Ciro Santilli @cirosantilli 37

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E. Coli Whole Cell Model by Covert Lab / Default run variant  Updated 2025-07-11  +Created 1970-01-01

The default run variant, if you don't pass any options, just has the minimal growth conditions set. What this means can be seen at condition.

Notably, this implies a growth medium that includes glucose and salt. It also includes oxygen, which is not strictly required, but greatly benefits cell growth, and is of course easier to have than not have as it is part of the atmosphere!

But the medium does not include amino acids, which the bacteria will have to produce by itself.

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E. Coli Whole Cell Model by Covert Lab / Other run variants  Updated 2025-07-11  +Created 1970-01-01

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Besides time series run variants, conditions can also be selected directly without a time series as in:

python runscripts/manual/runSim.py --variant condition 1 1

which select row indices from reconstruction/ecoli/flat/condition/condition_defs.tsv. The above 1 1 would mean the second line of that file which starts with:

"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"]

so 1 means no_oxygen.

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E. Coli Whole Cell Model by Covert Lab / Publications  Updated 2025-07-11  +Created 1970-01-01

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Unfortunately, due to lack of one page to rule them all, the on-Git tree publication list is meager, some of the most relevant ones seems to be:

2021 open access review paper: journals.asm.org/doi/full/10.1128/ecosalplus.ESP-0001-2020 "The E. coli Whole-Cell Modeling Project". They should just past that stuff in a README :-) The article mentions that it is a follow up to the previous M. genitalium whole cell model by Covert lab. Only 43% of known genes modelled at this point however, a shame.
2020 under Science paywall: www.science.org/doi/10.1126/science.aav3751 "Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation"

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E. Coli Whole Cell Model by Covert Lab / Run variants  Updated 2025-07-11  +Created 1970-01-01

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It would be boring if we could only simulate the same condition all the time, so let's have a look at the different boundary conditions that we can apply to the cell!

We are able to alter things like the composition of the external medium, and the genome of the bacteria, which will make the bacteria behave differently.

The variant selection is a bit cumbersome as we have to use indexes instead of names, but one you know what you are doing, it is fine.

Of course, genetic modification is limited only to experimentally known protein interactions due to the intractability of computational protein folding and computational chemistry in general, solving those would bsai.

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Edge (graph)  Updated 2025-07-11  +Created 1970-01-01

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Edit war  Updated 2025-07-11  +Created 1970-01-01

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Education  Updated 2025-07-11  +Created 1970-01-01

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One of the causes Ciro Santilli care the most about: motivation.

Ciro Santilli's view of the ideal teaching method: how to teach.

A list of complaints against education: Section "Education is broken".

How to improve education? Simple:

tax the fuck out of the rich people and companies: wealth tax and invest it in education
invest intelligently as mentioned at what poor countries have to do to get richer:
- focus on fewer higher excellence schools that select the most promising poor students, rather than giving crappy average to everyone
- use OurBigBook.com

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Educational technology  Updated 2025-07-11  +Created 1970-01-01

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Edward Teller  Updated 2025-07-11  +Created 1970-01-01

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www.youtube.com/playlist?list=PLVV0r6CmEsFw1phnddYWXtVkRW8eUVlqx Edward Teller interview by Web of Stories (1996) Date shown at: www.webofstories.com/play/edward.teller/1. Listener: John H. Nuckolls

Video 1.

Witnessing the test explosion Edward Teller interview by Web of Stories (1996)

Source.

Video 2.

Edward Teller, An Early Time

. Source. Comissioned by the Los Alamos National Laboratory in 1979. Producer: Mario Balibreraa.

youtu.be/Goim-4MF_uE?t=338; holy fuck he almost cut his foot off on a stupid tram accident!
youtu.be/Goim-4MF_uE?t=457: he plays the piano
youtu.be/Goim-4MF_uE?t=965: he drove Szilard to propose to Einstein the Einstein-Szilard letter

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Effective field theory  Updated 2025-07-11  +Created 1970-01-01

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www.youtube.com/watch?v=WB8r7CU7clk&list=PLUl4u3cNGP60TvpbO5toEWC8y8w51dtvm by Iain Stewart. Basically starts by explaining how quantum field theory is so generic that it is hard to get any numerical results out of it :-)

But in particular, we want to describe those subtheories in a way that we can reach arbitrary precision of the full theory if desired.

