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Add models with exact and simplified NMDA dynamics according to Brunel and Wang (2001) #2979

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merged 201 commits into from
Jun 26, 2024
Merged

Add models with exact and simplified NMDA dynamics according to Brunel and Wang (2001) #2979

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6149e4e
add nest names
Sep 13, 2023
297dcab
Files from Stine, fixed 0->nullptr and port->size_t
Sep 13, 2023
4ccecdf
change variable name
Sep 14, 2023
8d3d96c
add nest names
Sep 14, 2023
b17358c
compiles!
Sep 14, 2023
41a8136
cleaning up code, wip
Sep 23, 2023
f20c745
some changes, not sure what
Oct 3, 2023
4731cde
new dynamics in place, not tested yet
Oct 6, 2023
c5347b2
solution verified analytically
Oct 18, 2023
abc08d4
fix receptor port for external input, WIP reproduce wang2002
Oct 25, 2023
fc17cf5
lower case s for gating variable
Oct 25, 2023
9ac0012
test works
Oct 30, 2023
7dee211
Merge remote-tracking branch 'nest/master' into wong_wang
Oct 30, 2023
ca4a7ec
remove unneccessary lines
Nov 6, 2023
406ec50
Merge remote-tracking branch 'nest/master' into wong_wang
Nov 6, 2023
d9653da
compilation bug wip
Nov 6, 2023
5293f73
fix register_model, wip reproduce paper
Nov 10, 2023
7cea3b2
add separate synaptic channel for external AMPA
Nov 14, 2023
d9a4670
adjust rate
Nov 14, 2023
691a5e7
work on replication of (Wang, 2002), still not working
Nov 14, 2023
8614377
script works, but something wrong with dynamics
Nov 15, 2023
2138a99
bughunting, s_NMDA explodes
Nov 17, 2023
ffb55c4
fixed bug, uninitialized variable
Nov 17, 2023
422c1c9
reintroduce receptor type
Nov 17, 2023
7e6ec79
various fixes from review
Nov 17, 2023
9171873
update examples so that they run with receptor types again
Nov 17, 2023
6a04fb1
fix spike recorders
Nov 22, 2023
0929a5a
Merge remote-tracking branch 'nest/master' into wong_wang
Nov 25, 2023
9459757
exact model from Stine, wip
Nov 26, 2023
37d1133
add test for exact wang
Nov 27, 2023
5b1715b
exact version, rports work, WIP
Nov 30, 2023
8c651ff
formatting
Nov 30, 2023
8e76c45
exact model seems to work
Dec 12, 2023
4b3f7a3
compare to brian, off by constant factor
Dec 19, 2023
3253ff9
Getting exactly same results as Brian
Dec 21, 2023
12ac8df
reproduces brian exactly
Jan 3, 2024
0f6356c
Check NMDA approximation numerically
Jan 12, 2024
a721ef0
clean up
Jan 19, 2024
c4d03cf
implement new S_NMDA jump
Jan 19, 2024
f9ed575
add comment
Jan 19, 2024
b9f2979
add approx t variable
Jan 19, 2024
72085ab
remove print
Jan 19, 2024
2465108
remove max(S_NMDA), no need with approx. model
Jan 19, 2024
906b443
remove min(S_NMDA, 1), no need with approximation
Jan 19, 2024
3bc2ffd
correct inhibitory weight sign
Jan 19, 2024
04139d4
reproduces dynamics frfom wang 2002 paper
Jan 19, 2024
4517b28
Merge remote-tracking branch 'nest/master' into wong_wang
Jan 22, 2024
4797887
documentation iaf_wang_2002_exact
Jan 22, 2024
4a97fe2
commit all wong files, delete later
Jan 22, 2024
bf4c4b6
clean up
Jan 24, 2024
9e5d932
add benchmarking script
Jan 26, 2024
