E. Coli Whole Cell Model by Covert Lab / Source code overview by Ciro Santilli 37 Updated +Created
The key model database is located in the source code at reconstruction/ecoli/flat.
Let's try to understand some interesting looking, with a special focus on our understanding of the tiny E. Coli K-12 MG1655 operon thrLABC part of the metabolism, which we have well understood at Section "E. Coli K-12 MG1655 operon thrLABC".
We'll realize that a lot of data and IDs come from/match BioCyc quite closely.
  • reconstruction/ecoli/flat/compartments.tsv contains cellular compartment information:
    "abbrev" "id"
    "n" "CCO-BAC-NUCLEOID"
    "j" "CCO-CELL-PROJECTION"
    "w" "CCO-CW-BAC-NEG"
    "c" "CCO-CYTOSOL"
    "e" "CCO-EXTRACELLULAR"
    "m" "CCO-MEMBRANE"
    "o" "CCO-OUTER-MEM"
    "p" "CCO-PERI-BAC"
    "l" "CCO-PILUS"
    "i" "CCO-PM-BAC-NEG"
  • reconstruction/ecoli/flat/promoters.tsv contains promoter information. Simple file, sample lines:
    "position" "direction" "id" "name"
    148 "+" "PM00249" "thrLp"
    corresponds to E. Coli K-12 MG1655 promoter thrLp, which starts as position 148.
  • reconstruction/ecoli/flat/proteins.tsv contains protein information. Sample line corresponding to e. Coli K-12 MG1655 gene thrA:
    "aaCount" "name" "seq" "comments" "codingRnaSeq" "mw" "location" "rnaId" "id" "geneId"
    [91, 46, 38, 44, 12, 53, 30, 63, 14, 46, 89, 34, 23, 30, 29, 51, 34, 4, 20, 0, 69] "ThrA" "MRVL..." "Location information from Ecocyc dump." "AUGCGAGUGUUG..." [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 89103.51099999998, 0.0, 0.0, 0.0, 0.0] ["c"] "EG10998_RNA" "ASPKINIHOMOSERDEHYDROGI-MONOMER" "EG10998"
    so we understand that:
  • reconstruction/ecoli/flat/rnas.tsv: TODO vs transcriptionUnits.tsv. Sample lines:
    "halfLife" "name" "seq" "type" "modifiedForms" "monomerId" "comments" "mw" "location" "ntCount" "id" "geneId" "microarray expression"
    174.0 "ThrA [RNA]" "AUGCGAGUGUUG..." "mRNA" [] "ASPKINIHOMOSERDEHYDROGI-MONOMER" "" [0.0, 0.0, 0.0, 0.0, 790935.00399999996, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] ["c"] [553, 615, 692, 603] "EG10998_RNA" "EG10998" 0.0005264904
  • reconstruction/ecoli/flat/sequence.fasta: FASTA DNA sequence, first two lines:
    >E. coli K-12 MG1655 U00096.2 (1 to 4639675 = 4639675 bp)
    AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTG
  • reconstruction/ecoli/flat/transcriptionUnits.tsv: transcription units. We can observe for example the two different transcription units of the E. Coli K-12 MG1655 operon thrLABC in the lines:
    "expression_rate" "direction" "right" "terminator_id"  "name"    "promoter_id" "degradation_rate" "id"       "gene_id"                                   "left"
    0.0               "f"         310     ["TERM0-1059"]   "thrL"    "PM00249"     0.198905992329492 "TU0-42486" ["EG11277"]                                  148
    657.057317358791  "f"         5022    ["TERM_WC-2174"] "thrLABC" "PM00249"     0.231049060186648 "TU00178"   ["EG10998", "EG10999", "EG11000", "EG11277"] 148
  • reconstruction/ecoli/flat/genes.tsv
    "length" "name"                      "seq"             "rnaId"      "coordinate" "direction" "symbol" "type" "id"      "monomerId"
    66       "thr operon leader peptide" "ATGAAACGCATT..." "EG11277_RNA" 189         "+"         "thrL"   "mRNA" "EG11277" "EG11277-MONOMER"
    2463     "ThrA"                      "ATGCGAGTGTTG"    "EG10998_RNA" 336         "+"         "thrA"   "mRNA" "EG10998" "ASPKINIHOMOSERDEHYDROGI-MONOMER"
  • reconstruction/ecoli/flat/metabolites.tsv contains metabolite information. Sample lines:
    "id"                       "mw7.2" "location"
    "HOMO-SER"                 119.12  ["n", "j", "w", "c", "e", "m", "o", "p", "l", "i"]
    "L-ASPARTATE-SEMIALDEHYDE" 117.104 ["n", "j", "w", "c", "e", "m", "o", "p", "l", "i"]
    In the case of the enzyme thrA, one of the two reactions it catalyzes is "L-aspartate 4-semialdehyde" into "Homoserine".