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eGroups  Updated 2025-07-11  +Created 1970-01-01

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Company co-founded by Scott Hassan, early Google programmer at Stanford University, and Carl Victor Page, Jr., Larry Page's older brother.

They were an email list management website, and became Yahoo! Groups after the acquisition.

The company was sold to Yahoo! in August 2000 for $432m and became Yahoo! Groups. They managed to miraculously dodge the Dot-com bubble, which mostly poppet in 2021. After the acquisition, Yahoo started to redirect them to: groups.yahoo.com as can be seen on the Wayback Machine: web.archive.org/web/20000401000000*/egroups.com The first archive of groups.yahoo.com is from February 2001: web.archive.org/web/20010202055100/http://groups.yahoo.com/ and it unsurprisingly looks basically exactly like eGroups.

Figure 1.

eGroups logo

. From the earliest archive of their "about" page: web.archive.org/web/19991004062653/http://www.egroups.com/info/top.html in 1999.

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Electronic test equipment  Updated 2025-07-11  +Created 1970-01-01

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Electron microscope  Updated 2025-07-11  +Created 1970-01-01

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All of them need a vacuum because you can't shoot elecrons through air, as mentioned at Video "50,000,000x Magnification by AlphaPhoenix (2022)".

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Electrum  Updated 2025-07-11  +Created 1970-01-01

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electrum.org/

askubuntu.com/questions/281233/how-can-i-install-the-electrum-bitcoin-wallet/1384053#1384053

For the love of God, on Ubuntu install from the official AppImage downloaded from electrum.org/#download, not this random outdated Snap snapcraft.io/electrum:

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ELF Hello World Tutorial / Backlinks  Updated 2025-07-11  +Created 1970-01-01

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News aggregators:

2017-05: news.ycombinator.com/item?id=14359159 web.archive.org/web/20170517174951/https://news.ycombinator.com/news

Personal websites:

www.etherington.xyz/elfguide

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ELF Hello World Tutorial / .data section  Updated 2025-07-11  +Created 1970-01-01

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.data is section 1:

00000080  01 00 00 00 01 00 00 00  03 00 00 00 00 00 00 00  |................|
00000090  00 00 00 00 00 00 00 00  00 02 00 00 00 00 00 00  |................|
000000a0  0d 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000000b0  04 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|

80 0: sh_name = 01 00 00 00: index 1 in the .shstrtab string table
Here, 1 says the name of this section starts at the first character of that section, and ends at the first NUL character, making up the string .data.
.data is one of the section names which has a predefined meaning according to www.sco.com/developers/gabi/2003-12-17/ch4.strtab.html:
These sections hold initialized data that contribute to the program's memory image.

80 4: sh_type = 01 00 00 00: SHT_PROGBITS: the section content is not specified by ELF, only by how the program interprets it. Normal since a .data section.
80 8: sh_flags = 03 7x 00: SHF_WRITE and SHF_ALLOC: www.sco.com/developers/gabi/2003-12-17/ch4.sheader.html#sh_flags, as required from a .data section
90 0: sh_addr = 8x 00: TODO: standard says:
If the section will appear in the memory image of a process, this member gives the address at which the section's first byte should reside. Otherwise, the member contains 0.
but I don't understand it very well yet.
90 8: sh_offset = 00 02 00 00 00 00 00 00 = 0x200: number of bytes from the start of the program to the first byte in this section
a0 0: sh_size = 0d 00 00 00 00 00 00 00
If we take 0xD bytes starting at sh_offset 200, we see:
```
00000200  48 65 6c 6c 6f 20 77 6f  72 6c 64 21 0a 00        |Hello world!..  |
```
AHA! So our "Hello world!" string is in the data section like we told it to be on the NASM.
Once we graduate from hd, we will look this up like:
```
readelf -x .data hello_world.o
```
which outputs:
```
Hex dump of section '.data':
  0x00000000 48656c6c 6f20776f 726c6421 0a       Hello world!.
```
NASM sets decent properties for that section because it treats .data magically: www.nasm.us/doc/nasmdoc7.html#section-7.9.2
Also note that this was a bad section choice: a good C compiler would put the string in .rodata instead, because it is read-only and it would allow for further OS optimizations.
- a0 8: sh_link and sh_info = 8x 0: do not apply to this section type. www.sco.com/developers/gabi/2003-12-17/ch4.sheader.html#special_sections
- b0 0: sh_addralign = 04 = TODO: why is this alignment necessary? Is it only for sh_addr, or also for symbols inside sh_addr?
- b0 8: sh_entsize = 00 = the section does not contain a table. If != 0, it means that the section contains a table of fixed size entries. In this file, we see from the readelf output that this is the case for the .symtab and .rela.text sections.