565bf1b
add all examples scripts, remove later
Jan 30, 2024
3dd27a0
Merge remote-tracking branch 'nest/master' into wong_wang
Jan 30, 2024
490814c
Add documentation to iaf_psc_wang, remove unused variable t_approx
Feb 5, 2024
a59c6af
remove unused var
Feb 5, 2024
1b7076a
remove test scripts
Feb 5, 2024
ed03c83
clean up
Feb 5, 2024
9ba059c
add comments to wang_decision_making.py
Feb 5, 2024
c980c87
update doc
Feb 7, 2024
99766ed
update test
Feb 7, 2024
a2dae5b
remove comment
Feb 7, 2024
79e383f
add receptor types dictionary
Feb 7, 2024
5c14f8a
black
Feb 7, 2024
24d21ce
clang-format
Feb 7, 2024
7c9c02a
formatting
Feb 7, 2024
6bee519
test for exact version
Feb 7, 2024
cf8b82a
rename NMDA_sum
Feb 7, 2024
d8774f8
correct copyright header
Feb 7, 2024
bd8e101
remove plotting
Feb 7, 2024
be9f99f
update docstring
Feb 7, 2024
3743147
flake8
Feb 7, 2024
a303a29
more comments
Feb 7, 2024
041a7b4
fixes from review
Feb 13, 2024
4810fe8
update inhibitory weight signs
Feb 13, 2024
55e5d60
fix bug, wrong SynapseTypes:: logic
Feb 13, 2024
4536e59
specify AMPA/GABA by receptor_type instead of weight sign
Feb 13, 2024
301eb01
change expn function to avoid truncation of n
Feb 15, 2024
05403da
begin model_details notebook, still missing a bit
Feb 15, 2024
f840d77
finish notebook
Feb 19, 2024
9de4414
raise error if NMDA connection is made from other neuron types
Feb 19, 2024
49235c7
clang-format
Feb 19, 2024
01ae1f6
clang-format
Feb 19, 2024
9c443d1
G_NMDA -> s_NMDA
Feb 19, 2024
cd4bfc4
black/flake8
Feb 19, 2024
33c8082
black
Feb 19, 2024
94abdc8
remove constant weight constraint
Feb 19, 2024
a04e2a7
black
Feb 19, 2024
eff0767
black
Feb 19, 2024
cbe9b0a
add conc_Mg2
Feb 19, 2024
4e6d56e
remove duplicates
Feb 19, 2024
7928d82
remove duplicates
Feb 19, 2024
d7af047
removed unused names
Feb 19, 2024
af9fd6e
let NMDA currents be recorded
Feb 19, 2024
c59f6ad
fix handle ( SpikeEvent ) method
Mar 6, 2024
d66457b
Update models/iaf_wang_2002.h
janskaar Mar 9, 2024
8f17ac3
fix GABA sign
Mar 9, 2024
9970524
Merge remote-tracking branch 'origin/wong_wang' into wong_wang
Mar 9, 2024
0273e34
Merge remote-tracking branch 'nest/master' into wong_wang
Mar 9, 2024
1754ee5
Update models/iaf_wang_2002.cpp
janskaar Mar 9, 2024
d12d331
Update models/iaf_wang_2002_exact.cpp
janskaar Mar 9, 2024
f9f058b
Update models/iaf_wang_2002_exact.cpp
janskaar Mar 9, 2024
ef7ca53
reintroduce constant weight requirement
Mar 10, 2024
a6021b4
Merge remote-tracking branch 'refs/remotes/origin/wong_wang' into won…
Mar 10, 2024
7a0bffc
clang-format
Mar 10, 2024
4be3dca
ignore iaf_wang_2002
Mar 10, 2024
1473fe7
remove s_NMDA recording, update tests
Mar 11, 2024
5ef7c71
check that tau_NMDA_rise gte 0
Mar 11, 2024
1f6b41d
remove unused code
Mar 11, 2024
829a351
add extra params for iaf_wang_2002*
Mar 11, 2024
338824c
black
Mar 11, 2024
8afd569
add extra params to iaf_wang_2002_*
Mar 11, 2024
247f1e0
expand decision making example
Mar 12, 2024
f23430d
black
Mar 12, 2024
5e2b7cd
move wong notebook to correct directory
Mar 12, 2024
cd94b19
update wang_decision_making example
Mar 14, 2024
5150338