    Starting from the enzyme page: biocyc.org/gene?orgid=ECOLI&id=EG10998 we reach the reaction page: biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=HOMOSERDEHYDROG-RXN which has reaction ID HOMOSERDEHYDROG-RXN, and that page which clarifies the IDs:
    so these are the compounds that we care about.
  • reconstruction/ecoli/flat/reactions.tsv contains chemical reaction information. Sample lines:
    "reaction id" "stoichiometry" "is reversible" "catalyzed by"
    
    "HOMOSERDEHYDROG-RXN-HOMO-SER/NAD//L-ASPARTATE-SEMIALDEHYDE/NADH/PROTON.51."
      {"NADH[c]": -1, "PROTON[c]": -1, "HOMO-SER[c]": 1, "L-ASPARTATE-SEMIALDEHYDE[c]": -1, "NAD[c]": 1}
      false
      ["ASPKINIIHOMOSERDEHYDROGII-CPLX", "ASPKINIHOMOSERDEHYDROGI-CPLX"]
    
    "HOMOSERDEHYDROG-RXN-HOMO-SER/NADP//L-ASPARTATE-SEMIALDEHYDE/NADPH/PROTON.53."
      {"NADPH[c]": -1, "NADP[c]": 1, "PROTON[c]": -1, "L-ASPARTATE-SEMIALDEHYDE[c]": -1, "HOMO-SER[c]": 1
      false
      ["ASPKINIIHOMOSERDEHYDROGII-CPLX", "ASPKINIHOMOSERDEHYDROGI-CPLX"]
    • catalized by: here we see ASPKINIHOMOSERDEHYDROGI-CPLX, which we can guess is a protein complex made out of ASPKINIHOMOSERDEHYDROGI-MONOMER, which is the ID for the thrA we care about! This is confirmed in complexationReactions.tsv.
  • reconstruction/ecoli/flat/complexationReactions.tsv contains information about chemical reactions that produce protein complexes:
    "process" "stoichiometry" "id" "dir"
    "complexation"
      [
        {
          "molecule": "ASPKINIHOMOSERDEHYDROGI-CPLX",
          "coeff": 1,
          "type": "proteincomplex",
          "location": "c",
          "form": "mature"
        },
        {
          "molecule": "ASPKINIHOMOSERDEHYDROGI-MONOMER",
          "coeff": -4,
          "type": "proteinmonomer",
          "location": "c",
          "form": "mature"
        }
      ]
    "ASPKINIHOMOSERDEHYDROGI-CPLX_RXN"
    1
    The coeff is how many monomers need to get together for form the final complex. This can be seen from the Summary section of ecocyc.org/gene?orgid=ECOLI&id=ASPKINIHOMOSERDEHYDROGI-MONOMER:
    Aspartate kinase I / homoserine dehydrogenase I comprises a dimer of ThrA dimers. Although the dimeric form is catalytically active, the binding equilibrium dramatically favors the tetrameric form. The aspartate kinase and homoserine dehydrogenase activities of each ThrA monomer are catalyzed by independent domains connected by a linker region.
    Fantastic literature summary! Can't find that in database form there however.
  • reconstruction/ecoli/flat/proteinComplexes.tsv contains protein complex information:
    "name" "comments" "mw" "location" "reactionId" "id"
    "aspartate kinase / homoserine dehydrogenase"
    ""
    [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 356414.04399999994, 0.0, 0.0, 0.0, 0.0]
    ["c"]
    "ASPKINIHOMOSERDEHYDROGI-CPLX_RXN"
    "ASPKINIHOMOSERDEHYDROGI-CPLX"
  • reconstruction/ecoli/flat/protein_half_lives.tsv contains the half-life of proteins. Very few proteins are listed however for some reason.
  • reconstruction/ecoli/flat/tfIds.csv: transcription factors information:
    "TF"   "geneId"  "oneComponentId"  "twoComponentId" "nonMetaboliteBindingId" "activeId" "notes"
    "arcA" "EG10061" "PHOSPHO-ARCA"    "PHOSPHO-ARCA"
    "fnr"  "EG10325" "FNR-4FE-4S-CPLX" "FNR-4FE-4S-CPLX"
    "dksA" "EG10230"
AlphaGo by Ciro Santilli 37 Updated +Created
CPT symmetry by Ciro Santilli 37 Updated +Created
These are of course likely all made by AtomSea & EMBII themselves while developing/testing their upload system.
