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History Graph
History Graph
Commit | Author | Details | Committed | ||||
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8478fde7a5d4 | tlemaire | Automated getModel using automatically generated dictionary of models with… | Jan 14 2020 | ||||
382b41779471 | tlemaire | Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic | Dec 14 2019 | ||||
a0b6724a45a5 | tlemaire | removed plotVarQSSDynamics function from QSS and plot_QSS | Dec 14 2019 | ||||
dd4bcd97ad83 | vicari | Merge solved | Dec 13 2019 | ||||
cad5a41a29b0 | vicari | Correction in of the find_tpeaks function in postpro.py | Dec 13 2019 | ||||
5c9777d249d7 | tlemaire | updated STN neuron notebook with correct model parameters and enabled… | Dec 10 2019 | ||||
4a918211cc11 | tlemaire | added boundDataframe method to postpro module | Dec 9 2019 | ||||
d0b57c5e137d | tlemaire | re-ran and completed STN notebook | Dec 6 2019 | ||||
82b1e406d267 | tlemaire | updated README with instructions on how to cite. | Dec 4 2019 | ||||
bac984960467 | tlemaire | corrected nbls fullDerivatives, simFull and simHybrid methods (removed phi… | Dec 4 2019 | ||||
a29eea02e330 | tlemaire | changed Lookup repr method. added test_lkp test file. | Dec 4 2019 | ||||
f8107574d0a8 | tlemaire | added threshold module with isolated threshold function (now used for all… | Dec 2 2019 | ||||
19881e729753 | tlemaire | mofified SPIKE_MIN_QAMP and SPIKE_MIN_VAMP from 5 (nC/cm2 - mV) to 3 | Nov 27 2019 | ||||
d27e95459175 | tlemaire | added sundt lookups | Nov 27 2019 | ||||
6797e5e1f52b | tlemaire | moved pushbullet key file to package root | Nov 26 2019 | ||||
977bea19e55e | tlemaire | commented useless parameters in Sundt class | Nov 26 2019 | ||||
6deb0da8868d | tlemaire | added internal bls.simUntilConvergence method (without decorators) to enable… | Nov 26 2019 | ||||
647c007ad5d7 | tlemaire | added Eleak logging upon Sundt class creation. | Nov 25 2019 | ||||
974a5f7d7fef | tlemaire | cleaned up Sundt class | Nov 22 2019 | ||||
b46ab57b16d3 | tlemaire | corrected borg-graham formalism methods | Nov 22 2019 | ||||
6197f85f0709 | tlemaire | corrected Astim factor error in pneuron desc. added extra parsing methods | Nov 20 2019 | ||||
456fa71d226b | tlemaire | added qss_vars and pulse-avg run options to nbls simSonic method. | Nov 20 2019 | ||||
d14a124a4078 | tlemaire | implemented GenericPlot.wraptitle method | Nov 15 2019 | ||||
681033068b15 | tlemaire | updated titrations log | Nov 15 2019 | ||||
5da540f0f401 | tlemaire | moved model.simAndSave to utils to facilitate use in ExSONIC | Nov 14 2019 | ||||
36119dd01aec | tlemaire | moved filecode function to utils | Nov 14 2019 | ||||
de255e65bccc | tlemaire | Major update: | Nov 14 2019 | ||||
a26469ca67dc | tlemaire | added equality operators to TimeProtocol and PulsedProtocol classes. | Nov 14 2019 | ||||
4a5626da478c | tlemaire | improved filecodes generation from meta dictionary in Model.filecode | Nov 13 2019 | ||||
bc1800471252 | tlemaire | created Timeprotocol and PulsedProtocol classes, now used in pneuron, nbls and… | Nov 13 2019 | ||||
fa8f94b4198c | tlemaire | checked iM taup against ref. (Yamada 1989) | Nov 7 2019 | ||||
f1d2ab4cfb4b | tlemaire | added PointNeuron alphaBorgGaham and betaBorgGraham methods, now used for sundt… | Nov 7 2019 | ||||
163afcce99af | tlemaire | renamed PhaseDiagram to SpikePlot (more appropriate). simplified Sundt model… | Nov 6 2019 | ||||
a2c1e3e2eb02 | tlemaire | modified nbls.QSSderivatives and nbls.__simQSS to work with any specified… | Nov 6 2019 | ||||
