Documentation for working with clock (circadian) model

[csnazell]

Drafted description of clock model and how to create a new clock model from scratch.

Outstanding:

• [x] - need to verify code examples work as per expectation.

[csnazell]

Addresses Issue #1

[csnazell]

Tried out new clock example, identified areas where it didn't work & updated the docs accordingly.

[csnazell]

Explain what “sunset” and ConstantModel mean and what is needed to define the environment. ...

I've created issue #6 to cover documentation of environment model & included task to update this document (linking &c) when the environment model docs exist.

[csnazell]

Would be nice for parameters to say which “sets” are available (which possible genotype values are predefined).

I'll add an additional doc covering implemented models. I think this are the red * blue variants for the F2014 COP1 model.

[csnazell]

For the “Using a Clock Model” section where you explain entrainment, ...

I think adding some expansion of what's going on with entrainment probably needs to be in both locations. Probably a quick note in the docs and a few lines in the code. From a purely functional point of view this step essentially produces the initial conditions for clock model simulation run. I think it's necessary to give the clock model a chance to align with the environmental inputs to the model.

The Framework V2 Model paper doesn't really touch on what's happening but it does reference a couple of papers:

Locke JC, Southern MM, Kozma-Bognar L, Hibberd V, Brown PE, Turner MS, Millar AJ. 2005. Extension of a genetic network model by iterative experimentation and mathematical analysis. Molecular Systems Biology 1:2005–0013.

Haydon MJ, Mielczarek O, Robertson FC, Hubbard KE, Webb AA. 2013. Photosynthetic entrainment of the Arabidopsis thaliana cir- cadian clock. Nature 502:689–692.

[csnazell]

You say that it is good to review one of the existing implementations. ...

I 'll add some detail on where the clock elements of the framework are within the package with some info on the structure and how they work with one another.

I'll add a call out the F2014.jl source.

[csnazell]

In Dependencies, your clock model does not have “using PlantModelFramework”, right? Why is that not necessary in that case but necessary for the Experimental Clock?

My intention was that step "#2 Create The Boilerplate" is literally just a blank first step with the comments indicating the overall structure. Each subsequent step fills in the blanks. I'll add the comment lines into these steps to make it clearer.

[csnazell]

Is midnight really the middle of the night or is it the 24h timepoint? ...

It's just the 24h / 0h timepoint. I'll change the wording to clarify matters. With the sunset set to 8 the daylight period is effectively 0h through to 8h for an 8 hour photoperiod.

[csnazell]

Why are there negative values in the 41-element Vector? What does this represent? They are also all the same.

These are the caluclated outcomes of the differential equations as written. I just made the DEs up as simple example boilerplate. SciML complains they're not stable but it does run.

I'll add some text highlighting that the DEs are merely illustrative and don't represent anything in particular.