Ciro Santilli @cirosantilli  40

10 8: st_name = 01000000 = character 1 in the .strtab, which until the following \0 makes hello_world.asm
This piece of information file may be used by the linker to decide on which segment sections go: e.g. in ld linker script we write:
```
segment_name :
{
    file(section)
}
```
to pick a section from a given file.
Most of the time however, we will just dump all sections with a given name together with:
```
segment_name :
{
    *(section)
}
```
10 12: st_info = 04
Bits 0-3 = ELF64_R_TYPE = Type = 4 = STT_FILE: the main purpose of this entry is to use st_name to indicate the name of the file which generated this object file.
Bits 4-7 = ELF64_ST_BIND = Binding = 0 = STB_LOCAL. Required value for STT_FILE.
10 13: st_shndx = Symbol Table Section header Index = f1ff = SHN_ABS. Required for STT_FILE.
20 0: st_value = 8x 00: required for value for STT_FILE
20 8: st_size = 8x 00: no allocated size

Now from the readelf, we interpret the others quickly.

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ELF Hello World Tutorial / STT_SECTION Updated 2025-07-16

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There are two such entries, one pointing to .data and the other to .text (section indexes 1 and 2).

Num:    Value          Size Type    Bind   Vis      Ndx Name
  2: 0000000000000000     0 SECTION LOCAL  DEFAULT    1
  3: 0000000000000000     0 SECTION LOCAL  DEFAULT    2

TODO what is their purpose?

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ELF Hello World Tutorial / STT_NOTYPE Updated 2025-07-16

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Then come the most important symbols:

Num:    Value          Size Type    Bind   Vis      Ndx Name
  4: 0000000000000000     0 NOTYPE  LOCAL  DEFAULT    1 hello_world
  5: 000000000000000d     0 NOTYPE  LOCAL  DEFAULT  ABS hello_world_len
  6: 0000000000000000     0 NOTYPE  GLOBAL DEFAULT    2 _start

hello_world string is in the .data section (index 1). It's value is 0: it points to the first byte of that section.

_start is marked with GLOBAL visibility since we wrote:

global _start

in NASM. This is necessary since it must be seen as the entry point. Unlike in C, by default NASM labels are local.

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ELF Hello World Tutorial / SHT_SYMTAB on the executable Updated 2025-07-16

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By default, NASM places a .symtab on the executable as well.

This is only used for debugging. Without the symbols, we are completely blind, and must reverse engineer everything.

You can strip it with objcopy, and the executable will still run. Such executables are called "stripped executables".

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ELF Hello World Tutorial / .rel.text Updated 2025-07-16

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Besides sh_type == SHT_RELA, there also exists SHT_REL, which would have section name .text.rel (not present in this object file).

Those represent the same struct, but without the addend, e.g.:

typedef struct {
    Elf64_Addr  r_offset;
    Elf64_Xword r_info;
} Elf64_Rela;

The ELF standard says that in many cases the both can be used, and it is just a matter of convenience.

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ELF Hello World Tutorial / SHT_NULL Updated 2025-07-16

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In index 0, SHT_NULL is mandatory. Are there any other uses for it: stackoverflow.com/questions/26812142/what-is-the-use-of-the-sht-null-section-in-elf ?

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ELF Hello World Tutorial / PT_INTERP Updated 2025-07-16

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Contains the path to the dynamic loader, i.e. /lib64/ld-linux-x86-64.so.2 in Ubuntu 18.10. Explained at: stackoverflow.com/questions/8040631/checking-if-a-binary-compiled-with-static/55664341#55664341

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ELF Hello World Tutorial / Dynamic section Updated 2025-07-16

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Contains a lot of different flag masks.

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History of the electromagnetic theory of light Updated 2025-07-16

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Continent Updated 2025-07-16

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Moon Updated 2025-07-16

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Earth science Updated 2025-07-16

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E. Coli Whole Cell Model by Covert Lab / Condition Updated 2025-07-16

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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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