7a48bab58176 | tlemaire | renamed iKm to iM and kmk gate to p in Sundt to match formalism ot Cortical… | Nov 5 2019 | ||||
54b7854b35c3 | tlemaire | parametrized Caiinf in sundt model (checked for correct equivalence at Vm0) | Nov 5 2019 | ||||
15f0e82253ac | tlemaire | corrected error in effvars for plotGatingKinetics | Nov 5 2019 | ||||
7a4a9166c1ad | tlemaire | corrected Ikd kinetics (n and l zeta signs matching those of Borg-Graham 1991… | Nov 5 2019 | ||||
58e5ce4415c8 | vicari | Sign correction and comments | Nov 5 2019 | ||||
fc00bf556d5f | vicari | Correction in potassium kinetics | Nov 5 2019 | ||||
a35753429a7e | vicari | Correction of the delayed rectifier potassium kinetics | Nov 5 2019 | ||||
83ea55354a98 | tlemaire | added time step reduction to sundt class. code is running but simulations and… | Nov 1 2019 | ||||
894410e31f4a | tlemaire | debugged sundt class (estim now running) | Nov 1 2019 | ||||
3d652adfb7ce | tlemaire | further corrections to the sundt class, and implementation of Eleak computation… | Nov 1 2019 | ||||
5a508487f9f1 | tlemaire | identified parameters in Sundt expressions and highlighted discrepancies with… | Nov 1 2019 | ||||
eb70f6afb883 | tlemaire | corrected errors in sundt class (now compiling). minf and taum both seem off… | Nov 1 2019 | ||||
ab186ad4e8bf | tlemaire | Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic | Nov 1 2019 | ||||
0394f06c57fd | tlemaire | modified README | Nov 1 2019 | ||||
1a18aaa3abec | vicari | implemented Sundt model | Nov 1 2019 | ||||
0638d724be40 | tlemaire | added sundt import to neurons. corrected pushbullet requirement in setup | Oct 15 2019 | ||||
aee2c4e6cb21 | tlemaire | added Lookup.tile and modified SmartLookup.projectDC. modified nbls. | Oct 10 2019 | ||||
20f96c135bce | tlemaire | defined Lookup algorihtmic operators. defined OnOffSimulator class. defined… | Oct 7 2019 | ||||
d992992a3693 | tlemaire | commented out numdifftools import. updated README.md | Oct 2 2019 | ||||
06580e30545f | tlemaire | corrected addThresholdCurve. updated astim_titrations.log with latest batch | Oct 1 2019 | ||||
21401e741886 | tlemaire | updated ActivationMap (removed correctAmp method). corrected TimeSeriesPlot. | Sep 30 2019 | ||||
fedd732d1290 | tlemaire | changed TimeSeriesPlot.addLegend from static method to instance method | Sep 27 2019 | ||||
a4e909590831 | tlemaire | corrected unwanted changes to sublime-project file | Sep 26 2019 | ||||
ed57fe2edc40 | tlemaire | added rotAroundPoint2D function to utils | Sep 23 2019 | ||||
43cdd51258a0 | tlemaire | added nan return in pow2Search if x > xmax. added getPow10 to utils | Sep 20 2019 | ||||
d0cc76d4af6b | tlemaire | changed log level for logCache found entry | Sep 19 2019 | ||||
ec466c361f8c | tlemaire | added fillLine function to utils. added Parser.addOverwrite method (opposite of… | Sep 19 2019 | ||||
dd102470b272 | tlemaire | added method type in nbls.simulate logging | Sep 18 2019 | ||||
6fb96a1716d1 | tlemaire | corrected tirations log file | Sep 18 2019 | ||||
69faba51e2c1 | tlemaire | in PWSimulator.compute: added division of offset interval in several slices if… | Sep 17 2019 | ||||
133c0ab1ac73 | tlemaire | changed outputdir to keyword argument in queue items in Model.checkOutputDir… | Sep 17 2019 | ||||
f1092e3356eb | tlemaire | added Parser.addCheckForOutput method, now used in run_*** scripts to… | Sep 17 2019 | ||||
89e117f6ffaa | tlemaire | add handling of positional and keyword arguments in Batch queues. added… | Sep 17 2019 | ||||
