| 9aa8f57 | David C Sterratt | 06 January 2017, 14:21:12 UTC | Merge branch 'master' of github.com:davidcsterratt/KappaNEURON | 06 January 2017, 14:21:12 UTC |
| 07d9253 | David C Sterratt | 06 January 2017, 14:19:28 UTC | Customise which version of NEURON is installed | 06 January 2017, 14:19:28 UTC |
| 352799b | David C Sterratt | 05 January 2017, 14:32:13 UTC | Update INSTALL.md Link to INSTALL-neuron | 05 January 2017, 14:32:13 UTC |
| d23e6ad | David C Sterratt | 04 February 2016, 11:20:58 UTC | Corrected DOI | 04 February 2016, 11:20:58 UTC |
| 73fd22f | David C Sterratt | 04 February 2016, 11:18:52 UTC | Updated publication details | 04 February 2016, 11:18:52 UTC |
| 5385240 | David C Sterratt | 07 January 2016, 13:30:56 UTC | Updated publication details | 07 January 2016, 13:30:56 UTC |
| 11afed9 | David C. Sterratt | 16 November 2014, 23:04:45 UTC | Font size now 7pt - looks better | 16 November 2014, 23:04:45 UTC |
| 8b25d93 | David C. Sterratt | 16 November 2014, 22:21:32 UTC | Plotting tweaks | 16 November 2014, 22:21:32 UTC |
| e6aa676 | David C. Sterratt | 16 November 2014, 22:21:19 UTC | Made stimulation protocol more like Markram et al (1998) | 16 November 2014, 22:21:19 UTC |
| 36be3e3 | David C. Sterratt | 16 November 2014, 22:20:17 UTC | Image presentation tweaks | 16 November 2014, 22:20:17 UTC |
| aad330c | David C Sterratt | 14 November 2014, 16:14:00 UTC | Tweaks to plotting | 14 November 2014, 16:14:00 UTC |
| 06a799f | David C Sterratt | 14 November 2014, 14:18:52 UTC | Tweaked presentation of ca_pulse demo | 14 November 2014, 14:18:52 UTC |
| 30f8969 | David C. Sterratt | 29 September 2014, 17:27:46 UTC | Enabled elongated demo simulation | 29 September 2014, 17:27:46 UTC |
| c070cd7 | David C. Sterratt | 29 September 2014, 06:13:40 UTC | Updated to use UnchargedSpecies | 29 September 2014, 06:13:40 UTC |
| 2ca7d66 | David C. Sterratt | 28 September 2014, 15:05:47 UTC | Fixed #8: Added UnchargedSpecies class and don't set membrane_flux This is to be applied to species who have had their net current cancelled out int he mod file. The new tests test_twoMembraneSpecies and test_twoMembraneSpeciesOneUncharged demonstrate this. | 28 September 2014, 15:05:47 UTC |
| c2d79f0 | David C. Sterratt | 27 September 2014, 18:25:18 UTC | Further to #8, test showing two fluxes in one compartment | 27 September 2014, 18:25:18 UTC |
| c31aaa7 | David C. Sterratt | 27 September 2014, 13:31:06 UTC | Refactoring to address issue #8: multiple fluxes | 27 September 2014, 13:31:06 UTC |
| c1d47c0 | David C. Sterratt | 27 September 2014, 13:28:37 UTC | Improved comments | 27 September 2014, 13:28:37 UTC |
| 8977f36 | David C. Sterratt | 27 September 2014, 11:16:17 UTC | Merge branch 'master' of github.com:davidcsterratt/KappaNEURON | 27 September 2014, 11:16:17 UTC |
| a4ca590 | David C. Sterratt | 27 September 2014, 11:09:06 UTC | Ignore more files and directories | 27 September 2014, 11:09:06 UTC |
| 4fccb1c | David C. Sterratt | 27 September 2014, 11:07:08 UTC | Removed test_currents.py | 27 September 2014, 11:07:08 UTC |
| 2b9939a | David C Sterratt | 26 September 2014, 10:55:13 UTC | Update README.md Angle bracket round address | 26 September 2014, 10:55:13 UTC |
| 5170a70 | David C Sterratt | 26 September 2014, 10:52:29 UTC | Licence set to GPL v3 | 26 September 2014, 10:52:29 UTC |
| f72bf42 | David C. Sterratt | 26 September 2014, 09:26:15 UTC | Updated documentation | 26 September 2014, 09:26:15 UTC |
| eb699f7 | David C Sterratt | 25 September 2014, 10:04:00 UTC | Set glu charge to 0 | 25 September 2014, 10:04:00 UTC |
