Add astrocyte_lr_1994 to NEST for the modeling of astrocytes and neuron-astrocyte interactions
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… NEST version. Also add a python example of using the astrocyte component
…oulliAstroBuilder
… when p_astro is not given; assigning or overlapping not possible yet
…astrocytes connecting to neurons without presynaptic sources
… paired with astrocyte" instead of "target neurons paired with astrocyte"; "weight_astro" in syn_spec renamed as "weight_sic"
- True/False for Deterministic/Probabilistic selection of astrocyte pool per target neuron. - Rename "p_astro" to "p_syn_astro" since this parameter defines the probability of a neuron-neuron synapse being paired with an astrocyte.
- Set default to true - When true, the default of "max_astro_per_target" is 1 - When false, the default of "max_astro_per_target" is 0 (all astrocytes can connect)
…_per_target_det and (B) max_astro_per_target. - A=True, B=None: Distribute the neurons according to N_neuron/N_astrocyte. - A=True, B=n: Make overlapping in uneven cases more balanced (still to be improved). - Debug: p=1 is OK now, but autapses must be allowed. To be discussed.
…mber of max_astro_per_target.
…ivity - Fix the special case of: autapses not allowed, p=1, target overlaps with sources
…ator into hanjia_lr_1994
Pull request to fix test problem
pnbabu
suggested changes
Sep 15, 2023
pnbabu
approved these changes
Sep 15, 2023
heplesser
approved these changes
Sep 15, 2023
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@HanjiaJiang Thank you very much for your efforts in polishing the PR. It is fine now and we can merge as soon as the tests have completed successfully.
terhorstd
changed the title
astrocyte_lr_1994 to NEST for the modeling of astrocytes and neuron-astrocyte interactions
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We implemented an astrocyte model (astrocyte_lr_1994) based on the paper by Li & Rinzel (1994), for the study of astrocytes and neuron-astrocyte interactions in NEST. A new connection type (sic_connection) and a new neuron type (aeif_cond_alpha_astro) were also implemented for this purpose. We also created two example scripts for astrocyte dynamics, two test files for astrocyte_lr_1994 and sic_connection respectively, and one jupyter notebook file as a reference of model implementation.
The code is co-authored by Jugoslava Aćimović, Jan Hahne, Han-Jia Jiang, Mikko Lehtimäki, Tiina Manninen, and Jonas Stapmanns.