• 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

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