| bdb01ae | David C Sterratt | 25 September 2014, 10:03:12 UTC | Only pass flux to membrane_species, but regardless of species charge | 25 September 2014, 10:03:12 UTC |
| 43ff52c | David C Sterratt | 24 September 2014, 16:42:46 UTC | Brought in line with ca_pulse tests; now works | 24 September 2014, 16:42:46 UTC |
| 0fdad93 | David C Sterratt | 24 September 2014, 14:25:40 UTC | Added file to run ca_pulse demo | 24 September 2014, 14:25:40 UTC |
| 409e099 | David C Sterratt | 24 September 2014, 14:23:43 UTC | New test_injectCalciumPump2k2 with actual pumping | 24 September 2014, 14:23:43 UTC |
| 8566ad3 | David C Sterratt | 24 September 2014, 14:22:16 UTC | Use the caPump2.la and caPump2.mod from test directory | 24 September 2014, 14:22:16 UTC |
| a8e9318 | David C Sterratt | 24 September 2014, 14:17:13 UTC | Use self._cur_mapped to map current induced by Kappa onto _db | 24 September 2014, 14:17:13 UTC |
| ce2f896 | David C Sterratt | 24 September 2014, 10:09:28 UTC | Don't try to set initial value of species which are variables but not agents | 24 September 2014, 10:09:28 UTC |
| a43e382 | David C Sterratt | 24 September 2014, 09:27:30 UTC | Make setting observables for membrane_species optional | 24 September 2014, 09:27:30 UTC |
| 817f0bb | David C Sterratt | 24 September 2014, 09:15:46 UTC | Generalised setting up of membrane species | 24 September 2014, 09:15:46 UTC |
| 382242a | David C Sterratt | 23 September 2014, 16:25:41 UTC | Tidying and commenting | 23 September 2014, 16:25:41 UTC |
| 3985cf1 | David C Sterratt | 23 September 2014, 16:04:58 UTC | Put in instructions to run ca_pulse demo | 23 September 2014, 16:04:58 UTC |
| ccd9bf7 | David C Sterratt | 23 September 2014, 16:02:25 UTC | Tidied and commmented | 23 September 2014, 16:02:25 UTC |
| 7bae869 | David C Sterratt | 23 September 2014, 15:34:35 UTC | Ignore build | 23 September 2014, 15:34:35 UTC |
| a531f2d | David C Sterratt | 23 September 2014, 15:33:15 UTC | Moved old tests to demo directory | 23 September 2014, 15:33:15 UTC |
| 5d98ba8 | David C Sterratt | 23 September 2014, 14:29:23 UTC | Reorganised INSTALL instructions | 23 September 2014, 14:29:23 UTC |
| b597a59 | David C Sterratt | 23 September 2014, 14:26:53 UTC | Reorganisation of demo directory | 23 September 2014, 14:26:53 UTC |
| 28ffda5 | David C Sterratt | 23 September 2014, 14:24:22 UTC | Experiment with markdown formatting | 23 September 2014, 14:24:22 UTC |
| 8c32c84 | David C Sterratt | 23 September 2014, 12:00:45 UTC | Fixed links in README.md | 23 September 2014, 12:00:45 UTC |
| c820568 | David C Sterratt | 23 September 2014, 11:53:31 UTC | Skeleton of page now organised | 23 September 2014, 11:53:31 UTC |
| 1463833 | David C Sterratt | 23 September 2014, 11:46:49 UTC | Second attempt at getting links working | 23 September 2014, 11:46:49 UTC |
| 6290264 | David C Sterratt | 23 September 2014, 11:43:54 UTC | Added figures | 23 September 2014, 11:43:54 UTC |
| 42dab67 | David C Sterratt | 23 September 2014, 11:28:49 UTC | Added links to NEURON and SpatialKappa | 23 September 2014, 11:28:49 UTC |
| 9b95065 | David C Sterratt | 22 September 2014, 16:34:25 UTC | Fixed typos | 22 September 2014, 16:34:25 UTC |
| 09b6fbf | David C Sterratt | 22 September 2014, 16:30:36 UTC | Create README.md | 22 September 2014, 16:30:36 UTC |
| 5013263 | David C Sterratt | 22 September 2014, 16:20:43 UTC | More documentation improvements | 22 September 2014, 16:20:43 UTC |
| 282713e | David C Sterratt | 22 September 2014, 16:09:32 UTC | Removed redundant verbose argument and improved docstring | 22 September 2014, 16:09:32 UTC |
