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Add models with NMDA dynamics according to Wang (2002) #2979

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Add models with NMDA dynamics according to Wang (2002) #2979

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Commits on Sep 13, 2023

  1. add nest names

    janeirik committed Sep 13, 2023
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  2. Files from Stine, fixed 0->nullptr and port->size_t

    janeirik committed Sep 13, 2023
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Commits on Sep 14, 2023

  1. change variable name

    janeirik committed Sep 14, 2023
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  2. add nest names

    janeirik committed Sep 14, 2023
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  3. compiles!

    janeirik committed Sep 14, 2023
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Commits on Sep 23, 2023

  1. cleaning up code, wip

    janeirik committed Sep 23, 2023
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Commits on Oct 3, 2023

  1. some changes, not sure what

    janeirik committed Oct 3, 2023
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Commits on Oct 6, 2023

  1. new dynamics in place, not tested yet

    janeirik committed Oct 6, 2023
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Commits on Oct 18, 2023

  1. solution verified analytically

    janeirik committed Oct 18, 2023
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Commits on Oct 25, 2023

  1. fix receptor port for external input, WIP reproduce wang2002

    janeirik committed Oct 25, 2023
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  2. lower case s for gating variable

    janeirik committed Oct 25, 2023
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Commits on Oct 30, 2023

  1. test works

    janeirik committed Oct 30, 2023
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  2. Merge remote-tracking branch 'nest/master' into wong_wang

    janeirik committed Oct 30, 2023
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Commits on Nov 6, 2023

  1. remove unneccessary lines

    janeirik committed Nov 6, 2023
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  2. Merge remote-tracking branch 'nest/master' into wong_wang

    janeirik committed Nov 6, 2023
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  3. compilation bug wip

    janeirik committed Nov 6, 2023
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Commits on Nov 10, 2023

  1. fix register_model, wip reproduce paper

    janeirik committed Nov 10, 2023
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Commits on Nov 14, 2023

  1. add separate synaptic channel for external AMPA

    janeirik committed Nov 14, 2023
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  2. adjust rate

    janeirik committed Nov 14, 2023
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  3. work on replication of (Wang, 2002), still not working

    janeirik committed Nov 14, 2023
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Commits on Nov 15, 2023

  1. script works, but something wrong with dynamics

    janeirik committed Nov 15, 2023
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Commits on Nov 17, 2023

  1. bughunting, s_NMDA explodes

    janeirik committed Nov 17, 2023
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  2. fixed bug, uninitialized variable

    janeirik committed Nov 17, 2023
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  3. reintroduce receptor type

    janeirik committed Nov 17, 2023
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  4. various fixes from review

    janeirik committed Nov 17, 2023
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  5. update examples so that they run with receptor types again

    janeirik committed Nov 17, 2023
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Commits on Nov 22, 2023

  1. fix spike recorders

    janeirik committed Nov 22, 2023
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Commits on Nov 25, 2023

  1. Merge remote-tracking branch 'nest/master' into wong_wang

    janeirik committed Nov 25, 2023
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Commits on Nov 26, 2023

  1. exact model from Stine, wip

    janeirik committed Nov 26, 2023
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Commits on Nov 27, 2023

  1. add test for exact wang

    janeirik committed Nov 27, 2023
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Commits on Nov 30, 2023

  1. exact version, rports work, WIP

    janeirik committed Nov 30, 2023
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  2. formatting

    janeirik committed Nov 30, 2023
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Commits on Dec 12, 2023

  1. exact model seems to work

    janeirik committed Dec 12, 2023
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Commits on Dec 19, 2023

  1. compare to brian, off by constant factor

    janeirik committed Dec 19, 2023
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Commits on Dec 21, 2023

  1. Getting exactly same results as Brian

    janeirik committed Dec 21, 2023
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Commits on Jan 3, 2024

  1. reproduces brian exactly

    janeirik committed Jan 3, 2024
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Commits on Jan 12, 2024

  1. Check NMDA approximation numerically

    janeirik committed Jan 12, 2024
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Commits on Jan 19, 2024

