Ciro Santilli @cirosantilli 35

Notably, more people would try to "game" the system by quickly answering lots of small impact answers which could tilt things off a bit. Not to mention straight out fraud.

So basically less money into developers doing useless new features for the website, and more money back into meaningful contributors.

How about 2k USD / month for the number one contributor of the year, going linearly down to 0 for the 200th? This would be 100k USD / month, so about 12 developers.

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Fall term by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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Spring term by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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This actually happens in Winter. But they are so fucking euphemistic that winter has to be removed from the calendar.

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Summer term by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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This actually happens in spring. But because they are so euphemistic winter had to be removed from the calendar, it gets shifted a left.

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Chinese scholar by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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On Wikipedia we only find the term Scholar-official. But the idea of the ancient Chinese scholar is a bit wider as a concept, and even people who were not trying to be officials could thrive to follow certain aspects of the scholar way of life.

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Convert PDF to text by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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ELF Hello World Tutorial / Specified file formats by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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The ELF standard specifies multiple file formats:

Object files (.o).
Intermediate step to generating executables and other formats:
```
Source code

    |
    | Compilation
    |
    v

Object file

    |
    | Linking
    |
    v

Executable
```
Object files exist to make compilation faster: with make, we only have to recompile the modified source files based on timestamps.
We have to do the linking step every time, but it is much less expensive.

Executable files (no standard Linux extension).
This is what the Linux kernel can actually run.

Archive files (.a).
Libraries meant to be embedded into executables during the Linking step.

Shared object files (.so).
Libraries meant to be loaded when the executable starts running.

Core dumps.
Such files may be generated by the Linux kernel when the program does naughty things, e.g. segfault.
They exist to help debugging the program.

In this tutorial, we consider only object and executable files.

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Diffraction of Cathode Rays by a Thin Film by Thomson and Reid (1927) by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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www.nature.com/articles/119890a0

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Infrared by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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E. Coli Whole Cell Model by Covert Lab / Output overview by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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Run output is placed under out/:

Some of the output data is stored as .cpickle files. To observe those files, you need the original Python classes, and therefore you have to be inside Docker, from the host it won't work.

We can list all the plots that have been produced under out/ with

find -name '*.png'

Plots are also available in SVG and PDF formats, e.g.:

PNG: ./out/manual/plotOut/low_res_plots/massFractionSummary.png
SVG: ./out/manual/plotOut/svg_plots/massFractionSummary.svg The SVGs write text as polygons, see also: SVG fonts.
PDF: ./out/manual/plotOut/massFractionSummary.pdf

The output directory has a hierarchical structure of type:

./out/manual/wildtype_000000/000000/generation_000000/000000/

where:

wildtype_000000: variant conditions. wildtype is a human readable label, and 000000 is an index amongst the possible wildtype conditions. For example, we can have different simulations with different nutrients, or different DNA sequences. An example of this is shown at run variants.
000000: initial random seed for the initial cell, likely fed to NumPy's np.random.seed
genereation_000000: this will increase with generations if we simulate multiple cells, which is supported by the model
000000: this will presumably contain the cell index within a generation

We also understand that some of the top level directories contain summaries over all cells, e.g. the massFractionSummary.pdf plot exists at several levels of the hierarchy:

./out/manual/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/000000/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut/massFractionSummary.pdf

Each of thoes four levels of plotOut is generated by a different one of the analysis scripts:

./out/manual/plotOut: generated by python runscripts/manual/analysisVariant.py. Contains comparisons of different variant conditions. We confirm this by looking at the results of run variants.
./out/manual/wildtype_000000/plotOut: generated by python runscripts/manual/analysisCohort.py --variant_index 0. TODO not sure how to differentiate between two different labels e.g. wildtype_000000 and somethingElse_000000. If -v is not given, a it just picks the first one alphabetically. TODO not sure how to automatically generate all of those plots without inspecting the directories.
./out/manual/wildtype_000000/000000/plotOut: generated by python runscripts/manual/analysisMultigen.py --variant_index 0 --seed 0
./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut: generated by python runscripts/manual/analysisSingle.py --variant_index 0 --seed 0 --generation 0 --daughter 0. Contains information about a single specific cell.

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E. Coli Whole Cell Model by Covert Lab / Publications by

Ciro Santilli 35  Updated 2025-04-24  +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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David Tong's 2009 Quantum Field Theory lectures at the Perimeter Institute / Lecture 1 by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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www.youtube.com/watch?v=H3AFzbrqH68

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Undergraduate course of the University of Oxford by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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Cool data embedded in the Bitcoin blockchain / AtomSea & EMBII data format by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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For a detailed analysis of one transaction see: Nelson-Mandela.jpg.

Best guess so far, all in ASCII hex of output scripts:

remove the single output value different from first one from payload, that's the change, and it is randomly placed as far as I see
64 bytes: hex address of top level text
1 byte: some random punctuation
decimal number of bytes of some payload
1 byte: some random punctuation
64 bytes: same as the first address
CR LF
ends in NUL

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Classification of 3-transitive groups by

Ciro Santilli 35  Updated 2025-04-24  +Created 1970-01-01

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Might be a bit complex: math.stackexchange.com/questions/698327/classification-of-triply-transitive-finite-groups

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