opensourcebrain/l23pyramidalcelltutorial

A tutorial introducing OSB's ability to visualise, analyse and simulate biophysically realistic, multicompartmental cells.

L2/3 Pyramidal Cell Tutorial

A tutorial introducing OSB's ability to visualise, analyse and simulate biophysically realistic, multicompartmental cells.

Uses a detailed Layer 2/3 Pyramidal cell from the Blue Brain Project Neocortical Microcircuit model as an example.

To follow this tutorial, please click here.

l23pyramidalcelltutorial's Issues

Power operator '^' is not replaced by '**' by pyneuroml

L23PyramidalCellTutorial/NeuroML2/K_Tst.channel.nml

Line 60 in afc4e6e

<DerivedVariable name="t" exposure="t" dimension="time" value="(0.34 + 0.92 * (exp (-1 *((V+81)/59)^2))) * TIME_SCALE"/>

When evaluating this using pyneuroml, I am getting the following error:

unsupported operand type(s) for ^: 'float' and 'int'
pyNeuroML >>> v = -0.15
pyNeuroML >>> vShift = 0.0
pyNeuroML >>> temperature = 307.15
pyNeuroML >>> TIME_SCALE = 0.001
pyNeuroML >>> VOLT_SCALE = 0.001
pyNeuroML >>> V = v / VOLT_SCALE
pyNeuroML >>> return_vals["V"] = V
pyNeuroML >>> t = (0.34 + 0.92 * (exp (-1 *((V+81)/59)^2))) * TIME_SCALE
pyNeuroML >>> return_vals["t"] = t
pyNeuroML >>> 
Traceback (most recent call last):

Suggestions for improvements to tutorial

• explain what continuous accomodating is (or is it adapting?) - more info to be added here: https://bbp.epfl.ch/nmc-portal/glossary
• links for inputs are broken (related to OpenSourceBrain/geppetto-osb#194)

Some from Fred...

• once you highlight the cell regions with the different colors you can't go back to the cell in one color. not really important.
• how do you get from properties of the cell to properties of the K_Pst channel without the tutorial? Just add a sentence that say that you have to click on ion channels K_Pst.
• in ion channels/ activation variable, the scale is in Volt. It's OK but we are used to scale in mV.
• the control panel section should be better explained before it opens. indicate how to open it from the left hand side and how to close it (by clicking outside the box).
• ask people to log in before starting if they want to run a simulation. because when you refresh the page it starts from the beginning of the tutorial.
• I run the simulations/changing current input but it says that there is no data to display in the control panel?
• in the sodium channel sim., you say high transient Na+ but in the section below where you can change the density it says Fast, transient Na+
• you should put the default values somewhere so we can come back to the original model.
• I was not able to download the data.
• What's missing in the tutorial is how do you run a protocol by yourself. How can I do an input/output curve?