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Add tutorials and examples for SDE #1987

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5 of 6 tasks
thorstenhater opened this issue Sep 26, 2022 · 2 comments · Fixed by #2030 or #2044
Closed
5 of 6 tasks

Add tutorials and examples for SDE #1987

thorstenhater opened this issue Sep 26, 2022 · 2 comments · Fixed by #2030 or #2044
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enhancement Feature Request help wanted neuroscience
Milestone
v0.8

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@thorstenhater
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thorstenhater commented Sep 26, 2022 •
edited by boeschf

#1884 is about to get merged, we should add a few basic examples at least to
show how to use it from Python and C++. Also, some standard mechanisms could
be included in a 'stochastic' catalogue.

TODO

  • add a simple example
    • C++
    • Python
  • add stochastic catalogue
    • O-U process point source
  • Optional: add tutorial
@thorstenhater thorstenhater added this to the v0.8 milestone Sep 26, 2022
@thorstenhater thorstenhater mentioned this issue Oct 18, 2022
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@schmitts
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schmitts commented Nov 3, 2022

I can contribute the Graupner-Brunel example.

@thorstenhater
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That'd be cool.

@brenthuisman brenthuisman linked a pull request Nov 7, 2022 that will close this issue
SDE examples #2030
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@boeschf boeschf mentioned this issue Nov 8, 2022
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boeschf added a commit that referenced this issue Nov 15, 2022
@boeschf
SDE examples (#2030)
1b268ec 
Addresses #1987

* reproducibility test for random number generator
* C++ example demonstrating Ornstein-Uhlenbeck process
* Python example featuring stochastic mechanism
* stochastic mechanism catalogue

The Python example is contributed by Jannik Luboeinski's (@jlubo): https://github.com/jlubo/arbor_ou_lif_example
and adapted to fit into Arbor.
@boeschf boeschf mentioned this issue Nov 21, 2022
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brenthuisman pushed a commit that referenced this issue Dec 12, 2022
@boeschf
Sde Tutorial (#2044)
abbf6bb 
Implementation of stochastic calcium plasticity curves, originally
authored by Sebastian Schmitt @schmitts, and adapted here for Arbor
inclusion.
- python example plasticity_stdp.py
- stochastic mechanism calcium_based_synapse.mod
- tutorial

Closes #1987
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enhancement Feature Request help wanted neuroscience
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SDE examples boeschf/arbor
Sde Tutorial boeschf/arbor
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@schmitts @thorstenhater