to random sampling from the prior, which provides more benefits in my hands... | 28 January 2015, 13:51:05 UTC |
| 4cee49a | Wolfgang Mader | 28 January 2015, 10:38:06 UTC | Merge | 28 January 2015, 10:38:06 UTC |
| d486249 | Wolfgang Mader | 28 January 2015, 10:37:26 UTC | Checking for missing x-plot handle, using default system libs for pdflatex. | 28 January 2015, 10:37:26 UTC |
| 3d4e6d4 | Andreas Raue | 28 January 2015, 00:52:32 UTC | merge and added -dmeta as output format for windows systems (.emf files, vector graphic that can be imported to powerpoint directly) | 28 January 2015, 00:52:32 UTC |