| 436ae8c | David C Sterratt | 22 September 2014, 15:37:41 UTC | Improved function documentation. | 22 September 2014, 15:37:41 UTC |
| efc80c4 | David C Sterratt | 22 September 2014, 15:33:37 UTC | Updated notes on variables and functions in KappaNEURON | 22 September 2014, 15:33:37 UTC |
| 5c193be | David C Sterratt | 22 September 2014, 13:47:31 UTC | Removed print statement | 22 September 2014, 13:47:31 UTC |
| cf42004 | David C Sterratt | 19 September 2014, 15:37:35 UTC | Finally computed volume to area ratio using _do_memb_scales() | 19 September 2014, 15:37:35 UTC |
| 45f6e5c | David C Sterratt | 16 September 2014, 14:43:11 UTC | Some basic documentation comments | 16 September 2014, 14:43:11 UTC |
| f424b9f | David C. Sterratt | 15 September 2014, 16:19:11 UTC | Allow multiple membrane_species | 15 September 2014, 16:19:11 UTC |
| 2e12169 | David C. Sterratt | 15 September 2014, 16:18:38 UTC | Increased tolerance in test_injectCalciumPump to 0.15 | 15 September 2014, 16:18:38 UTC |
| fbfbd30 | David C Sterratt | 12 September 2014, 10:47:48 UTC | Ignore sundry files | 12 September 2014, 10:47:48 UTC |
| 7f39ed6 | David C Sterratt | 12 September 2014, 10:46:26 UTC | Documentation updates | 12 September 2014, 10:46:26 UTC |
| 047228a | David C Sterratt | 12 September 2014, 10:45:50 UTC | Switched to keyword arguments for Kappa class | 12 September 2014, 10:45:50 UTC |
| d677467 | David C Sterratt | 12 September 2014, 10:44:54 UTC | Cleaned up _get_memb_flux() | 12 September 2014, 10:44:54 UTC |
| 541a3c9 | David C Sterratt | 12 September 2014, 08:58:03 UTC | Removed redundant _kn_currents() and callback | 12 September 2014, 08:58:03 UTC |
| a3f8cd7 | David C Sterratt | 12 September 2014, 08:47:26 UTC | KappaNEURON class now working as reaction It uses _get_memb_flux() to determine the membrane current, which is read in rxd._currents(). This has required computation of _db to be changed so that its length corresponds to the number of membrane fluxes. It is only computed for Species in self._sources | 12 September 2014, 08:47:26 UTC |
| 3515871 | David C Sterratt | 08 September 2014, 14:23:02 UTC | Create kappa sims in new function _create_kappa_sims(), not _update_indices() This is _update_indicies is called whenever init() is called. This meant that kappa sims (and any associated variables set with setVariable()) were being overridden, leading to failed tests. | 08 September 2014, 14:23:02 UTC |
| bab7c2a | David C Sterratt | 08 September 2014, 14:14:22 UTC | Increase dt for speed and new assertEqualWithinTol() function | 08 September 2014, 14:14:22 UTC |
| 85654fb | David C. Sterratt | 05 September 2014, 16:27:46 UTC | Merge in updated tests | 05 September 2014, 16:27:46 UTC |
| 1cef29e | David C. Sterratt | 05 September 2014, 16:24:05 UTC | Refactored tests | 05 September 2014, 16:24:05 UTC |
| c685d1c | David C. Sterratt | 05 September 2014, 15:49:25 UTC | Fixed bug in simple Ca pump test due to P existing in caPump1.ka | 05 September 2014, 15:49:25 UTC |
| c9d0581 | David C. Sterratt | 05 September 2014, 15:47:57 UTC | Improved debugging output | 05 September 2014, 15:47:57 UTC |
| 198f6b3 | David C. Sterratt | 05 September 2014, 15:47:14 UTC | Taken out duplicated test | 05 September 2014, 15:47:14 UTC |
| bc5300f | David C. Sterratt | 05 September 2014, 10:15:57 UTC | Used get_mode() function in all tests | 05 September 2014, 10:15:57 UTC |
| 28efe3d | David C. Sterratt | 05 September 2014, 10:02:16 UTC | First steps towards generalising the code to allow kappa mechanisms in arbitrary sections | 05 September 2014, 10:02:16 UTC |
