Run output is placed under `out/`:

Some of the output data is stored as `.cpickle` files. To observe those files, you need the original Python classes, and therefore you have to be inside Docker, from the host it won't work.

We can list all the plots that have been produced under `out/` with
``
find -name '*.png'
``
Plots are also available in <SVG> and <PDF> formats, e.g.:
* <PNG>: `./out/manual/plotOut/low_res_plots/massFractionSummary.png`
* <SVG>: `./out/manual/plotOut/svg_plots/massFractionSummary.svg` The SVGs write text as polygons, see also: <SVG fonts>.
* <PDF>: `./out/manual/plotOut/massFractionSummary.pdf`

The output directory has a hierarchical structure of type:
``
./out/manual/wildtype_000000/000000/generation_000000/000000/
``
where:
* `wildtype_000000`: variant conditions. `wildtype` is a human readable label, and `000000` is an index amongst the possible `wildtype` conditions. For example, we can have different simulations with different nutrients, or different <DNA> sequences. An example of this is shown at <run variants>.
* `000000`: initial random seed for the initial cell, likely fed to <NumPy>'s `np.random.seed`
* `genereation_000000`: this will increase with generations if we simulate multiple cells, which is supported by the model
* `000000`: this will presumably contain the cell index within a generation

We also understand that some of the top level directories contain summaries over all cells, e.g. the `massFractionSummary.pdf` plot exists at several levels of the hierarchy:
``
./out/manual/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/000000/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut/massFractionSummary.pdf
``

Each of thoes four levels of `plotOut` is generated by a different one of the analysis scripts:
* `./out/manual/plotOut`: generated by `python runscripts/manual/analysisVariant.py`. Contains comparisons of different variant conditions. We confirm this by looking at the results of <run variants>.
* `./out/manual/wildtype_000000/plotOut`: generated by `python runscripts/manual/analysisCohort.py --variant_index 0`. TODO not sure how to differentiate between two different labels e.g. `wildtype_000000` and `somethingElse_000000`. If `-v` is not given, a it just picks the first one alphabetically. TODO not sure how to automatically generate all of those plots without inspecting the directories.
* `./out/manual/wildtype_000000/000000/plotOut`: generated by `python runscripts/manual/analysisMultigen.py --variant_index 0 --seed 0`
* `./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut`: generated by `python runscripts/manual/analysisSingle.py --variant_index 0 --seed 0 --generation 0 --daughter 0`. Contains information about a single specific cell.


Discussion on "Output overview" by Ciro Santilli 32