Revised and renamed Wang example notebook
heplesser Apr 26, 2024
e80488a
Merge pull request #5 from heplesser/wang_model_hep
janskaar Apr 28, 2024
1b7b628
record spikes in steps instead of time
Apr 28, 2024
c76834c
update notebook, wip
Apr 28, 2024
12480be
update notebook equations
Apr 28, 2024
6fc3164
simplify equations
Apr 28, 2024
9852cb4
black
Apr 28, 2024
1776278
clang-format
Apr 29, 2024
c63b8e7
fix equations, add examples to model docs
Apr 29, 2024
bb67d3c
fix modeldoc
Apr 29, 2024
04b832d
Update models/iaf_wang_2002_exact.cpp
janskaar Apr 29, 2024
78fdb30
clang-format
Apr 29, 2024
ac80cf2
change wording in documentation note
Apr 29, 2024
cfe61a5
add note explaining spikes must be recorded with time_in_steps
Apr 29, 2024
4817bc3
add example to modeldoc
Apr 29, 2024
ef16d2a
remove unnecessary blank lines
Apr 29, 2024
1c6b1d7
clang-format
Apr 29, 2024
690a3eb
fix equation for NMDA spike update
Apr 29, 2024
94f9f7c
add newline between equations
Apr 29, 2024
ef313bf
Some more polishing and questions in notebook
heplesser Apr 29, 2024
0d51f65
Merge branch 'wong_wang' of github.com:janskaar/nest-simulator into w…
heplesser Apr 29, 2024
f0a72ed
Merge pull request #6 from heplesser/wang_model_hep
janskaar Apr 30, 2024
1603774
Merge remote-tracking branch 'refs/remotes/origin/wong_wang' into won…
Apr 30, 2024
d036f03
make it possible to record s_NMDA
May 1, 2024
afcd5b5
update notebook
May 1, 2024
3feb295
clang-format
May 1, 2024
5ea17eb
update documentation
May 2, 2024
70e8e56
Further polishing of notebook
heplesser May 2, 2024
a1b6b59
Update models/iaf_wang_2002.cpp
janskaar May 2, 2024
92a3e26
Merge pull request #7 from heplesser/wang_model_hep
janskaar May 3, 2024
ea254fe
change iaf_wang_2002 to iaf_bw_2001
May 4, 2024
14c34d4
rename tests to iaf_bw_2001
May 4, 2024
1fab22f
clang-format
May 4, 2024
489237f
add check that we don't add NMDA synapses after buffers have been cre…
May 4, 2024
bf595de
update tests
May 4, 2024
442a5d8
add comment
May 4, 2024
1b44488
update example
May 4, 2024
fd08380
change variable names S_jump_* -> k_*
May 4, 2024
9469e6b
Update models/iaf_bw_2001_exact.h
janskaar May 7, 2024
0ced8d2
Update models/iaf_bw_2001.h
janskaar May 7, 2024
06cf6c7
Update pynest/examples/wang_decision_making.py
janskaar May 7, 2024
863653d
Update pynest/examples/wang_decision_making.py
janskaar May 7, 2024
7fd6f85
Update models/iaf_bw_2001.h
janskaar May 7, 2024
623297b
Update models/iaf_bw_2001.h
janskaar May 7, 2024
5db64d5
Update models/iaf_bw_2001.h
janskaar May 7, 2024
21c1281
Update models/iaf_bw_2001.h
janskaar May 7, 2024
548f2ab
Update pynest/examples/wang_decision_making.py
janskaar May 7, 2024
4fb08e6
Update pynest/examples/wang_decision_making.py
janskaar May 7, 2024
9ac9b50
Update pynest/examples/wang_decision_making.py
janskaar May 7, 2024
4080558
Update models/iaf_bw_2001_exact.h
janskaar May 7, 2024
0e9fb5b
Update models/iaf_bw_2001.h
janskaar May 7, 2024
0197ab3
Update models/iaf_bw_2001_exact.h
janskaar May 7, 2024
47b38af
Update models/iaf_bw_2001.h
janskaar May 7, 2024
1643d9f
correct citaton
