Diffusion PySONIC (old) (master) History

neurons
masterfe5b0a532e32201006403ef…

Jul 21 2020

specified logger handler stream to sys.stdout to avoid red background in…
fd4b6531e872
·tlemaire on Jul 21 2020, 20:03.
introduced default celsius (36°C) as a PointNeuron property shared by all…
42a3be29b47b
·tlemaire on Jul 21 2020, 16:18.
added celsius parameter (36.0) to cortical and thalamic neurons.
133be2f739dd
·tlemaire on Jul 21 2020, 15:41.
added HH point neuron
4884f5695b3e
·tlemaire on Jul 21 2020, 15:28.

Jul 15 2020

removed SilentMRGNode class (now generated on-the-fly in analysis notebook)
c9894bdbd61c
·tlemaire on Jul 15 2020, 21:24.
implemented passiveNeuron wrapper function to generate PassiveNeuron class…
a8ba89d095f5
·tlemaire on Jul 15 2020, 12:18.
added LogBatch getSerlializedOutput and getEntryOutput methods.
3998f71a5a6f
·tlemaire on Jul 15 2020, 10:41.

Jun 3 2020

updated MANIFEST file.
bebce73d9405
·tlemaire on Jun 3 2020, 16:57.

Apr 23 2020

added TCtweak70 and TCtweak50 cases.
5b268a756bc5
·tlemaire on Apr 23 2020, 12:41.
added TC2 class
a6e6abff99bc
·tlemaire on Apr 23 2020, 12:06.

Apr 21 2020

placed StimObject class in a separate stimobj module. added boltons dependency…
67531a20cdce
·tlemaire on Apr 21 2020, 12:18.

Mar 31 2020

added ASTIM_REL_CONV_THR to constants file.
9239911c1f35
·tlemaire on Mar 31 2020, 18:41.

Mar 30 2020

added MRG fs lookup.
4e96a816343e
·tlemaire on Mar 30 2020, 13:16.

Mar 27 2020

renamed fibers point-neuron models for better interpretability. completed fiber…
8f0bbde630a7
·tlemaire on Mar 27 2020, 20:37.

Mar 26 2020

corrected typo in SweeneyNode description.
a4eafd9f8059
·tlemaire on Mar 26 2020, 21:16.

Mar 19 2020

added polyfit amd extrapolate capabilities to Lookup class.
066e8e416305
·tlemaire on Mar 19 2020, 12:13.

Feb 27 2020

added better handling of ybounds in timeseries. added MRG neuron class.
a46f7227e040
·tlemaire on Feb 27 2020, 23:02.

Feb 11 2020

added copy method to all model classes. added TI US notebook. updated…
68961385d17e
·tlemaire on Feb 11 2020, 07:55.

Feb 3 2020

Initialized LFS. deleted lookup files from neuron folder.
ed7412335d9f
·tlemaire on Feb 3 2020, 14:32.
Created AcousticSource class to be used for US simulations.
9d0666784d2d
·tlemaire on Feb 3 2020, 14:26.

Jan 26 2020

added sundt fs lookups. adapted RS fs lookups. adapted nbls.getLookup2D method…
eec847e65a7a
·tlemaire on Jan 26 2020, 23:37.
Modified Lookup class (new properties, corrected methods).
c995e8999df7
·tlemaire on Jan 26 2020, 19:15.

Jan 22 2020

added membrane area attributes to IB and STN neurons
5e77509ee19d
·tlemaire on Jan 22 2020, 15:37.

Jan 14 2020

Automated getModel using automatically generated dictionary of models with…
8478fde7a5d4
·tlemaire on Jan 14 2020, 17:18.

Dec 10 2019

updated STN neuron notebook with correct model parameters and enabled…
5c9777d249d7
·tlemaire on Dec 10 2019, 17:14.

Nov 27 2019

added sundt lookups
d27e95459175
·tlemaire on Nov 27 2019, 15:23.

Nov 26 2019

commented useless parameters in Sundt class
977bea19e55e
·tlemaire on Nov 26 2019, 18:40.

