Tutorial alpha user feedback: Bottom-up construction of a neural assembly

[sbrincat]

General

• I like how this tutorial builds complexity step-by-step, but I think it would be helpful to add like a 1-2 sentence description, in a conversational tone, of what is being added at each step and how it is different from/build upon the previous steps (some steps have this already, but many don’t). I’d suggest the PING tutorial for a good model of how to do this. For example, for the “Creating lateral inhibition WTA circuit” section, you might say something like: “So far, we’ve built a winner-take-all circuit by creating and connecting single neurons. Neuroblox also provides built-in functions that abstract all of this into a single function call. Here, we use WinnerTakeAllBlox() to generate an entire WTA circuit in one step.”
• I also like how it shows the effects of each step in the same plot types. But this leads to a lot of code cutting and pasting for users following along. I wonder if we might bundle each of the sets of spiking/meanfield/spectrum plots into a single figure with multiple subplots? Also, maybe we want to use the higher-level plotting functions used in the “Basal Ganglia Model and Parkinson's Disease” tutorial instead of the low-level lines!() calls?
• Do we need to redefine(?) the namespace (global_namespace=:g) in each cell? Other tutorials only set it once. (I also have zero understanding of what this line actually does…shouldn’t everything not within a function be in the same namespace already?)

Intro

• References – we should update this to the newest version (Pathak et al. “Biomimetic model of corticostriatal micro-assemblies discovers new neural code” Biorxiv 2024) and include a link to the paper
• References – should we include a reference to Byrne et. al. 2020?

Cell 7/8

• Could we label “neuron1/2/3…” on y-axis here? I initially assumed it was descending order, was confused.
• This is the first usage of stackplot() in the tutorials. Could we get a brief description of it in the associated text? Eg. “Here we use the high-level plotting function stackplot(), which plots a vertically-stacked series of neural activity curves.”

Cell 9 (“Creating lateral inhibition "winner-take-all"…”)

• Should have a note explaining the relationship to previous cells. I assume this would be something along the lines of “Instead of building a winner-take-all circuit by hand, we can use an pre-built composite ‘blox’ function to automatically build one.”
• Since this is the first usage of get_neurons(), which seems important, can we also include a brief description of that in the associated text? Eg, “Here we introduce the get_neurons() function, which allows you to extract pointers to(?) all individual neurons within a composite blox.”

Cell 15 (“Connecting the cortical superficial layer block to an ascending system block”)

• Should clarify “ascending system” means “neuromodulatory/brainstem ascending system”, rather than feedforward sensory inputs (which might be confusing since this is also the first tutorial with sensory input)