www.wholecellviz.org/viz.php awesome visualization of simtk, paper: www.ncbi.nlm.nih.gov/pmc/articles/PMC3413483/ A Whole-Cell Computational Model Predicts Phenotype from Genotype - 2013 - Jonathan R. Karr.
Followed up by the E. Coli Whole Cell Model by Covert Lab.
DNA stuff at: human mtDNA.
Ciro Santilli once talked to a man who had been working on high-frequency trading for the last six years.
He was quite nice.
Ciro asked him in what way did he feel his job contributed to the benefit of society.
He replied that it didn't contribute at all. It was completely useless. More than that, it so completely useless, that it was even pure. A bit like advanced mathematics, but not even providing beauty for anybody outside of the company, since everything is a closely guarded trade secret, unlike mathematics which is normally published for the vanity recognition.
And so, Ciro was enlightened.
Sections with
sh_type == SHT_STRTAB are called string tables.They hold a null separated array of strings.
Such sections are used by other sections when string names are to be used. The using section says:
- which string table they are using
- what is the index on the target string table where the string starts
So for example, we could have a string table containing:
Data: \0 a b c \0 d e f \0
Index: 0 1 2 3 4 5 6 7 8And if another section wants to use the string
d e f, they have to point to index 5 of this section (letter d).Notable string table sections:
.shstrtab.strtab
Holds strings for the symbol table.
This section has
sh_type == SHT_STRTAB.It is pointed to by outputs:
sh_link == 5 of the .symtab section.readelf -x .strtab hello_world.oHex dump of section '.strtab':
0x00000000 0068656c 6c6f5f77 6f726c64 2e61736d .hello_world.asm
0x00000010 0068656c 6c6f5f77 6f726c64 0068656c .hello_world.hel
0x00000020 6c6f5f77 6f726c64 5f6c656e 005f7374 lo_world_len._st
0x00000030 61727400 art.This implies that it is an ELF level limitation that global variables cannot contain NUL characters.
Spin like mad between:
- standards
- high level generators. We use the assembler
asand linkerld. - hexdumps
- file decompilers. We use
readelf. It makes it faster to read the ELF file by turning it into human readable output. But you must have seen one byte-by-byte example first, and think howreadelfoutput maps to the standard. - low-level generators: stand-alone libraries that let you control every field of the ELF files you generated. github.com/BR903/ELFkickers, github.com/sqall01/ZwoELF and many more on GitHub.
- consumer: the
execsystem call of the Linux kernel can parse ELF files to starts processes: github.com/torvalds/linux/blob/v4.11/fs/binfmt_elf.c, stackoverflow.com/questions/8352535/how-does-kernel-get-an-executable-binary-file-running-under-linux/31394861#31394861
This is likely the easiest one to produce as the frequencies are lower, which is why it was discovered first. TODO original setup.
Also because it is transparent to brick and glass, (though not metal) it becomes good for telecommunication.
Some notable subranges:
E. Coli Whole Cell Model by Covert Lab Install and first run by 
Ciro Santilli 37 Updated 2025-07-16
Ciro Santilli 37 Updated 2025-07-16At 7e4cc9e57de76752df0f4e32eca95fb653ea64e4 you basically need to use the Docker image on Ubuntu 21.04 due to pip breaking changes... (not their fault). Perhaps pyenv would solve things, but who has the patience for that?!?!
The Docker setup from README does just work. The image download is a bit tedius, as it requires you to create a GitHub API key as described in the README, but there must be reasons for that.
Once the image is downloaded, you really want to run is from the root of the source tree:This mounts the host source under The meaning of each of the analysis commands is described at Section "Output overview".
sudo docker run --name=wcm -it -v "$(pwd):/wcEcoli" docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full/wcEcoli, so you can easily edit and view output images from your host. Once inside Docker we can compile, run the simulation, and analyze results with:make clean compile &&
python runscripts/manual/runFitter.py &&
python runscripts/manual/runSim.py &&
python runscripts/manual/analysisVariant.py &&
python runscripts/manual/analysisCohort.py &&
python runscripts/manual/analysisMultigen.py &&
python runscripts/manual/analysisSingle.pyAs a Docker refresher, after you stop the container, e.g. by restarting your computer or running
sudo docker stop wcm, you can get back into it with:sudo docker start wcm
sudo docker run -it wcm bashrunscripts/manual/runFitter.py takes about 15 minutes, and it generates files such as reconstruction/ecoli/dataclasses/process/two_component_system.py (related) which is required to run the simulation, it is basically a part of the build.runSim.py does the main simulation, progress output contains lines of type:Time (s) Dry mass Dry mass Protein RNA Small mol Expected
(fg) fold change fold change fold change fold change fold change
======== ======== =========== =========== =========== =========== ===========
0.00 403.09 1.000 1.000 1.000 1.000 1.000
0.20 403.18 1.000 1.000 1.000 1.000 1.000 2569.18 783.09 1.943 1.910 2.005 1.950 1.963
Simulation finished:
- Length: 0:42:49
- Runtime: 0:09:13TODO compare with actual datasetes.
Generalization of AlphaGo Zero that plays Go, chess and shogi.
- www.science.org/doi/10.1126/science.aar6404 A general reinforcement learning algorithm that masters chess, shogi, and Go through self-play by Silver et al. (2018), published without source code
- www.quora.com/Is-there-an-Open-Source-version-of-AlphaZero-specifically-the-generic-game-learning-tool-distinct-from-AlphaGo
www.quora.com/Which-chess-engine-would-be-stronger-Alpha-Zero-or-Stockfish-12/answer/Felix-Zaslavskiy explains that it beat Stockfish 8. But then Stockfish was developed further and would start to beat it. We know this because although AlphaZero was closed source, they released the trained artificial neural network, so it was possible to replay AlphaZero at its particular stage of training.
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