janskaar May 7, 2024
14549d9
rename notebook
janskaar May 7, 2024
9e3ecba
correct notebook name in documentation
janskaar May 7, 2024
e64515b
Update models/iaf_bw_2001_exact.h
janskaar May 7, 2024
f0ce0df
allow recording of AMPA and GABA currents
janskaar May 19, 2024
c081fb6
Merge remote-tracking branch 'refs/remotes/origin/wong_wang' into won…
janskaar May 19, 2024
c20736b
Merge remote-tracking branch 'nest/master' into wong_wang
janskaar May 20, 2024
f2ebd3e
Merge remote-tracking branch 'nest/master' into wong_wang
janskaar Jun 20, 2024
99e8d70
add wang to example index
jessica-mitchell Jun 20, 2024
dc9cef8
Update models/iaf_bw_2001_exact.h
janskaar Jun 20, 2024
d1c5de2
Update pynest/examples/wang_decision_making.py
janskaar Jun 20, 2024
58b5cee
Update pynest/examples/wang_decision_making.py
janskaar Jun 20, 2024
5979ebd
Update testsuite/pytests/test_iaf_bw_2001_exact.py
janskaar Jun 21, 2024
fb5b716
Update pynest/examples/wang_decision_making.py
janskaar Jun 21, 2024
21c5568
Update pynest/examples/wang_decision_making.py
janskaar Jun 21, 2024
bdec79d
Update testsuite/pytests/test_iaf_bw_2001_exact.py
janskaar Jun 21, 2024
431d4ce
fix bug
janskaar Jun 21, 2024
eb05220
apply suggestions fro mreview
janskaar Jun 21, 2024
1dc31c4
rm lambda fn to please pylint
janskaar Jun 21, 2024
6c087b6
bugfix
janskaar Jun 21, 2024
713f102
rm unused imports
janskaar Jun 21, 2024
b898267
change docstring
janskaar Jun 21, 2024
6a599c7
Update models/iaf_bw_2001.h
janskaar Jun 25, 2024
2d67e02
Update models/iaf_bw_2001.h
janskaar Jun 25, 2024
d81d3b3
update short description
janskaar Jun 25, 2024
48979ba
Merge remote-tracking branch 'refs/remotes/origin/wong_wang' into won…
janskaar Jun 25, 2024
5dc04a1
Update models/iaf_bw_2001_exact.h
janskaar Jun 25, 2024
5f87054
Update pynest/examples/wang_decision_making.py
janskaar Jun 25, 2024
c7f7826
Update pynest/examples/wang_decision_making.py
janskaar Jun 25, 2024
ef363c0
Update testsuite/pytests/test_iaf_bw_2001.py
janskaar Jun 25, 2024
476b700
Update testsuite/pytests/test_iaf_bw_2001_exact.py
janskaar Jun 25, 2024
7cae37d
don't use getter directly
janskaar Jun 25, 2024
6fbb8c9
add hyphen
janskaar Jun 26, 2024
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7 changes: 7 additions & 0 deletions doc/htmldoc/examples/index.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -153,6 +153,12 @@ PyNEST examples

* :doc:`../auto_examples/CampbellSiegert`

.. grid:: 1 1 2 3

.. grid-item-card:: Decision making in recurrent network (after Wang 2002)
:img-top: ../static/img/nest_logo-faded.png

* :doc:`../auto_examples/wang_decision_making`

.. grid:: 1 1 2 3

Expand Down Expand Up @@ -351,6 +357,7 @@ PyNEST examples
../auto_examples/astrocytes/astrocyte_brunel
../auto_examples/EI_clustered_network/index
../auto_examples/eprop_plasticity/index
../auto_examples/wang_decision_making

.. toctree::
:hidden:
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595 changes: 595 additions & 0 deletions doc/htmldoc/model_details/Brunel_Wang_2001_Model_Approximation.ipynb
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