ELF Hello World Tutorial Sections Updated 2025-07-16
ELF Hello World Tutorial Program header table Updated 2025-07-16
Only appears in the executable.
Contains information of how the executable should be put into the process virtual memory.
The executable is generated from object files by the linker. The main jobs that the linker does are:
- determine which sections of the object files will go into which segments of the executable.
- do relocation according to the
.rela.textsection. This depends on how the multiple sections are put into memory.
readelf -l hello_world.out gives:Elf file type is EXEC (Executable file)
Entry point 0x4000b0
There are 2 program headers, starting at offset 64
Program Headers:
Type Offset VirtAddr PhysAddr
FileSiz MemSiz Flags Align
LOAD 0x0000000000000000 0x0000000000400000 0x0000000000400000
0x00000000000000d7 0x00000000000000d7 R E 200000
LOAD 0x00000000000000d8 0x00000000006000d8 0x00000000006000d8
0x000000000000000d 0x000000000000000d RW 200000
Section to Segment mapping:
Segment Sections...
00 .text
01 .dataOn the ELF header, and:
e_phoff, e_phnum and e_phentsize told us that there are 2 program headers, which start at 0x40 and are 0x38 bytes long each, so they are:00000040 01 00 00 00 05 00 00 00 00 00 00 00 00 00 00 00 |................|
00000050 00 00 40 00 00 00 00 00 00 00 40 00 00 00 00 00 |..@.......@.....|
00000060 d7 00 00 00 00 00 00 00 d7 00 00 00 00 00 00 00 |................|
00000070 00 00 20 00 00 00 00 00 |.. ..... |00000070 01 00 00 00 06 00 00 00 | ........|
00000080 d8 00 00 00 00 00 00 00 d8 00 60 00 00 00 00 00 |..........`.....|
00000090 d8 00 60 00 00 00 00 00 0d 00 00 00 00 00 00 00 |..`.............|
000000a0 0d 00 00 00 00 00 00 00 00 00 20 00 00 00 00 00 |.......... .....|Structure represented www.sco.com/developers/gabi/2003-12-17/ch5.pheader.html:
typedef struct {
Elf64_Word p_type;
Elf64_Word p_flags;
Elf64_Off p_offset;
Elf64_Addr p_vaddr;
Elf64_Addr p_paddr;
Elf64_Xword p_filesz;
Elf64_Xword p_memsz;
Elf64_Xword p_align;
} Elf64_Phdr;Breakdown of the first one:
- 40 0:
p_type=01 00 00 00=PT_LOAD: this is a regular segment that will get loaded in memory. - 40 4:
p_flags=05 00 00 00= execute and read permissions. No write: we cannot modify the text segment. A classic way to do this in C is with string literals: stackoverflow.com/a/30662565/895245 This allows kernels to do certain optimizations, like sharing the segment amongst processes. This member gives the offset from the beginning of the file at which the first byte of the segment resides.
But it looks like offsets from the beginning of segments, not file?- 50 0:
p_vaddr=00 00 40 00 00 00 00 00: initial virtual memory address to load this segment to - 50 8:
p_paddr=00 00 40 00 00 00 00 00: unspecified effect. Intended for systems in which physical addressing matters. TODO example? - 60 0:
p_filesz=d7 00 00 00 00 00 00 00: size that the segment occupies in memory. If smaller thanp_memsz, the OS fills it with zeroes to fit when loading the program. This is how BSS data is implemented to save space on executable files. i368 ABI says onPT_LOAD:The bytes from the file are mapped to the beginning of the memory segment. If the segment’s memory size (p_memsz) is larger than the file size (p_filesz), the ‘‘extra’’ bytes are defined to hold the value 0 and to follow the segment’s initialized area. The file size may not be larger than the memory size.
The second segment (
.data) is analogous. TODO: why use offset 0x0000d8 and address 0x00000000006000d8? Why not just use 0 and 0x00000000006000d8?Then the:section of the
Section to Segment mapping:readelf tells us that:TODO where does this information come from? stackoverflow.com/questions/23018496/section-to-segment-mapping-in-elf-files
ELF Hello World Tutorial Backlinks Updated 2025-07-16
Organization developing electron on helium quantum computer Updated 2025-07-16
Elementary charge Updated 2025-07-16
Experiments to measure it:
The 2019 redefinition of the SI base units defines it precisely and uses it as a measure of charge: en.wikipedia.org/wiki/2019_redefinition_of_the_SI_base_units#Ampere
Electron rest mass Updated 2025-07-16
Positron Updated 2025-07-16
Ben Bernanke Updated 2025-07-16
Yanis Varoufakis Updated 2025-07-16
He beats the The European Union is a failure drum pretty well.