Nov 25 2019

added Eleak logging upon Sundt class creation.
647c007ad5d7
·tlemaire on Nov 25 2019, 12:22.

Nov 22 2019

cleaned up Sundt class
974a5f7d7fef
·tlemaire on Nov 22 2019, 18:42.
corrected borg-graham formalism methods
b46ab57b16d3
·tlemaire on Nov 22 2019, 18:36.

Nov 7 2019

checked iM taup against ref. (Yamada 1989)
fa8f94b4198c
·tlemaire on Nov 7 2019, 14:43.
added PointNeuron alphaBorgGaham and betaBorgGraham methods, now used for sundt…
f1d2ab4cfb4b
·tlemaire on Nov 7 2019, 12:44.

Nov 6 2019

renamed PhaseDiagram to SpikePlot (more appropriate). simplified Sundt model…
163afcce99af
·tlemaire on Nov 6 2019, 19:33.
modified nbls.QSSderivatives and nbls.__simQSS to work with any specified…
a2c1e3e2eb02
·tlemaire on Nov 6 2019, 15:46.

Nov 5 2019

renamed iKm to iM and kmk gate to p in Sundt to match formalism ot Cortical…
7a48bab58176
·tlemaire on Nov 5 2019, 22:35.
parametrized Caiinf in sundt model (checked for correct equivalence at Vm0)
54b7854b35c3
·tlemaire on Nov 5 2019, 18:16.
corrected error in effvars for plotGatingKinetics
15f0e82253ac
·tlemaire on Nov 5 2019, 17:17.
corrected Ikd kinetics (n and l zeta signs matching those of Borg-Graham 1991…
7a4a9166c1ad
·tlemaire on Nov 5 2019, 16:14.
Sign correction and comments
58e5ce4415c8
·vicari on Nov 5 2019, 14:31.
Correction in potassium kinetics
fc00bf556d5f
·vicari on Nov 5 2019, 13:29.
Correction of the delayed rectifier potassium kinetics
a35753429a7e
·vicari on Nov 5 2019, 13:15.

Nov 1 2019

added time step reduction to sundt class. code is running but simulations and…
83ea55354a98
·tlemaire on Nov 1 2019, 17:49.
debugged sundt class (estim now running)
894410e31f4a
·tlemaire on Nov 1 2019, 17:38.
further corrections to the sundt class, and implementation of Eleak computation…
3d652adfb7ce
·tlemaire on Nov 1 2019, 17:36.
identified parameters in Sundt expressions and highlighted discrepancies with…
5a508487f9f1
·tlemaire on Nov 1 2019, 17:08.
corrected errors in sundt class (now compiling). minf and taum both seem off…
eb70f6afb883
·tlemaire on Nov 1 2019, 14:54.
implemented Sundt model
1a18aaa3abec
·vicari on Nov 1 2019, 14:40.

Oct 15 2019

added sundt import to neurons. corrected pushbullet requirement in setup
0638d724be40
·tlemaire on Oct 15 2019, 17:33.

Oct 10 2019

added Lookup.tile and modified SmartLookup.projectDC. modified nbls.
aee2c4e6cb21
·tlemaire on Oct 10 2019, 16:48.

Sep 18 2019

corrected tirations log file
6fb96a1716d1
·tlemaire on Sep 18 2019, 18:05.

Sep 13 2019

Merge branch 'master' of https://c4science.ch/diffusion/4670/pysonic
1d0578736cc2
·tlemaire on Sep 13 2019, 14:28.
added vsteprange to VlcampParser. changed timeseries default onset from…
0c9e09419d16
·tlemaire on Sep 13 2019, 14:27.
Merge branch 'master' of https://c4science.ch/diffusion/4670/pointnice
9b11f9b84f6e
·tlemaire on Sep 13 2019, 14:17.
re-computed lookups of FH, FS, IB, LTS, RE, RS, STN and TC neurons
5f918009eb20
·tlemaire on Sep 13 2019, 14:16.