  1. clean up

    janeirik committed Jan 19, 2024
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  2. implement new S_NMDA jump

    janeirik committed Jan 19, 2024
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  3. add comment

    janeirik committed Jan 19, 2024
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  4. add approx t variable

    janeirik committed Jan 19, 2024
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  5. remove print

    janeirik committed Jan 19, 2024
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  6. remove max(S_NMDA), no need with approx. model

    janeirik committed Jan 19, 2024
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  7. remove min(S_NMDA, 1), no need with approximation

    janeirik committed Jan 19, 2024
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  8. correct inhibitory weight sign

    janeirik committed Jan 19, 2024
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  9. reproduces dynamics frfom wang 2002 paper

    janeirik committed Jan 19, 2024
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Commits on Jan 22, 2024

  1. Merge remote-tracking branch 'nest/master' into wong_wang

    janeirik committed Jan 22, 2024
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  2. documentation iaf_wang_2002_exact

    janeirik committed Jan 22, 2024
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  3. commit all wong files, delete later

    janeirik committed Jan 22, 2024
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Commits on Jan 24, 2024

  1. clean up

    janeirik committed Jan 24, 2024
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Commits on Jan 26, 2024

  1. add benchmarking script

    janeirik committed Jan 26, 2024
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Commits on Jan 30, 2024

  1. add all examples scripts, remove later

    janeirik committed Jan 30, 2024
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  2. Merge remote-tracking branch 'nest/master' into wong_wang

    janeirik committed Jan 30, 2024
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Commits on Feb 5, 2024

  1. Add documentation to iaf_psc_wang, remove unused variable t_approx

    janeirik committed Feb 5, 2024
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  2. remove unused var

    janeirik committed Feb 5, 2024
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  3. remove test scripts

    janeirik committed Feb 5, 2024
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  4. clean up

    janeirik committed Feb 5, 2024
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  5. add comments to wang_decision_making.py

    janeirik committed Feb 5, 2024
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Commits on Feb 7, 2024

  1. update doc

    janeirik committed Feb 7, 2024
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  2. update test

    janeirik committed Feb 7, 2024
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  3. remove comment

    janeirik committed Feb 7, 2024
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  4. add receptor types dictionary

    janeirik committed Feb 7, 2024
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  5. black

    janeirik committed Feb 7, 2024
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  6. clang-format

    janeirik committed Feb 7, 2024
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  7. formatting

    janeirik committed Feb 7, 2024
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  8. test for exact version

    janeirik committed Feb 7, 2024
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  9. rename NMDA_sum

    janeirik committed Feb 7, 2024
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  10. correct copyright header

    janeirik committed Feb 7, 2024
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  11. remove plotting

    janeirik committed Feb 7, 2024
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  12. update docstring

    janeirik committed Feb 7, 2024
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  13. flake8

    janeirik committed Feb 7, 2024
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  14. more comments

    janeirik committed Feb 7, 2024
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Commits on Feb 13, 2024

  1. fixes from review

    janeirik committed Feb 13, 2024
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  2. update inhibitory weight signs

    janeirik committed Feb 13, 2024
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  3. fix bug, wrong SynapseTypes:: logic

    janeirik committed Feb 13, 2024
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  4. specify AMPA/GABA by receptor_type instead of weight sign

    janeirik committed Feb 13, 2024
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Commits on Feb 15, 2024

  1. change expn function to avoid truncation of n

    janeirik committed Feb 15, 2024
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  2. begin model_details notebook, still missing a bit

    janeirik committed Feb 15, 2024
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Commits on Feb 19, 2024