| e6b7cea | David C Sterratt | 03 September 2014, 16:08:04 UTC | Removed some print cruft | 03 September 2014, 16:08:04 UTC |
| e4cabd4 | David C Sterratt | 02 September 2014, 16:00:41 UTC | Nonlinear calcium pump test working | 02 September 2014, 16:00:41 UTC |
| bbe3504 | David C Sterratt | 02 September 2014, 16:00:04 UTC | Updated comment | 02 September 2014, 16:00:04 UTC |
| 33019d5 | David C Sterratt | 02 September 2014, 15:59:18 UTC | Updated comments | 02 September 2014, 15:59:18 UTC |
| fbd8ab3 | David C Sterratt | 02 September 2014, 15:55:41 UTC | Updated comments | 02 September 2014, 15:55:41 UTC |
| 3422cc2 | David C Sterratt | 29 August 2014, 15:29:29 UTC | Run all tests from Makefile | 29 August 2014, 15:29:29 UTC |
| 23c40da | David C Sterratt | 29 August 2014, 14:26:10 UTC | Added test_injectCalciumPumpGHK | 29 August 2014, 14:26:10 UTC |
| 0328298 | David C Sterratt | 29 August 2014, 13:27:59 UTC | Test 2 (Ca accumulation with pump) now working | 29 August 2014, 13:27:59 UTC |
| 7c03453 | David C Sterratt | 29 August 2014, 13:22:18 UTC | Changed suffix to caPump2 | 29 August 2014, 13:22:18 UTC |
| 6e09d76 | David C Sterratt | 29 August 2014, 13:21:30 UTC | Added GHK flag | 29 August 2014, 13:21:30 UTC |
| de3ff5f | David C Sterratt | 29 August 2014, 13:20:49 UTC | Added vclamp argument to functions | 29 August 2014, 13:20:49 UTC |
| 84a44cd | David C Sterratt | 29 August 2014, 13:19:35 UTC | Added the calculations for Calcium pump test | 29 August 2014, 13:19:35 UTC |
| 9c5b636 | David C Sterratt | 28 August 2014, 11:32:14 UTC | Refactored test code | 28 August 2014, 11:32:14 UTC |
| a1478ff | David C Sterratt | 27 August 2014, 10:58:13 UTC | Work on GHK test case including factoring out shared code | 27 August 2014, 10:58:13 UTC |
| a7f316c | David C Sterratt | 26 August 2014, 15:11:41 UTC | Completed tests of simple calcium injection | 26 August 2014, 15:11:41 UTC |
| 24e77b6 | David C Sterratt | 26 August 2014, 12:23:31 UTC | Added comment and numpy->np | 26 August 2014, 12:23:31 UTC |
| 1038f44 | David C Sterratt | 21 August 2014, 16:35:54 UTC | Intermediate stage in which it looks as though calcium accumulation is working | 21 August 2014, 16:35:54 UTC |
| 1a2751b | David C Sterratt | 19 August 2014, 15:10:19 UTC | Graphs plotted to help debug | 19 August 2014, 15:10:19 UTC |
| cd2d472 | David C Sterratt | 12 August 2014, 16:00:34 UTC | Merged simple Ca accumulation test from master | 12 August 2014, 16:00:34 UTC |
| b0b200d | David C Sterratt | 12 August 2014, 15:57:43 UTC | Test of simple Ca accumulation added | 12 August 2014, 15:57:43 UTC |
| 5101bbd | David C Sterratt | 12 August 2014, 15:53:29 UTC | Commented out _kn_currents callback | 12 August 2014, 15:53:29 UTC |
| c956327 | David C Sterratt | 08 August 2014, 16:21:24 UTC | Shorter simulations for faster tests | 08 August 2014, 16:21:24 UTC |
| 3cb3638 | David C Sterratt | 08 August 2014, 16:11:38 UTC | Merge branch 'master' into continuous_influx_currents2_db | 08 August 2014, 16:11:38 UTC |
| 26b9c39 | David C Sterratt | 08 August 2014, 14:04:49 UTC | Moved boilerplate code to class to allow for multiple runs | 08 August 2014, 14:04:49 UTC |
| f8501f1 | David C Sterratt | 08 August 2014, 14:04:15 UTC | More informative error message when failure to set initial concentration | 08 August 2014, 14:04:15 UTC |
| 7fb57b6 | David C Sterratt | 08 August 2014, 14:03:18 UTC | Fixed error in file which caused test to fail | 08 August 2014, 14:03:18 UTC |
| 64e9bd6 | David C Sterratt | 06 August 2014, 16:25:20 UTC | Basis for multiple tests now working | 06 August 2014, 16:25:20 UTC |
