* `reconstruction/ecoli/flat/condition/nutrient/minimal.tsv` contains the nutrients in a minimal environment in which the cell survives:
  ``
  "molecule id" "lower bound (units.mmol / units.g / units.h)" "upper bound (units.mmol / units.g / units.h)"
  "ADP[c]" 3.15 3.15
  "PI[c]" 3.15 3.15
  "PROTON[c]" 3.15 3.15
  "GLC[p]" NaN 20
  "OXYGEN-MOLECULE[p]" NaN NaN
  "AMMONIUM[c]" NaN NaN
  "PI[p]" NaN NaN
  "K+[p]" NaN NaN
  "SULFATE[p]" NaN NaN
  "FE+2[p]" NaN NaN
  "CA+2[p]" NaN NaN
  "CL-[p]" NaN NaN
  "CO+2[p]" NaN NaN
  "MG+2[p]" NaN NaN
  "MN+2[p]" NaN NaN
  "NI+2[p]" NaN NaN
  "ZN+2[p]" NaN NaN
  "WATER[p]" NaN NaN
  "CARBON-DIOXIDE[p]" NaN NaN
  "CPD0-1958[p]" NaN NaN
  "L-SELENOCYSTEINE[c]" NaN NaN
  "GLC-D-LACTONE[c]" NaN NaN
  "CYTOSINE[c]" NaN NaN
  ``
  If we compare that to `reconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv`, we see that it adds the 20 <amino acids> on top of the minimal condition:
  ``
  "L-ALPHA-ALANINE[p]" NaN NaN
  "ARG[p]" NaN NaN
  "ASN[p]" NaN NaN
  "L-ASPARTATE[p]" NaN NaN
  "CYS[p]" NaN NaN
  "GLT[p]" NaN NaN
  "GLN[p]" NaN NaN
  "GLY[p]" NaN NaN
  "HIS[p]" NaN NaN
  "ILE[p]" NaN NaN
  "LEU[p]" NaN NaN
  "LYS[p]" NaN NaN
  "MET[p]" NaN NaN
  "PHE[p]" NaN NaN
  "PRO[p]" NaN NaN
  "SER[p]" NaN NaN
  "THR[p]" NaN NaN
  "TRP[p]" NaN NaN
  "TYR[p]" NaN NaN
  "L-SELENOCYSTEINE[c]" NaN NaN
  "VAL[p]" NaN NaN
  ``
  so we guess that `NaN` in the `upper mound` likely means infinite.

  We can try to understand the less obvious ones:
  * `ADP`: TODO
  * `PI`: TODO
  * `PROTON[c]`: presumably a measure of <pH>
  * `GLC[p]`: <glucose>, this can be seen by comparing `minimal.tsv` with `minimal_no_glucose.tsv`
  * `AMMONIUM`: <ammonium>. This appears to be the primary source of <nitrogen> <atoms> for producing <amino acids>.
  * `CYTOSINE[c]`: hmmm, why is external <cytosine> needed? Weird.
* ``
  reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/` contains sequences of conditions for each time. For example:
  * 
  ``
  reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000000_basal.tsv` contains:
    ``  "time (units.s)" "nutrients"
    0 "minimal"
    ``  which means just using `reconstruction/ecoli/flat/condition/nutrient/minimal.tsv` until infinity. That is the default one used by `runSim.py`, as can be seen from `./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Environment/attributes/nutrientTimeSeriesLabel` which contains just `000000_basal`.
  * ``reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000001_cut_glucose.tsv` is more interesting and contains:
    
  ``
    "time (units.s)" "nutrients"
    0 "minimal"
    1200 "minimal_no_glucose"
    
  ``
    so we see that this will shift the conditions half-way to a condition that will eventually kill the bacteria because it will run out of <glucose> and thus energy!

    Timeseries can be selected with `--variant nutrientTimeSeries X Y`, see also: <run variants>.

    We can use that variant with:
    
  ``
    VARIANT="condition" FIRST_VARIANT_INDEX=1 LAST_VARIANT_INDEX=1 python runscripts/manual/runSim.py
    
  ``
* `reconstruction/ecoli/flat/condition/condition_defs.tsv` contains lines of form:
  ``
  "condition" "nutrients"                "genotype perturbations" "doubling time (units.min)" "active TFs"
  "basal"     "minimal"                  {}                       44.0                        []
  "no_oxygen" "minimal_minus_oxygen"     {}                       100.0                       []
  "with_aa"   "minimal_plus_amino_acids" {}                       25.0                        ["CPLX-125", "MONOMER0-162", "CPLX0-7671", "CPLX0-228", "MONOMER0-155"]
  ``

  * `condition` refers to entries in `reconstruction/ecoli/flat/condition/condition_defs.tsv`
  * `nutrients` refers to entries under `reconstruction/ecoli/flat/condition/nutrient/`, e.g. `reconstruction/ecoli/flat/condition/nutrient/minimal.tsv` or `reconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv`
  * `genotype perturbations`: there aren't any in the file, but this suggests that genotype modifications can also be incorporated here
  * `doubling time`: TODO experimental data? Because this should be a simulation output, right? Or do they cheat and fix doubling by time?
  * `active TFs`: this suggests that they are cheating <transcription factors> here, as those would ideally be functions of other more basic inputs


E coli whole cell model by covert lab/condition

ID: e-coli-whole-cell-model-by-covert-lab/condition