They are also artsy peoeple themselves, and as pointed at twitter.com/AllenVandever/status/1563964396656812034 what they were doing was basicaly non-fungible token art, which became much much more popular a few years later around 2021.
The first upload that we could find at github.com/cirosantilli/bitcoin-inscription-indexer/tree/3f53e152ec9bb0d070dbcb8f9249d92f89effa70#atomsea-index was tx 44e80475dc363de2c7ee17b286f8cd49eb146165a79968a62c1c2c4cf80772c9 on block 272573 (2013-12-01) but it does not show on Bitfossil: bitfossil.org/44e80475dc363de2c7ee17b286f8cd49eb146165a79968a62c1c2c4cf80772c9/. This is was due to an upload bug explained by the following entry. By looking at the ASCII data at github.com/cirosantilli/bitcoin-inscription-indexer/blob/master/data/out/0272.txt#L449 that this is meant to contain the same content as the following message: a quote from the Bhagavad Gita, so this is definitely a bugged version of the following one.
The next one is tx c9d1363ea517cd463950f83168ce8242ef917d99cd6518995bd1af927d335828 block 272577 (2013-12-02). It actually shows on bifossil and it reads:
I WONDER WHAT HISTORY WILL THINK ABOUT THESE FIRST FEW BUGS...HA HA HA. NOBODY IS PERFECT.
followed by:
He who regards
With an eye that is equal
Friends and comrades,
The foe and the kinsman,
The vile, the wicked,
The men who judge him,
And those who belong
To neither faction:
He is the greatest.
The bug message is definitely a reference to the previous non-visible bugged upload bitfossil.org/4b72a223007eab8a951d43edc171befeabc7b5dca4213770c88e09ba5b936e17/, TODO understand exactly how they fucked up. This illustrates the beauty of the blockchain very well: unlike with version control, you don't just see selected snapshots: you see actual debug logs!!!
Figure 1.
WeAreStarStuff.jpg
. Source.
The third AtomSea & EMBII upload, and the first actual image.
Message:
Photo etchin' test. #AtomSea #embii (photo by Travis Ehrich)
The image shows showingAtomSea and EMBII together, presumably photographed by this dude.
The filename is of course a reference to the quote/idea: We Are Made of Star-Stuff that was much popularized by Carl Sagan.
bitfossil.org/fac0b9a4f90414710b806fd286e020aea2404498946845ef3783f305dd4cd3a7 (2024-01-13) contains a cropped version with only AtomSea persent.
Figure 2.
HugPuddle.jpg
. Source.
The fourth AtomSea & EMBII upload, and the second image. Message:
HugPuddle Testing Apertus Disk Drive
And then finally we meet Chiharu, EMBII's partner, with her hair painted blond (she's Japanese): ILoveYouMore.jpg.
Then there's an approximation of pi as ASCII decimal fraction on tx 70fd289901bae0409f27237506c330588d917716944c6359a8711b0ad6b4ce76 from block 273522 (2013-12-07):
3.1415926535897932384626433832795028841971693993751058209749445923078164062862089986280348253421170679821480865132823066470938446095505822317253594081284811174502841027019385211055596446229489549303819644288109756659334461284756482337867831652712019091456485669234603486104543266482133936072602491412737245870066063155881748815209209628292540917153643678925903600113305305488204665213841469519415116094330572703657595919530921861173819326117931051185480744623799627495673518857527248912279381830119491298336733624406566430860213949463952247371907021798609437027705392171762931767523846748184676694051320005681271452635608277857713427577896091736371787214684409012249534301465495853710507922796892589235420199561121290219608640344181598136297747713099605187072113499999983729780499510597317328160963185950244594553469083026425223082533446850352619311881710100031378387528865875332083814206171776691473035982534904287554687311595628638823537875937519577818577805321712268066130019278766111959092164201989
tx b8b9f50a354166c46b69ecd47a0fbd20ee78c3471d2557bf275aff1b4cf4752d (2013-12-07) on bitfossil.org) contains Where the Sidewalk Ends by Shel Silverstein:
There is a place where the sidewalk ends
And before the street begins,
And there the grass grows soft and white,
And there the sun burns crimson bright,
And there the moon-bird rests from his flight
To cool in the peppermint wind.
Let us leave this place where the smoke blows black
And the dark street winds and bends.
