= Condition
* `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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