  1. finish notebook

    janeirik committed Feb 19, 2024
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  2. raise error if NMDA connection is made from other neuron types

    janeirik committed Feb 19, 2024
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  3. clang-format

    janeirik committed Feb 19, 2024
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  4. clang-format

    janeirik committed Feb 19, 2024
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  5. G_NMDA -> s_NMDA

    janeirik committed Feb 19, 2024
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  6. black/flake8

    janeirik committed Feb 19, 2024
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  7. black

    janeirik committed Feb 19, 2024
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  8. remove constant weight constraint

    janeirik committed Feb 19, 2024
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  9. black

    janeirik committed Feb 19, 2024
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  10. black

    janeirik committed Feb 19, 2024
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  11. add conc_Mg2

    janeirik committed Feb 19, 2024
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  12. remove duplicates

    janeirik committed Feb 19, 2024
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  13. remove duplicates

    janeirik committed Feb 19, 2024
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  14. removed unused names

    janeirik committed Feb 19, 2024
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  15. let NMDA currents be recorded

    janeirik committed Feb 19, 2024
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Commits on Mar 6, 2024

  1. fix handle ( SpikeEvent ) method

    janeirik committed Mar 6, 2024
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Commits on Mar 9, 2024

  1. Update models/iaf_wang_2002.h 

    Co-authored-by: Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no>
    @janskaar @heplesser
    janskaar and heplesser committed Mar 9, 2024
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  2. fix GABA sign

    janeirik committed Mar 9, 2024
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  3. Merge remote-tracking branch 'origin/wong_wang' into wong_wang

    janeirik committed Mar 9, 2024
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  4. Merge remote-tracking branch 'nest/master' into wong_wang

    janeirik committed Mar 9, 2024
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  5. Update models/iaf_wang_2002.cpp 

    Co-authored-by: Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no>
    @janskaar @heplesser
    janskaar and heplesser committed Mar 9, 2024
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  6. Update models/iaf_wang_2002_exact.cpp 

    Co-authored-by: Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no>
    @janskaar @heplesser
    janskaar and heplesser committed Mar 9, 2024
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  7. Update models/iaf_wang_2002_exact.cpp 

    Co-authored-by: Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no>
    @janskaar @heplesser
    janskaar and heplesser committed Mar 9, 2024
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Commits on Mar 10, 2024

  1. reintroduce constant weight requirement

    janeirik committed Mar 10, 2024
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  2. Merge remote-tracking branch 'refs/remotes/origin/wong_wang' into won… 

    …g_wang
    janeirik committed Mar 10, 2024
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  3. clang-format

    janeirik committed Mar 10, 2024
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  4. ignore iaf_wang_2002

    janeirik committed Mar 10, 2024
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Commits on Mar 11, 2024

  1. remove s_NMDA recording, update tests

    janeirik committed Mar 11, 2024
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  2. check that tau_NMDA_rise gte 0

    janeirik committed Mar 11, 2024
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  3. remove unused code

    janeirik committed Mar 11, 2024
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  4. add extra params for iaf_wang_2002*

    janeirik committed Mar 11, 2024
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  5. black

    janeirik committed Mar 11, 2024
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  6. add extra params to iaf_wang_2002_*

    janeirik committed Mar 11, 2024
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Commits on Mar 12, 2024

  1. expand decision making example

    janeirik committed Mar 12, 2024
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  2. black

    janeirik committed Mar 12, 2024
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  3. move wong notebook to correct directory

    janeirik committed Mar 12, 2024
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Commits on Mar 14, 2024

  1. update wang_decision_making example

    janeirik committed Mar 14, 2024
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Commits on Apr 26, 2024

  1. Revised and renamed Wang example notebook

    @heplesser
    heplesser committed Apr 26, 2024
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Commits on Apr 28, 2024

  1. Merge pull request #5 from heplesser/wang_model_hep 

    Revised and renamed Wang example notebook
    @janskaar
    janskaar committed Apr 28, 2024
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  2. record spikes in steps instead of time

    janeirik committed Apr 28, 2024
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  3. update notebook, wip

    janeirik committed Apr 28, 2024
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  4. update notebook equations

    janeirik committed Apr 28, 2024
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  5. simplify equations

    janeirik committed Apr 28, 2024
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  6. black

    janeirik committed Apr 28, 2024
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Commits on Apr 29, 2024

  1. clang-format

    janeirik committed Apr 29, 2024
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  2. fix equations, add examples to model docs

    janeirik committed Apr 29, 2024
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  3. fix modeldoc

    janeirik committed Apr 29, 2024
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  4. Update models/iaf_wang_2002_exact.cpp 