Past the pits where the asphalt flowers grow
We shall walk with a walk that is measured and slow,
And watch where the chalk-white arrowls go
To the place where the sidewalk ends.
Yes we'll walk with a walk that is measured and slow,
And we'll go where the chalk-white arrows go,
For the children, they mark, and the children, they know
The place where the sidewalk ends.
bitfossil.org/73ca50321147bac9010bec43d63f7f76857fe9ede240cc89710e28723fdb242f/ (2013-12-14) has message:
MULTIFILE SUPPORT TEST
and links to 3 .txt files 1.txt, 2.txt, 3.txt containing single characters 1, 2, and 3.
Figure 3.
CompressedLogo.png
. Source.
2013-12-20. Message:
Colby Nelson and myself burnt the midnight oils designing the APERTUS imagery last night....
Thanks Colby for all your help.
Possibly www.linkedin.com/in/colby-nelson-59b538207/.
Contains an Apertus logo which is used on bitfossil.org/ itself, presumably they were designing that logo.
Permanent private hall by Ciro Santilli 37 Updated +Created
Similar to a college, but led by religious denomination leaders rather than fellows.
Mitochondrial carrier by Ciro Santilli 37 Updated +Created
Half-silvered mirror by Ciro Santilli 37 Updated +Created
Android Open Source Project by Ciro Santilli 37 Updated +Created
AMD GPU by Ciro Santilli 37 Updated +Created
x86 Paging Tutorial / Sample code by Ciro Santilli 37 Updated +Created
Like everything else in programming, the only way to really understand this is to play with minimal examples.
What makes this a "hard" subject is that the minimal example is large because you need to make your own small OS.
x86 Paging Tutorial / Example: simplified single-level paging scheme by Ciro Santilli 37 Updated +Created
This is an example of how paging operates on a simplified version of a x86 architecture to implement a virtual memory space with a 20 | 12 address split (4 KiB page size).
x86 Paging Tutorial / PAE and PSE page table schemes by Ciro Santilli 37 Updated +Created
If either PAE and PSE are active, different paging level schemes are used:
  • no PAE and no PSE: 10 | 10 | 12
  • no PAE and PSE: 10 | 22.
    22 is the offset within the 4Mb page, since 22 bits address 4Mb.
  • PAE and no PSE: 2 | 9 | 9 | 12
    The design reason why 9 is used twice instead of 10 is that now entries cannot fit anymore into 32 bits, which were all filled up by 20 address bits and 12 meaningful or reserved flag bits.
    The reason is that 20 bits are not enough anymore to represent the address of page tables: 24 bits are now needed because of the 4 extra wires added to the processor.
    Therefore, the designers decided to increase entry size to 64 bits, and to make them fit into a single page table it is necessary reduce the number of entries to 2^9 instead of 2^10.
    The starting 2 is a new Page level called Page Directory Pointer Table (PDPT), since it points to page directories and fill in the 32 bit linear address. PDPTs are also 64 bits wide.
    cr3 now points to PDPTs which must be on the fist four 4GB of memory and aligned on 32 bit multiples for addressing efficiency. This means that now cr3 has 27 significative bits instead of 20: 2^5 for the 32 multiples * 2^27 to complete the 2^32 of the first 4GB.
  • PAE and PSE: 2 | 9 | 21
    Designers decided to keep a 9 bit wide field to make it fit into a single page.
    This leaves 23 bits. Leaving 2 for the PDPT to keep things uniform with the PAE case without PSE leaves 21 for offset, meaning that pages are 2M wide instead of 4M.
WhatsApp profile information is public by default by Ciro Santilli 37 Updated +Created
Your profile picture, name and status are public by default as of 2022!!! OMG!!!
This means that all secret services in the world have alrady scraped this information for everyone that uses WhatsApp!!!
They just have to go incrementally through the list of all phone numbers... 001 0000 0000, 001 0000 0001, 001 0000 0002, etc. and then you can deduce who has which phone number.
OMG... it is analogous to the Facebook profile face dump.
Voltage by Ciro Santilli 37 Updated +Created
Oxford University Press by Ciro Santilli 37 Updated +Created
Course of the University of Oxford by Ciro Santilli 37 Updated +Created
The course outline is given in a "handbook", a one or more PDF files that contain what people will learn and other practicalities. There is a full list of handbooks at: www.ox.ac.uk/students/academic/guidance/undergraduate/handbooks, but many of them are closed. The system is so closed that even the fucking course list is closed, e.g. all links at: www2.physics.ox.ac.uk/students/undergraduates are closed. Insane.

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