Node.js ORM library by Ciro Santilli 35 Updated +Created
Copernican heliocentrism by Ciro Santilli 35 Updated +Created
Divorce of Jeff and MacKenzie Bezos by Ciro Santilli 35 Updated +Created
MacKenzie Bezos went on to marry a science teacher who taught their children.
The contrast with Bezos's girlfriend is simply comical. MacKenzie married the idealistic morally upright science teacher, while Bezos went for a silly sex bomb. Ah, bruta flor, do querer!
M. genitalium whole cell model by Covert lab by Ciro Santilli 35 Updated +Created
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.
Sergey Brin by Ciro Santilli 35 Updated +Created
Human mitochondrion by Ciro Santilli 35 Updated +Created
GDSII by Ciro Santilli 35 Updated +Created
Figure 1.
3D rendering of a GDSII file.
Source.
High-frequency trading as a form of Nirvana by Ciro Santilli 35 Updated +Created
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.
A great mind can work in the most useless branches of finance, without the desire to improve the world, nor make it worse. Not to compete, nor be afraid, nor anxious. A sand mandala.
Only being. Being, in the exact fraction of a moment where bid meets ask.
Synoptic Gospels by Ciro Santilli 35 Updated +Created
Rogue trader by Ciro Santilli 35 Updated +Created
University of Stanford spinout company by Ciro Santilli 35 Updated +Created
SHT_STRTAB by Ciro Santilli 35 Updated +Created
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  8
The first byte must be a 0. TODO rationale?
And 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
.strtab by Ciro Santilli 35 Updated +Created
Holds strings for the symbol table.
This section has sh_type == SHT_STRTAB.
It is pointed to by sh_link == 5 of the .symtab section.
readelf -x .strtab hello_world.o
outputs:
Hex 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.
How to learn by Ciro Santilli 35 Updated +Created
Spin like mad between:
Anomalous magnetic dipole moment by Ciro Santilli 35 Updated +Created
Radio wave by Ciro Santilli 35 Updated +Created
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:
Install and first run by Ciro Santilli 35 Updated +Created
At 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:
sudo docker run --name=wcm -it -v "$(pwd):/wcEcoli" docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full
This mounts the host source under /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.py
The meaning of each of the analysis commands is described at Section "Output overview".
As 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 bash
runscripts/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
and then it ended on the Lenovo ThinkPad P51 (2017) at:
 2569.18    783.09        1.943        1.910        2.005        1.950        1.963

Simulation finished:
 - Length: 0:42:49
 - Runtime: 0:09:13
when the cell had almost doubled, and presumably divided in 42 minutes of simulated time, which could make sense compared to the 20 under optimal conditions.

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