Ciro Santilli
OurBigBook.comreconstruction/ecoli/flat/condition/nutrient/minimal.tsvcontains the nutrients in a minimal environment in which the cell survives:If we compare that to"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 NaNreconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv, we see that it adds the 20 amino acids on top of the minimal condition:so we guess that"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 NaNNaNin theupper moundlikely means infinite.We can try to understand the less obvious ones:ADP: TODOPI: TODOPROTON[c]: presumably a measure of pHGLC[p]: glucose, this can be seen by comparingminimal.tsvwithminimal_no_glucose.tsvAMMONIUM: 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/000000_basal.tsv
reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/` contains sequences of conditions for each time. For example: *contains:"time (units.s)" "nutrients" 0 "minimal"which means just usingreconstruction/ecoli/flat/condition/nutrient/minimal.tsvuntil infinity. That is the default one used byrunSim.py, as can be seen from./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Environment/attributes/nutrientTimeSeriesLabelwhich contains just000000_basal. *reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000001_cut_glucose.tsvis more interesting and contains:
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!"time (units.s)" "nutrients" 0 "minimal" 1200 "minimal_no_glucose"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.tsvcontains 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"]conditionrefers to entries inreconstruction/ecoli/flat/condition/condition_defs.tsvnutrientsrefers to entries underreconstruction/ecoli/flat/condition/nutrient/, e.g.reconstruction/ecoli/flat/condition/nutrient/minimal.tsvorreconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsvgenotype perturbations: there aren't any in the file, but this suggests that genotype modifications can also be incorporated heredoubling 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