Examples by Matthew Stroud --- Thanks to Tyler Banks, Ben Latimer, Pete Canfield, and Satish Nair for assisting in the creation of these models.
These examples were inspired by examples in Christophe Borgers' book, "Introduction to Modeling Neuronal Dynamics". Each example in this repository is written in Python and may use the packages NEURON and or BMTK. Some features of the original examples are ignored while implementing similar networks in these models.
The goal of these computational models is to display general network features and their affects apart from raw numerical solutions when possible.
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Python 3.6 or 2.7
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BMTK version 0.0.9
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Neuron version 8.0.0
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H5py version 2.9.0
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Latest jupyter notebook
Compile all .mod files in each example by using mknrndll Windows app or nrnivmodl command in terminal.
Recommended: Download latest Anaconda app to download each of the above in an Anaconda Environment. You can then open jupyter notebooks from the Anaconda terminal.
Chapters 30 and 32 are skipped
Section 23.1 — Figure 23.3: WB neuron 1:1 entrainment (page 185) Omit: Section 23.2
Section 24.2 – Figure 24.6: RTM_E_TO_E_Heterogeneous example (page 196) Omit: Section 24.1
Section 25.1 – Figure 25.2: RTM_PRC example (page 201). Omit: Sections 25.2, 25.3, and 25.4
Section 26.3 – Figure 26.7: and Figure 26.8 (page 219) Omit: Sections 26.1, 26.2, 26.4, 26.5, and 26.6
Section 27.1 – Figure 27.1 (page 231) Omit Section 27.2 and 27.3
Section 28.1 – Figure 28.1 and Figure 28.2 (page 237) Omit Section 28.2
Section 29.2 – Figure 29.4: RTM_With_Inhibitory_Pulse (page 248) Omit: Section 29.1 and 29.3
Section 31.6 – Figure 31.14: ING_ENTRAINING_E_CELLS (page 277) Omit: Sections 31.1, 31.2, 31.3, 31.4, 31.5
Section 33.1 – Figure 33.2: PINB_2 (page 295) Omit: Section 33.2 and 33.3
Erisir Model, RTM Model, and WB Model completed using BMTK.