History Graph
History Graph
Commit | Author | Details | Committed | |||
---|---|---|---|---|---|---|
4884f5695b3e | tlemaire | added HH point neuron | Jul 21 2020 | |||
c9894bdbd61c | tlemaire | removed SilentMRGNode class (now generated on-the-fly in analysis notebook) | Jul 15 2020 | |||
a8ba89d095f5 | tlemaire | implemented passiveNeuron wrapper function to generate PassiveNeuron class… | Jul 15 2020 | |||
3998f71a5a6f | tlemaire | added LogBatch getSerlializedOutput and getEntryOutput methods. | Jul 15 2020 | |||
bebce73d9405 | tlemaire | updated MANIFEST file. | Jun 3 2020 | |||
5b268a756bc5 | tlemaire | added TCtweak70 and TCtweak50 cases. | Apr 23 2020 | |||
a6e6abff99bc | tlemaire | added TC2 class | Apr 23 2020 | |||
67531a20cdce | tlemaire | placed StimObject class in a separate stimobj module. added boltons dependency… | Apr 21 2020 | |||
9239911c1f35 | tlemaire | added ASTIM_REL_CONV_THR to constants file. | Mar 31 2020 | |||
4e96a816343e | tlemaire | added MRG fs lookup. | Mar 30 2020 | |||
8f0bbde630a7 | tlemaire | renamed fibers point-neuron models for better interpretability. completed fiber… | Mar 27 2020 | |||
a4eafd9f8059 | tlemaire | corrected typo in SweeneyNode description. | Mar 26 2020 | |||
066e8e416305 | tlemaire | added polyfit amd extrapolate capabilities to Lookup class. | Mar 19 2020 | |||
a46f7227e040 | tlemaire | added better handling of ybounds in timeseries. added MRG neuron class. | Feb 27 2020 | |||
68961385d17e | tlemaire | added copy method to all model classes. added TI US notebook. updated… | Feb 11 2020 | |||
ed7412335d9f | tlemaire | Initialized LFS. deleted lookup files from neuron folder. | Feb 3 2020 | |||
9d0666784d2d | tlemaire | Created AcousticSource class to be used for US simulations. | Feb 3 2020 | |||
eec847e65a7a | tlemaire | added sundt fs lookups. adapted RS fs lookups. adapted nbls.getLookup2D method… | Jan 26 2020 | |||
c995e8999df7 | tlemaire | Modified Lookup class (new properties, corrected methods). | Jan 26 2020 | |||
5e77509ee19d | tlemaire | added membrane area attributes to IB and STN neurons | Jan 22 2020 | |||
8478fde7a5d4 | tlemaire | Automated getModel using automatically generated dictionary of models with… | Jan 14 2020 | |||
5c9777d249d7 | tlemaire | updated STN neuron notebook with correct model parameters and enabled… | Dec 10 2019 | |||
d27e95459175 | tlemaire | added sundt lookups | Nov 27 2019 | |||
977bea19e55e | tlemaire | commented useless parameters in Sundt class | 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 | |||
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 | |||
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 | |||
6fb96a1716d1 | tlemaire | corrected tirations log file | Sep 18 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 | |||
6f5a204770f8 | tlemaire | added sweeney lookups | Sep 3 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 | |||
4f5fb5ee0829 | tlemaire | implemented SweeneyNode class. added PointNeuron.chooseTimeStep method to… | Aug 26 2019 | |||
db880034dc26 | tlemaire | harmonized peaks/spikes detection process across the package. | Aug 22 2019 | |||
3146cab6bade | tlemaire | added iCap to plot variables. added colormap option for comparative plots even… | Aug 15 2019 | |||
1b242e25ca45 | tlemaire | added plot_intensity_vs_amplitude.py script | Aug 14 2019 | |||
ec01e1e58099 | tlemaire | fixed error in bls.filecodes | Jul 29 2019 | |||
8e1403abecb9 | tlemaire | updated README to latest changes. | Jul 24 2019 | |||
dc37f0afbd17 | tlemaire | removed all static quasiSteadyStates definition in neuron classes. | Jul 17 2019 | |||
bce60bf70097 | tlemaire | adapted findModifiedEq to work with iterables as inputs | Jul 17 2019 | |||