8cf15b137151 | tlemaire | abstracted Model.simQueue method (now defined in children classes). changed… | Sep 17 2019 | ||||
83cf10bbf6e7 | tlemaire | replaced hypersampling error by warning message PWSimulator.downsample | Sep 17 2019 | ||||
6d8b2b3d4804 | tlemaire | updated titrations log | Sep 16 2019 | ||||
1d0578736cc2 | tlemaire | Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic | Sep 13 2019 | ||||
0c9e09419d16 | tlemaire | added vsteprange to VlcampParser. changed timeseries default onset from… | Sep 13 2019 | ||||
9b11f9b84f6e | tlemaire | Merge branch 'master' of https://c4science.ch/diffusion/4670/pointnice | Sep 13 2019 | ||||
5f918009eb20 | tlemaire | re-computed lookups of FH, FS, IB, LTS, RE, RS, STN and TC neurons | Sep 13 2019 | ||||
d65e74f5c30c | tlemaire | implemmented inheritance scheme for PointNeuron.chooseTimeStep method | Sep 11 2019 | ||||
737ddddddd46 | tlemaire | added sweeney neuron lookups | Sep 11 2019 | ||||
bd840351d13f | tlemaire | corrected SweeneyNode alpham equation according to Basser and Roth, 1991. | Sep 10 2019 | ||||
01c2a27636c1 | tlemaire | added prependDataframe method to postpro module. | Sep 6 2019 | ||||
c4d24a293f93 | tlemaire | renamed Simulator.resample method to downsample in order to avoid confusion… | Sep 6 2019 | ||||
107df2b92970 | tlemaire | corrected minor issues in spike detection functions (dt bounding for resampling… | Sep 6 2019 | ||||
ec87894d9435 | tlemaire | modified find_tpeaks to work with irregular time vectors. | Sep 6 2019 | ||||
614c56792d61 | tlemaire | expanded charge range for pneuron.getLookup | Sep 4 2019 | ||||
fdf554e5e6ab | tlemaire | updated notebooks | Sep 4 2019 | ||||
6f5a204770f8 | tlemaire | added sweeney lookups | Sep 3 2019 | ||||
8102e979f684 | tlemaire | updated SPIKE_MIN_VAMP to allow robust spike detection for sweeney model | Sep 3 2019 | ||||
fd4639a4c602 | tlemaire | parametrised Qm plot range to be neuron-specific. Solved issue with pbar update. | Sep 2 2019 | ||||
d2ccd21d9889 | tlemaire | corrected crucial error in nbls.spatialAverage method. corrected Cm0 and Qm0… | Sep 2 2019 | ||||
4c34c2a9dc9a | tlemaire | adapted test_sims (avoiding sweeney neuron) | Aug 29 2019 | ||||
f19b1648b5ed | tlemaire | remoed sweeney lookups (need to figure out the reason for weird profiles first). | Aug 29 2019 | ||||
1b3cffe95e7a | tlemaire | added sweeney lookups (ASTIM not working yet). added fixLookup to remove single… | Aug 29 2019 | ||||
8226a9490c9b | tlemaire | adapted constants to enable sweeney lookups creation. | Aug 26 2019 | ||||
4f5fb5ee0829 | tlemaire | implemented SweeneyNode class. added PointNeuron.chooseTimeStep method to… | Aug 26 2019 | ||||
d7855a1dd087 | tlemaire | implemented pow2Search function using an incremental power of 2 search to… | Aug 26 2019 | ||||
4821f3c94b73 | tlemaire | corrected minor mistake in getCommonLabel | Aug 24 2019 | ||||
fdf57ea352bd | tlemaire | added getCommonLabel method to ComparativePlot (now used to determine figure… | Aug 24 2019 | ||||
db880034dc26 | tlemaire | harmonized peaks/spikes detection process across the package. | Aug 22 2019 | ||||
3c76710406c6 | tlemaire | removed paper figures folder (now in separate repo) | Aug 19 2019 | ||||
0d24b201dea4 | tlemaire | added figtitle and getModel as GenericPlot methods | Aug 16 2019 | ||||
3146cab6bade | tlemaire | added iCap to plot variables. added colormap option for comparative plots even… | Aug 15 2019 | ||||
2278e599a753 | tlemaire | added automatic solution prepending to all simulate methods (to treat initial… | Aug 14 2019 |
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