Minor formatting updates

[agchesebro]

Collection of minor things I've noticed (will append to list as I continue looking at the website):

• Short website name (shown on tab view) still says "Franklin Example | Vela" and the non-Neuroblox logo
• Menu name of website is "Vela Template"
• Circuit Models in the menu is "Circuit Modelis"
• PING network structure image isn't shown (just ?)
• Under "Introduction to Julia" it lists a bunch of resources as "prerequisites", which sounds like they should read all of these resources, is this intentional? Maybe it should just be called "Resources"?
• PING tutorial HH equation is set as code rather than rendered LaTeX
• PING tutorial markdown is behaving weirdly - subsection headers like "Define the neurons" and "Alternative graph creation" are not bold and just plain text
• Citations in tutorials without bulleted lists are not separated (numbered lists are rendered as a single paragraph).
• In the Circuit Models Introduction page, both of the links to the tutorials are 404
• In the spDCM tutorial, the challenge problems have titles but these aren't bolded so they just look like incomplete sentences.
• spDCM figures need to be fixed to render on website
• semicolons for code suppression
• in "Biomimetic model...." page the t_stimulus and t_pause in the exercises are rendered as italics and no underline so it's messing with the formatting
• in "Biomimetic model...." Exercise has two colons after it.
• in "Introduction to Julia" the links to the outside course are plain text, not hyperlinks (first block only, main links work).

[sbrincat]

Note: I don't have write access to to Anthony's issue, so I am adding my typos/formatting comments here. Feel free to cut and paste them into the main issue if you want.

• Link in “Plotting with Makie: Challenge problems” is 404
• In “Blox and Connections in Neuroblox: Custom Connections” – typo: variery → variety
• In “Blox and Connections in Neuroblox: Connection callbacks” – typos: Currenlty → Currently; affect → effect?
• In “Neurons, Neural Masses and Sources: Neurons and neural masses” – typo: Exhitatation → Excitation; ‘int he’ → ‘in the’
• In “Neurons, Neural Masses and Sources: Sources” – typo: ‘as a particular Blox subtype’ → ‘are a particular Blox subtype’; shiften → shifted
• Typos in “Circuit Models in Neuroblox”: in text and code ‘WinnerTakesAllBlox’ should be ‘WinnerTakeAllBlox’
• Even with typo fix above, code still throws error: UndefKeywordError: keyword argument name not assigned
• In "PING": 'Reasons for each non-Neuroblox package are given in the comments' – these are actually not given
• In “Decisions”: Populations A and B are reversed in my output (and the text matches my plots, rather than the plots in the tutorial)
• In “Decisions”: Plot title "Competing Firing Rates" isn’t showing up
• In “Synaptic Plasticity”: Plot titles are not showing up
• In “Inverse problems”: typo: ‘optimizatoin’ should be ‘optimization’

[sbrincat]

Since this issue is still open, I will just add additional minor comments that arose from the course here...

• In "Intro to Julia", cells 80-81 (h.(x)) seem to be a repeat of 78
• In "Intro to Diff Eq", the 1st plot outputs twice, in cells 14 and 15
• In "Intro to Plotting", cells starting with “for i in eachindex(t_range[1:end-1])” don’t output any plot (need fig call)- - [ ] In "NB blox & connections", typo: ‘genric’ should be ‘generic’
• In "Neurons & neural masses", could we label axes on the plots, so people know what they are?
• In "Neurons & neural masses", the first cell in “Event-based spike sources” produced a bunch of warnings…then didn’t the second time I called it(?)

• In "Neurons & neural masses", would’ve been nice to have some brief intro to LIF vs Izh neurons, what their different parameters reflect
• In "Corticostriatal model", typo: ‘strutures’ should be ‘structures’
• In "Corticostriatal model", typo ‘number if WTA circuits’ should be ‘number of WTA circuits’
• In "Corticostriatal model", could we explain what I_bg is supposed to represent?
• In "DCM", typo: ‘euqations’ should be ‘equations’
• In "DCM", could we recode ecbarplot() to plot ground truth values in different color, in case they ever do overlap with the posterior bars

[harisorgn]

Thank you both! We will address these shortl

In "DCM", could we recode ecbarplot() to plot ground truth values in different color, in case they ever do overlap with the posterior bars

I'll open a PR for this now. You will be able to do ecbarplot(; color = :color_of_your_choice) like with other recipes.