f113d822d4fb | tlemaire | added findModifiedEq function to utils, using brentq to find a new equilibrium… | Jul 17 2019 | |||
17b59c14aa75 | tlemaire | modified TC neuron steadyStates method. | Jul 16 2019 | |||
d50bf6119d40 | tlemaire | started implementing SonicTranslator.parseSteadyStates method. Implemented… | Jul 15 2019 | |||
e34dcc6d2cb9 | tlemaire | reordered TC states. minor changes in translators. | Jul 5 2019 | |||
6755d10c0e98 | tlemaire | add permeability_constant_pattern to PointNeuronTranslator | Jul 4 2019 | |||
a788320b3aae | tlemaire | added new functionalities to Trnalsator class (now used in SonicTranslator). | Jul 4 2019 | |||
aa1ed8d9b040 | tlemaire | added getClosure method to Translator class. | Jul 4 2019 | |||
b427c3fd93df | tlemaire | added getClosure to translator. added getConstantsDict function in constants.py | Jul 3 2019 | |||
be3e09e67984 | tlemaire | removed test lookup file | Jul 1 2019 | |||
d1a3fbaefd83 | tlemaire | added option to provide simAndSave or simulate to batches. implemented addMeta… | Jul 1 2019 | |||
f22a47305c1e | tlemaire | improved SonicTranslator class | Jun 30 2019 | |||
4937955d0214 | tlemaire | adapted methods of all classes into classmethods and staticmethods when… | Jun 29 2019 | |||
b73594f4d58b | tlemaire | moved lookup to core module. moved getLookup methods to nbls class. | Jun 27 2019 | |||
dffee6926b85 | tlemaire | added fs (spatially-averaged) as input to nbls model. defined SmartLookup class… | Jun 26 2019 | |||
07c34eeed0f7 | tlemaire | added test at bottom of lookups module | Jun 26 2019 | |||
9965ddc0005d | tlemaire | improved steadyStates definition in TC and STN neurons. corrected dQdt pltvar… | Jun 25 2019 | |||
f83e0e973bd3 | tlemaire | corrected README | Jun 25 2019 | |||
acf299185987 | tlemaire | removed unnecessary functions from pneuron | Jun 25 2019 | |||
db8cc8e2b5ff | tlemaire | added automatic effRates function definition in pneuron.parse method. removed… | Jun 25 2019 | |||
4742d6a43494 | tlemaire | finished implementing pneuron.buildDerEffStates method to automatically create… | Jun 25 2019 | |||
83ff47370d86 | tlemaire | defined separate lookup decorator for bls.computePMparams method. updated… | Jun 24 2019 | |||
a96a900ad4b4 | tlemaire | define dLookUp class to perform lookup projections and interpolations | Jun 20 2019 | |||
6c10d4162d71 | tlemaire | added default output directory ("dump"). cleaned up neuron classes. | Jun 20 2019 | |||
fdebb58e8442 | tlemaire | refefined derEffstates construction to return a dictionary of function. | Jun 19 2019 | |||
becd2527f268 | tlemaire | corrected Cinf error in ThalamoCortical neuron | Jun 19 2019 | |||
98942bac6b56 | tlemaire | redefined derStates and steadyStates as dictionary of lambda functions | Jun 19 2019 | |||
26fe1e08a408 | tlemaire | cleaned up neuron classes. redefined currents to return functions instead of… | Jun 19 2019 | |||
7b2aee9851af | tlemaire | replaced obscur states list by explicit dictionary in all currents methods | Jun 18 2019 | |||
00f57af96cfb | tlemaire | replaced obscur states list by explicit states dictionary in derStates and… | Jun 18 2019 | |||
af7294977045 | tlemaire | adapted MechSimParser for use in run_lookups.py | Jun 13 2019 | |||
b42a0de93240 | tlemaire | updated all file headers | Jun 12 2019 | |||
0ab79b08684a | tlemaire | adapted README recipe to cleaned up neuron classes | Jun 12 2019 | |||
cc309fa78cd9 | tlemaire | cleaned-up all neuron classes | Jun 12 2019 | |||
0028dbdfe69f | tlemaire | added neuron templyte class. added procedure to follow to add new neuron types… | Jun 11 2019 | |||
50103226d72b | tlemaire | moved getLowIntensitiesSTN to STN class | Jun 6 2019 |
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