    Co-authored-by: Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no>
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    janskaar and heplesser committed Apr 29, 2024
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  5. clang-format

    janeirik committed Apr 29, 2024
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  6. change wording in documentation note

    janeirik committed Apr 29, 2024
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  7. add note explaining spikes must be recorded with time_in_steps

    janeirik committed Apr 29, 2024
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  8. add example to modeldoc

    janeirik committed Apr 29, 2024
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  9. remove unnecessary blank lines

    janeirik committed Apr 29, 2024
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  10. clang-format

    janeirik committed Apr 29, 2024
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  11. fix equation for NMDA spike update

    janeirik committed Apr 29, 2024
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  12. add newline between equations

    janeirik committed Apr 29, 2024
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  13. Some more polishing and questions in notebook

    @heplesser
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  14. Merge branch 'wong_wang' of github.com:janskaar/nest-simulator into w… 

    …ang_model_hep
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Commits on Apr 30, 2024

  1. Merge pull request #6 from heplesser/wang_model_hep 

    Further work on Notebook
    @janskaar
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  2. Merge remote-tracking branch 'refs/remotes/origin/wong_wang' into won… 

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Commits on May 1, 2024

  1. make it possible to record s_NMDA

    janeirik committed May 1, 2024
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  2. update notebook

    janeirik committed May 1, 2024
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  3. clang-format

    janeirik committed May 1, 2024
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  1. update documentation

    janeirik committed May 2, 2024
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  2. Further polishing of notebook

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    heplesser committed May 2, 2024
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  3. Update models/iaf_wang_2002.cpp 

    Co-authored-by: Hans Ekkehard Plesser <hans.ekkehard.plesser@nmbu.no>
    @janskaar @heplesser
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Commits on May 3, 2024

  1. Merge pull request #7 from heplesser/wang_model_hep 

    Notebook updates
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    janskaar committed May 3, 2024
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Commits on May 4, 2024

  1. change iaf_wang_2002 to iaf_bw_2001

    janeirik committed May 4, 2024
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  2. rename tests to iaf_bw_2001

    janeirik committed May 4, 2024
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  3. clang-format

    janeirik committed May 4, 2024
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  4. add check that we don't add NMDA synapses after buffers have been cre… 

    …ated
    janeirik committed May 4, 2024
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  5. update tests

    janeirik committed May 4, 2024
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  6. add comment

    janeirik committed May 4, 2024
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  7. update example

    janeirik committed May 4, 2024
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  8. change variable names S_jump_* -> k_*

    janeirik committed May 4, 2024
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Commits on May 7, 2024

  1. Update models/iaf_bw_2001_exact.h 

    Co-authored-by: jessica-mitchell <mitchell20j@gmail.com>
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  2. Update models/iaf_bw_2001.h 

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  3. Update pynest/examples/wang_decision_making.py 

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  4. Update pynest/examples/wang_decision_making.py 

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  5. Update models/iaf_bw_2001.h 

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  6. Update models/iaf_bw_2001.h 

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  7. Update models/iaf_bw_2001.h 

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  8. Update models/iaf_bw_2001.h 

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  9. Update pynest/examples/wang_decision_making.py 

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  10. Update pynest/examples/wang_decision_making.py 

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  11. Update pynest/examples/wang_decision_making.py 

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  12. Update models/iaf_bw_2001_exact.h 

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  13. Update models/iaf_bw_2001.h 

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  14. Update models/iaf_bw_2001_exact.h 

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  15. Update models/iaf_bw_2001.h 

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  16. correct citaton

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    janskaar committed May 7, 2024
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  17. rename notebook

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    janskaar committed May 7, 2024
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  18. correct notebook name in documentation

    @janskaar
    janskaar committed May 7, 2024
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  19. Update models/iaf_bw_2001_exact.h 

    Co-authored-by: jessica-mitchell <mitchell20j@gmail.com>
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    janskaar and jessica-mitchell committed May 7, 2024
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