Ciro Santilli @cirosantilli 34

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Condition  Updated 2024-12-15  +Created 1970-01-01

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.tsvcontains:"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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Sample collection  Updated 2024-12-15  +Created 1970-01-01

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As you would expect, not much secret here, we just dumped a 1 liter glass bottle with a rope attached around the neck in a few different locations of the river, and pulled it out with the rope.

And, in the name of science, we even wore gloves to not contaminate the samples!

Video 1.

Dumping the bottle into the river to collect the water sample

. Source. That was fun.

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