Sep 11 2019

implemmented inheritance scheme for PointNeuron.chooseTimeStep method
d65e74f5c30c
·tlemaire on Sep 11 2019, 15:51.
added sweeney neuron lookups
737ddddddd46
·tlemaire on Sep 11 2019, 14:03.

Sep 10 2019

corrected SweeneyNode alpham equation according to Basser and Roth, 1991.
bd840351d13f
·tlemaire on Sep 10 2019, 15:01.

Sep 3 2019

added sweeney lookups
6f5a204770f8
·tlemaire on Sep 3 2019, 18:43.

Aug 29 2019

remoed sweeney lookups (need to figure out the reason for weird profiles first).
f19b1648b5ed
·tlemaire on Aug 29 2019, 19:54.
added sweeney lookups (ASTIM not working yet). added fixLookup to remove single…
1b3cffe95e7a
·tlemaire on Aug 29 2019, 10:01.

Aug 26 2019

implemented SweeneyNode class. added PointNeuron.chooseTimeStep method to…
4f5fb5ee0829
·tlemaire on Aug 26 2019, 14:57.

Aug 22 2019

harmonized peaks/spikes detection process across the package.
db880034dc26
·tlemaire on Aug 22 2019, 15:31.

Aug 15 2019

added iCap to plot variables. added colormap option for comparative plots even…
3146cab6bade
·tlemaire on Aug 15 2019, 21:38.

Aug 14 2019

added plot_intensity_vs_amplitude.py script
1b242e25ca45
·tlemaire on Aug 14 2019, 11:49.

Jul 29 2019

fixed error in bls.filecodes
ec01e1e58099
·tlemaire on Jul 29 2019, 17:24.

Jul 24 2019

updated README to latest changes.
8e1403abecb9
·tlemaire on Jul 24 2019, 11:44.

Jul 17 2019

removed all static quasiSteadyStates definition in neuron classes.
dc37f0afbd17
·tlemaire on Jul 17 2019, 20:05.
adapted findModifiedEq to work with iterables as inputs
bce60bf70097
·tlemaire on Jul 17 2019, 17:19.
added findModifiedEq function to utils, using brentq to find a new equilibrium…
f113d822d4fb
·tlemaire on Jul 17 2019, 15:51.

Jul 16 2019

modified TC neuron steadyStates method.
17b59c14aa75
·tlemaire on Jul 16 2019, 18:57.

Jul 15 2019

started implementing SonicTranslator.parseSteadyStates method. Implemented…
d50bf6119d40
·tlemaire on Jul 15 2019, 20:22.

Jul 5 2019

reordered TC states. minor changes in translators.
e34dcc6d2cb9
·tlemaire on Jul 5 2019, 04:48.

Jul 4 2019

add permeability_constant_pattern to PointNeuronTranslator
6755d10c0e98
·tlemaire on Jul 4 2019, 23:41.
added new functionalities to Trnalsator class (now used in SonicTranslator).
a788320b3aae
·tlemaire on Jul 4 2019, 22:06.
added getClosure method to Translator class.
aa1ed8d9b040
·tlemaire on Jul 4 2019, 17:44.

Jul 3 2019

added getClosure to translator. added getConstantsDict function in constants.py
b427c3fd93df
·tlemaire on Jul 3 2019, 01:59.

Jul 1 2019

removed test lookup file
be3e09e67984
·tlemaire on Jul 1 2019, 16:53.
added option to provide simAndSave or simulate to batches. implemented addMeta…
d1a3fbaefd83
·tlemaire on Jul 1 2019, 16:46.

Jun 30 2019

improved SonicTranslator class
f22a47305c1e
·tlemaire on Jun 30 2019, 01:24.

Jun 29 2019

adapted methods of all classes into classmethods and staticmethods when…
4937955d0214
·tlemaire on Jun 29 2019, 20:27.

Jun 27 2019

moved lookup to core module. moved getLookup methods to nbls class.
b73594f4d58b
·tlemaire on Jun 27 2019, 14:34.

