Add Bouhadjar sequence learning network tutorial

[clinssen]

Should be merged after #1027.

• Add the following notes:

  lambda_plus is increasing facilitation: too many daps, decrease facilitation!
  lambda_minus is increasing depression: too many daps, increase depression!
  if you see overlap, increase lambda_h a bit
  

• eliminate the use of the "parameters" Python package

[github-actions]

Bencher Report

Branch	1026/merge
Testbed	ubuntu-latest

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Benchmark	Latency	nanoseconds (ns)
tests/nest_continuous_benchmarking/test_nest_continuous_benchmarking.py::TestNESTContinuousBenchmarking::test_stdp_nn_synapse	📈 view plot ⚠️ NO THRESHOLD	4,012,252,605.60

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[clinssen]

It seems as though the second line in the following snippet from the notebook causes an extreme memory consumption:

connections = nest.GetConnections(synapse_model=...)
connections.set({'Wmin': connections.weight})

There are around 165000 connections.

Edit: spun off to nest/nest-simulator#3359.

[pnbabu]

Thanks for this excellent tutorial! I have a few minor comments:

• When you describe the different terms in the STDP rule in the text, could you refer to the equation by number? For example, the second term on the right-hand side in (1)...
• Any reason behind setting the number of threads to 1?
• Under "Generating code with NESTML", do we need the try and except?
  • Remove the following lines

"""module_name = "/tmp/nestml_target_68digoes/nestml_27fd8d9de14b408f9e6181b2f2310d41_module.so"
neuron_model_name = "iaf_psc_exp_nonlineardendrite_neuron_nestml__with_stdsp_synapse_nestml"
synapse_model_name = "stdsp_synapse_nestml__with_iaf_psc_exp_nonlineardendrite_neuron_nestml" """

• The fig just before Experiment 2 is a bit hard to read. Can the three panels be a bit further apart?

[clinssen]

@pnbabu: much obliged for the review! I have cleaned up the notebook and the neuron model; this should address all your comments.

[YounesBouhadjar]

I have created a PR to your fork @clinssen with an update of the notebook.
Mainly minor things, except that I had to restructure a bit the third experiment,
for example, by adding new subtitles and changing the order of the subsections.

Remained to be done:

1. Add "taken from [1]" to the concerned figures.
2. We could add a legend describing the dashed and solid lines to the figure under experiment 1 showing the active dendrite simulations.
3. Could it be useful to provide the requirements of the packages to be installed? especially nest version? I saw also that a numpy<2.0.0 version is required.
4. The nest.Install(module_name) raises an error if called twice or more. A quick fix could be to do: try except

[clinssen]

Thanks very much for the review! The latest changes should address all your comments.

1. Add "taken from [1]" to the concerned figures.

Done.

2. We could add a legend describing the dashed and solid lines to the figure under experiment 1 showing the active dendrite simulations.

Done.

3. Could it be useful to provide the requirements of the packages to be installed? especially nest version? I saw also that a numpy<2.0.0 version is required.

numpy is constrained to be >= 1.8.2. Only sympy is limited (to <1.11) but this should soon be amended (nest/ode-toolbox#77 (comment)).

4. The nest.Install(module_name) raises an error if called twice or more. A quick fix could be to do: try except

This has been changed starting from NEST 3.7 (I noticed from the log messages in the notebook that you are using 3.6).

Please let me know if this addresses your comments; much obliged!

[clinssen]

Thank you for the review!