- www.youtube.com/watch?v=iVxaTC7Qp44 The Global Minotaur: The Crash of 2008 and the Euro-Zone Crisis in Historical Perspective (2011)
- youtu.be/vNhkYXhYSSs?t=368 proposes that there is something missing from utility maximization, citing a lotus-Eater Machine idea
E. Coli Whole Cell Model by Covert Lab Updated 2025-07-16
github.com/CovertLab/WholeCellEcoliRelease is a whole cell simulation model created by Covert Lab and other collaborators.
The project is written in Python, hurray!
But according to te README, it seems to be the use a code drop model with on-request access to master. Ciro Santilli asked at rationale on GitHub discussion, and they confirmed as expected that it is to:
- to prevent their publication ideas from being stolen. Who would steal publication ideas with public proof in an issue tracker without crediting original authors? Academia is broken. Academia should be the most open form of knowledge sharing. But instead we get this silly competition for publication points.
- to prevent noise from non-collaborators. But they only get like 2 issues as year on such a meganiche subject... Did you know that you can ignore people, and even block them if they are particularly annoying? Much more likely is that no one will every hear about your project and that it will die with its last graduate student slave.
The project is a followup to the earlier M. genitalium whole cell model by Covert lab which modelled Mycoplasma genitalium. E. Coli has 8x more genes (500 vs 4k), but it the undisputed bacterial model organism and as such has been studied much more thoroughly. It also reproduces faster than Mycoplasma (20 minutes vs a few hours), which is a huge advantages for validation/exploratory experiments.
The project has a partial dependency on the proprietary optimization software CPLEX which is freeware, for students, not sure what it is used for exactly, from the comment in the
requirements.txt the dependency is only partial.This project makes Ciro Santilli think of the E. Coli as an optimization problem. Given such external nutrient/temperature condition, which DNA sequence makes the cell grow the fastest? Balancing metabolites feels like designing a Factorio speedrun.
There is one major thing missing thing in the current model: promoters/transcription factor interactions are not modelled due to lack/low quality of experimental data: github.com/CovertLab/WholeCellEcoliRelease/issues/21. They just have a magic direct "transcription factor to gene" relationship, encoded at reconstruction/ecoli/flat/foldChanges.tsv in terms of type "if this is present, such protein is expressed 10x more". Transcription units are not implemented at all it appears.
Everything in this section refers to version 7e4cc9e57de76752df0f4e32eca95fb653ea64e4, the code drop from November 2020, and was tested on Ubuntu 21.04 with a docker install of
docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full with image id 502c3e604265, unless otherwise noted. Multi-Omics Model and Analytics Updated 2025-07-16
By Tagkopoulos lab at University of California, Davies.
- www.nature.com/articles/ncomms13090 Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli (2016)
- www.sciencedaily.com/releases/2016/10/161027173552.htm
E. Coli K-12 Updated 2025-07-16
E. Coli genome starting point Updated 2025-07-16
The conventional starting point is not at the E. Coli K-12 MG1655 origin of replication.
biocyc.org/ECOLI/NEW-IMAGE?type=EXTRAGENIC-SITE&object=G0-10506 explains:If it is a bit hard to understand what they mean by "origin of transfer" though, as that term is usually associated with the origin of transfer of bacterial conjugation.
This site is the origin of replication of the E. coli chromosome. It contains the binding sites for DnaA, which is critical for initiation of replication. Replication proceeds bidirectionally. For historical reasons, the numbering of E. coli's circular chromosome does not start at the origin of replication, but at the origin of transfer during conjugation.
Synchronous dynamic random-access memory Updated 2025-07-16
Knuth reward check Updated 2025-07-16
Yet another Updated 2026-10-19
The mandatory xkcd: xkcd 927: Standards.
It is hard for complex organisms to evolve because longer DNA means longer replication time Updated 2025-07-16
Because DNA replication is a key limiting factor of bacterial replication time, such organisms are therefore strongly incentivized to have very minimal DNAs.
Power, Sex, Suicide by Nick Lane (2006) 7 "Why bacteria are simple" page 169 puts this nicely:
Bacteria replicate at colossal speed. [...] In two days, the mass of exponentially doubling E. coli would be 2664 times larger than the mass of the Earth.Luckily this does not happen, and the reason is that bacteria are normally half starved. They swiftly consume all available food, whereupon their growth is limited once again by the lack of nutrients. Most bacteria spend most of their lives in stasis, waiting for a meal. Nonetheless, the speed at which bacteria do mobilize themselves to replicate upon feeding illustrates the overwhelming strength of the selection pressures at work.
Terminal deoxynucleotidyl transferase Updated 2025-07-16
Magnetoresistive disk head Updated 2025-07-16
N-V center quantum computer Updated 2025-07-16
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