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: TODOPI: TODOPROTON[c]: presumably a measure of pHGLC[p]: glucose, this can be seen by comparing minimal.tsv with minimal_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/` 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.tsvnutrients 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.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
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Ciro Santilli