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ELF Hello World Tutorial / Dynamic linking sections  Updated 2025-07-11  +Created 1970-01-01

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This program did not have certain dynamic linking related sections because we linked it minimally with ld.

However, if you compile a C hello world with GCC 8.2:

gcc -o main.out main.c

some other interesting sections would appear.

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ELF Hello World Tutorial / Global file structure  Updated 2025-07-11  +Created 1970-01-01

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An ELF file contains the following parts:

ELF header. Points to the position of the section header table and the program header table.
Section header table (optional on executable). Each has e_shnum section headers, each pointing to the position of a section.
N sections, with N <= e_shnum (optional on executable)
Program header table (only on executable). Each has e_phnum program headers, each pointing to the position of a segment.
N segments, with N <= e_phnum (only on executable)

The order of those parts is not fixed: the only fixed thing is the ELF header that must be the first thing on the file: Generic docs say:

Although the figure shows the program header table immediately after the ELF header, and the section header table following the sections, actual files may differ. Moreover, sections and segments have no specified order. Only the ELF header has a fixed position in the file.

In pictures: sample object file with three sections:

            +-------------------+
            | ELF header        |---+
+---------> +-------------------+   | e_shoff
|           |                   |<--+
| Section   | Section header 0  |
|           |                   |---+ sh_offset
| Header    +-------------------+   |
|           | Section header 1  |---|--+ sh_offset
| Table     +-------------------+   |  |
|           | Section header 2  |---|--|--+
+---------> +-------------------+   |  |  |
            | Section 0         |<--+  |  |
            +-------------------+      |  | sh_offset
            | Section 1         |<-----+  |
            +-------------------+         |
            | Section 2         |<--------+
            +-------------------+

But nothing (except sanity) prevents the following topology:

            +-------------------+
            | ELF header        |---+ e_shoff
            +-------------------+   |
            | Section 1         |<--|--+
+---------> +-------------------+   |  |
|           |                   |<--+  | sh_offset
| Section   | Section header 0  |      |
|           |                   |------|---------+
| Header    +-------------------+      |         |
|           | Section header 1  |------+         |
| Table     +-------------------+                |
|           | Section header 2  |---+            | sh_offset
+---------> +-------------------+   | sh_offset  |
            | Section 2         |<--+            |
            +-------------------+                |
            | Section 0         |<---------------+
            +-------------------+

But some newbies may prefer PNGs :-)

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ELF Hello World Tutorial / Implementations  Updated 2025-07-11  +Created 1970-01-01

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Compiler toolchains generate and read ELF files.
Sane compilers should use a separate standalone library to do the dirty work. E.g., Binutils uses BFD (in-tree and canonical source).

Operating systems read and run ELF files.
Kernels cannot link to a library nor use the C stlib, so they are more likely to implement it themselves.
This is the case of the Linux kernel 4.2 which implements it in th file fs/binfmt_elf.c.

Specialized libraries. Examples:
- github.com/eliben/pyelftools. By a hardcore Googler: plus.google.com/+EliBenderskyGplus/posts
- sourceforge.net/projects/elftoolchain

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ELF Hello World Tutorial / Object hd  Updated 2025-07-11  +Created 1970-01-01

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Running:

hd hello_world.o

gives:

