abi-tutorials / cellml-opencor-pmr Goto Github PK

As per https://groups.google.com/d/msgid/opencor-users/331a507d-3a77-4f6d-96a3-3ef3dde86436%40googlegroups.com?utm_medium=email&utm_source=footer

There is an extra E_Na being defined which when copy-pasted into OpenCOR will result in an overconstrained model. Linked SED-ML/CellML works fine and correctly only has one E_Na definition.

It would be good to link to appropriate example models in the repository wherever possible.

It would be nice (might be nice?) if we can state at the outset that "this tutorial is based on version X.Y.Z" and then we try to keep the tutorial in sync with each new release. Given limited resources it might not be every release, but perhaps significant releases or times when the tutorial is presented.

We could then maintain a collection of versions of this tutorial?

it would be good to consistently use the sphinx semantic elements for user interface elements: http://sphinx-doc.org/markup/inline.html#other-semantic-markup

particularly when referring to GUI labels and menu selections.

Eventually OpenCOR might support a similar colour coding as used in the example code given in the original PDF version. It would be good if this could be implemented in a way that was easily configurable (i.e., in the template?). See opencor/opencor#651 and opencor/opencor#652.

Should create a new version of figure 9 with Lorenz

It would probably be best to split the tutorial into several different documents, following the initial main section headings.

The ss_cur_volt.png file in the documentation has a label "needs checking" ... does it?

Hi all
I'm trying to replicate the behaviour of the tutorials using libcellml and am struggling with some of them. For example, in the sodium channel tutorial:

1. The second equation is confusing:
   
   ... this isn't true, it equals 38.511?

2. There's only equation including g_Na is Na_conductance=g_Na*pow(m, 3{dimensionless})*h; which doesn't change its value from the initial condition of 120. Where does the behaviour in the figure come from?

3. The initial conditions don't seem to make sense to me? The initial h value is 0.6 but in the figures it looks closer to 0.8ish? See: var h: dimensionless {init: 0.6, pub: out};

4. In the PDF the equation for Na_conductance has mismatched parentheses:
   Na_conductance=g_Na*pow(m, 3{dimensionless})*h);
   and defines E_Na twice? How come that's allowed?

If anyone can help me understand what I'm missing that would be great :) Thanks!