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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

merged 201 commits into from
Jun 26, 2024

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janskaar
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@janskaar janskaar commented Oct 30, 2023 •
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Update: Removed draft.

Adds iaf_wang_2002, a model with a conductance based exponential synapse with extra dynamics, from [1]. The model is simplified to allow efficient computation, by taking $t_\mathrm{AMPA,rise} \to 0$ and modelling it as a delta function. Since $t_\mathrm{AMPA,rise} \ll t_\mathrm{AMPA,decay}$, this should not make too much of a difference.

[1] Wang, X. J. (2002). Probabilistic decision making by slow reverberation in cortical circuits. Neuron, 36(5), 955-968.
DOI: https://doi.org/10.1016/S0896-6273(02)01092-9

@janskaar janskaar marked this pull request as draft October 30, 2023 11:26
@janskaar janskaar added T: Enhancement New functionality, model or documentation S: Normal Handle this with default priority I: No breaking change Previously written code will work as before, no one should note anything changing (aside the fix) labels Oct 30, 2023
@heplesser heplesser self-requested a review October 30, 2023 14:10
nicolossus
nicolossus suggested changes Oct 31, 2023
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@janskaar Thanks! Here is my initial review after looking at the implementation of the model.

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heplesser
heplesser requested changes Nov 16, 2023
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See my comments in the code, we can discuss directly later.

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@heplesser heplesser changed the title Wong wang Add model with NMDA dynamics after Wang (2002) Nov 16, 2023
janskaar and others added 12 commits June 20, 2024 18:24
@janskaar @heplesser
Update pynest/examples/wang_decision_making.py
d1c5de2 
Co-authored-by: Hans Ekkehard Plesser <[email protected]>
@janskaar @heplesser
Update pynest/examples/wang_decision_making.py
58b5cee 
Co-authored-by: Hans Ekkehard Plesser <[email protected]>
@janskaar @heplesser
Update testsuite/pytests/test_iaf_bw_2001_exact.py
5979ebd 
Co-authored-by: Hans Ekkehard Plesser <[email protected]>
@janskaar @heplesser
Update pynest/examples/wang_decision_making.py
fb5b716 
Co-authored-by: Hans Ekkehard Plesser <[email protected]>
@janskaar @heplesser
Update pynest/examples/wang_decision_making.py
21c5568 
Co-authored-by: Hans Ekkehard Plesser <[email protected]>
@janskaar @heplesser
Update testsuite/pytests/test_iaf_bw_2001_exact.py
bdec79d 
Co-authored-by: Hans Ekkehard Plesser <[email protected]>
@janskaar
fix bug
431d4ce
@janskaar
apply suggestions fro mreview
eb05220
@janskaar
rm lambda fn to please pylint
1dc31c4
@janskaar
bugfix
6c087b6
@janskaar
rm unused imports
713f102
@janskaar
change docstring
b898267
@janskaar janskaar requested a review from heplesser June 21, 2024 11:04
heplesser
heplesser approved these changes Jun 21, 2024
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@janskaar Thanks, looks good now!

nicolossus
nicolossus approved these changes Jun 24, 2024
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Impressive work! I only have a few non-critical comments that you may consider, so I'll go ahead and approve 👍

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janskaar and others added 11 commits June 25, 2024 13:51
@janskaar @nicolossus
Update models/iaf_bw_2001.h
6a599c7 
Co-authored-by: Nicolai Haug <[email protected]>
@janskaar @nicolossus
Update models/iaf_bw_2001.h
2d67e02 
Co-authored-by: Nicolai Haug <[email protected]>
@janskaar
update short description
d81d3b3
@janskaar
Merge remote-tracking branch 'refs/remotes/origin/wong_wang' into won…
48979ba 
…g_wang
@janskaar @nicolossus
Update models/iaf_bw_2001_exact.h
5dc04a1 
Co-authored-by: Nicolai Haug <[email protected]>
@janskaar @heplesser
Update pynest/examples/wang_decision_making.py
5f87054 
Co-authored-by: Hans Ekkehard Plesser <[email protected]>
@janskaar @nicolossus
Update pynest/examples/wang_decision_making.py
c7f7826 
Co-authored-by: Nicolai Haug <[email protected]>
@janskaar @nicolossus
Update testsuite/pytests/test_iaf_bw_2001.py
ef363c0 
Co-authored-by: Nicolai Haug <[email protected]>
@janskaar @nicolossus
Update testsuite/pytests/test_iaf_bw_2001_exact.py
476b700 
Co-authored-by: Nicolai Haug <[email protected]>
@janskaar
don't use getter directly
7cae37d
@janskaar
add hyphen
6fbb8c9
@heplesser heplesser changed the title Add models with NMDA dynamics according to Wang (2002) Add models with exact and simplified NMDA dynamics according to Brunel and Wang (2001) Jun 26, 2024
@heplesser heplesser merged commit ccb3d4e into nest:master Jun 26, 2024
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@BrewTestBot BrewTestBot mentioned this pull request Aug 2, 2024
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@heplesser heplesser heplesser approved these changes

@nicolossus nicolossus nicolossus approved these changes

@jessica-mitchell jessica-mitchell jessica-mitchell approved these changes

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I: No breaking change Previously written code will work as before, no one should note anything changing (aside the fix) S: Normal Handle this with default priority T: Enhancement New functionality, model or documentation
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@janskaar @heplesser @jessica-mitchell @nicolossus