00000000  7f 45 4c 46 02 01 01 00  00 00 00 00 00 00 00 00  |.ELF............|
00000010  01 00 3e 00 01 00 00 00  00 00 00 00 00 00 00 00  |..>.............|
00000020  00 00 00 00 00 00 00 00  40 00 00 00 00 00 00 00  |........@.......|
00000030  00 00 00 00 40 00 00 00  00 00 40 00 07 00 03 00  |....@.....@.....|
00000040  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
*
00000080  01 00 00 00 01 00 00 00  03 00 00 00 00 00 00 00  |................|
00000090  00 00 00 00 00 00 00 00  00 02 00 00 00 00 00 00  |................|
000000a0  0d 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000000b0  04 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000000c0  07 00 00 00 01 00 00 00  06 00 00 00 00 00 00 00  |................|
000000d0  00 00 00 00 00 00 00 00  10 02 00 00 00 00 00 00  |................|
000000e0  27 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |'...............|
000000f0  10 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000100  0d 00 00 00 03 00 00 00  00 00 00 00 00 00 00 00  |................|
00000110  00 00 00 00 00 00 00 00  40 02 00 00 00 00 00 00  |........@.......|
00000120  32 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |2...............|
00000130  01 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000140  17 00 00 00 02 00 00 00  00 00 00 00 00 00 00 00  |................|
00000150  00 00 00 00 00 00 00 00  80 02 00 00 00 00 00 00  |................|
00000160  a8 00 00 00 00 00 00 00  05 00 00 00 06 00 00 00  |................|
00000170  04 00 00 00 00 00 00 00  18 00 00 00 00 00 00 00  |................|
00000180  1f 00 00 00 03 00 00 00  00 00 00 00 00 00 00 00  |................|
00000190  00 00 00 00 00 00 00 00  30 03 00 00 00 00 00 00  |........0.......|
000001a0  34 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |4...............|
000001b0  01 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000001c0  27 00 00 00 04 00 00 00  00 00 00 00 00 00 00 00  |'...............|
000001d0  00 00 00 00 00 00 00 00  70 03 00 00 00 00 00 00  |........p.......|
000001e0  18 00 00 00 00 00 00 00  04 00 00 00 02 00 00 00  |................|
000001f0  04 00 00 00 00 00 00 00  18 00 00 00 00 00 00 00  |................|
00000200  48 65 6c 6c 6f 20 77 6f  72 6c 64 21 0a 00 00 00  |Hello world!....|
00000210  b8 01 00 00 00 bf 01 00  00 00 48 be 00 00 00 00  |..........H.....|
00000220  00 00 00 00 ba 0d 00 00  00 0f 05 b8 3c 00 00 00  |............<...|
00000230  bf 00 00 00 00 0f 05 00  00 00 00 00 00 00 00 00  |................|
00000240  00 2e 64 61 74 61 00 2e  74 65 78 74 00 2e 73 68  |..data..text..sh|
00000250  73 74 72 74 61 62 00 2e  73 79 6d 74 61 62 00 2e  |strtab..symtab..|
00000260  73 74 72 74 61 62 00 2e  72 65 6c 61 2e 74 65 78  |strtab..rela.tex|
00000270  74 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |t...............|
00000280  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000290  00 00 00 00 00 00 00 00  01 00 00 00 04 00 f1 ff  |................|
000002a0  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000002b0  00 00 00 00 03 00 01 00  00 00 00 00 00 00 00 00  |................|
000002c0  00 00 00 00 00 00 00 00  00 00 00 00 03 00 02 00  |................|
000002d0  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
000002e0  11 00 00 00 00 00 01 00  00 00 00 00 00 00 00 00  |................|
000002f0  00 00 00 00 00 00 00 00  1d 00 00 00 00 00 f1 ff  |................|
00000300  0d 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000310  2d 00 00 00 10 00 02 00  00 00 00 00 00 00 00 00  |-...............|
00000320  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000330  00 68 65 6c 6c 6f 5f 77  6f 72 6c 64 2e 61 73 6d  |.hello_world.asm|
00000340  00 68 65 6c 6c 6f 5f 77  6f 72 6c 64 00 68 65 6c  |.hello_world.hel|
00000350  6c 6f 5f 77 6f 72 6c 64  5f 6c 65 6e 00 5f 73 74  |lo_world_len._st|
00000360  61 72 74 00 00 00 00 00  00 00 00 00 00 00 00 00  |art.............|
00000370  0c 00 00 00 00 00 00 00  01 00 00 00 02 00 00 00  |................|
00000380  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  |................|
00000390

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