Jun 26 2019

added fs (spatially-averaged) as input to nbls model. defined SmartLookup class…
dffee6926b85
·tlemaire on Jun 26 2019, 19:50.
added test at bottom of lookups module
07c34eeed0f7
·tlemaire on Jun 26 2019, 16:50.

Jun 25 2019

improved steadyStates definition in TC and STN neurons. corrected dQdt pltvar…
9965ddc0005d
·tlemaire on Jun 25 2019, 23:21.
corrected README
f83e0e973bd3
·tlemaire on Jun 25 2019, 19:19.
removed unnecessary functions from pneuron
acf299185987
·tlemaire on Jun 25 2019, 18:17.
added automatic effRates function definition in pneuron.parse method. removed…
db8cc8e2b5ff
·tlemaire on Jun 25 2019, 17:57.
finished implementing pneuron.buildDerEffStates method to automatically create…
4742d6a43494
·tlemaire on Jun 25 2019, 14:59.

Jun 24 2019

defined separate lookup decorator for bls.computePMparams method. updated…
83ff47370d86
·tlemaire on Jun 24 2019, 20:21.

Jun 20 2019

define dLookUp class to perform lookup projections and interpolations
a96a900ad4b4
·tlemaire on Jun 20 2019, 17:35.
added default output directory ("dump"). cleaned up neuron classes.
6c10d4162d71
·tlemaire on Jun 20 2019, 10:09.

Jun 19 2019

refefined derEffstates construction to return a dictionary of function.
fdebb58e8442
·tlemaire on Jun 19 2019, 19:12.
corrected Cinf error in ThalamoCortical neuron
becd2527f268
·tlemaire on Jun 19 2019, 15:19.
redefined derStates and steadyStates as dictionary of lambda functions
98942bac6b56
·tlemaire on Jun 19 2019, 15:16.
cleaned up neuron classes. redefined currents to return functions instead of…
26fe1e08a408
·tlemaire on Jun 19 2019, 11:05.

Jun 18 2019

replaced obscur states list by explicit dictionary in all currents methods
7b2aee9851af
·tlemaire on Jun 18 2019, 18:21.
replaced obscur states list by explicit states dictionary in derStates and…
00f57af96cfb
·tlemaire on Jun 18 2019, 16:04.

Jun 13 2019

adapted MechSimParser for use in run_lookups.py
af7294977045
·tlemaire on Jun 13 2019, 15:22.

Jun 12 2019

updated all file headers
b42a0de93240
·tlemaire on Jun 12 2019, 23:15.
adapted README recipe to cleaned up neuron classes
0ab79b08684a
·tlemaire on Jun 12 2019, 17:16.

R4670/PySONIC/neuronsmasterfe5b0a532e32201006403ef…

Jul 21 2020

Jul 15 2020

Jun 3 2020

Apr 23 2020

Apr 21 2020

Mar 31 2020

Mar 30 2020

Mar 27 2020

Mar 26 2020

Mar 19 2020

Feb 27 2020

Feb 11 2020

Feb 3 2020

Jan 26 2020

Jan 22 2020

Jan 14 2020

Dec 10 2019

Nov 27 2019

Nov 26 2019

Nov 25 2019

Nov 22 2019

Nov 7 2019

Nov 6 2019

Nov 5 2019

Nov 1 2019

Oct 15 2019

Oct 10 2019

Sep 18 2019

Sep 13 2019

Sep 11 2019

Sep 10 2019

Sep 3 2019

Aug 29 2019

Aug 26 2019

Aug 22 2019

Aug 15 2019

Aug 14 2019

Jul 29 2019

Jul 24 2019

Jul 17 2019

Jul 16 2019

Jul 15 2019

Jul 5 2019

Jul 4 2019

Jul 3 2019

Jul 1 2019

Jun 30 2019

Jun 29 2019

Jun 27 2019

Jun 26 2019

Jun 25 2019

Jun 24 2019

Jun 20 2019

Jun 19 2019

Jun 18 2019

Jun 13 2019

Jun 12 2019

R4670/PySONIC/neurons
masterfe5b0a532e32201006403ef…