E. Coli Whole Cell Model by Covert Lab Install and first run Updated 2025-07-16
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:This mounts the host source under The meaning of each of the analysis commands is described at Section "Output overview".
sudo docker run --name=wcm -it -v "$(pwd):/wcEcoli" docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full/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.pyAs 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 bashrunscripts/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 2569.18 783.09 1.943 1.910 2.005 1.950 1.963
Simulation finished:
- Length: 0:42:49
- Runtime: 0:09:13 E. Coli Whole Cell Model by Covert Lab Output overview Updated 2025-07-16
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 Plots are also available in SVG and PDF formats, e.g.:
out/ withfind -name '*.png'The output directory has a hierarchical structure of type:where:
./out/manual/wildtype_000000/000000/generation_000000/000000/wildtype_000000: variant conditions.wildtypeis a human readable label, and000000is an index amongst the possiblewildtypeconditions. 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'snp.random.seedgenereation_000000: this will increase with generations if we simulate multiple cells, which is supported by the model000000: 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.pdfEach of thoes four levels of
plotOut is generated by a different one of the analysis scripts:./out/manual/plotOut: generated bypython 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 bypython runscripts/manual/analysisCohort.py --variant_index 0. TODO not sure how to differentiate between two different labels e.g.wildtype_000000andsomethingElse_000000. If-vis 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 bypython runscripts/manual/analysisMultigen.py --variant_index 0 --seed 0./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut: generated bypython runscripts/manual/analysisSingle.py --variant_index 0 --seed 0 --generation 0 --daughter 0. Contains information about a single specific cell.
E. Coli Whole Cell Model by Covert Lab Run variants Updated 2025-07-16
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.
E. Coli Whole Cell Model by Covert Lab Other run variants Updated 2025-07-16
Besides time series run variants, conditions can also be selected directly without a time series as in:which select row indices from so
python runscripts/manual/runSim.py --variant condition 1 1reconstruction/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"]1 means no_oxygen. E. Coli Whole Cell Model by Covert Lab Source code overview Updated 2025-07-16
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".
reconstruction/ecoli/flat/compartments.tsvcontains 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"CCO: "Celular COmpartment"BAC-NUCLEOID: nucleoidCELL-PROJECTION: cell projectionCW-BAC-NEG: TODO confirm: cell wall (of a Gram-negative bacteria)CYTOSOL: cytosolEXTRACELLULAR: outside the cellMEMBRANE: cell membraneOUTER-MEM: bacterial outer membranePERI-BAC: periplasmPILUS: pilusPM-BAC-NEG: TODO: plasma membrane, but that is the same as cell membrane no?
reconstruction/ecoli/flat/promoters.tsvcontains promoter information. Simple file, sample lines:corresponds to E. Coli K-12 MG1655 promoter thrLp, which starts as position 148."position" "direction" "id" "name" 148 "+" "PM00249" "thrLp"reconstruction/ecoli/flat/proteins.tsvcontains protein information. Sample line corresponding to e. Coli K-12 MG1655 gene thrA:so we understand that:"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"aaCount: amino acid count, how many of each of the 20 proteinogenic amino acid are thereseq: full sequence, using the single letter abbreviation of the proteinogenic amino acidsmw; molecular weight? The 11 components appear to be given atreconstruction/ecoli/flat/scripts/unifyBulkFiles.py:so they simply classify the weight? Presumably this exists for complexes that have multiple classes?molecular_weight_keys = [ '23srRNA', '16srRNA', '5srRNA', 'tRNA', 'mRNA', 'miscRNA', 'protein', 'metabolite', 'water', 'DNA', 'RNA' # nonspecific RNA ]23srRNA,16srRNA,5srRNAare the three structural RNAs present in the ribosome: 23S ribosomal RNA, 16S ribosomal RNA, 5S ribosomal RNA, all others are obvious:- tRNA
- mRNA
- protein. This is the seventh class, and this enzyme only contains mass in this class as expected.
- metabolite
- water
- DNA
- RNA: TODO
rnavsmiscRNA
location: cell compartment where the protein is present,cdefined atreconstruction/ecoli/flat/compartments.tsvas cytoplasm, as expected for something that will make an amino acid
reconstruction/ecoli/flat/rnas.tsv: TODO vstranscriptionUnits.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" 0.0005264904halfLife: half-lifemw: molecular weight, same as inreconstruction/ecoli/flat/proteins.tsv. This molecule only have weight in themRNAclass, as expected, as it just codes for a proteinlocation: same as inreconstruction/ecoli/flat/proteins.tsvntCount: nucleotide count for each of the ATGCmicroarray expression: presumably refers to DNA microarray for gene expression profiling, but what measure exactly?
reconstruction/ecoli/flat/sequence.fasta: FASTA DNA sequence, first two lines:>E. coli K-12 MG1655 U00096.2 (1 to 4639675 = 4639675 bp) AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGreconstruction/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"] 148promoter_id: matches promoter id inreconstruction/ecoli/flat/promoters.tsvgene_id: matches id inreconstruction/ecoli/flat/genes.tsvid: matches exactly those used in BioCyc, which is quite nice, might be more or less standardized:
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.tsvcontains metabolite information. Sample lines:In the case of the enzyme thrA, one of the two reactions it catalyzes is "L-aspartate 4-semialdehyde" into "Homoserine"."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"]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 IDHOMOSERDEHYDROG-RXN, and that page which clarifies the IDs:so these are the compounds that we care about.- biocyc.org/compound?orgid=ECOLI&id=L-ASPARTATE-SEMIALDEHYDE: "L-aspartate 4-semialdehyde" has ID
L-ASPARTATE-SEMIALDEHYDE - biocyc.org/compound?orgid=ECOLI&id=HOMO-SER: "Homoserine" has ID
HOMO-SER
- biocyc.org/compound?orgid=ECOLI&id=L-ASPARTATE-SEMIALDEHYDE: "L-aspartate 4-semialdehyde" has ID
reconstruction/ecoli/flat/reactions.tsvcontains 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 seeASPKINIHOMOSERDEHYDROGI-CPLX, which we can guess is a protein complex made out ofASPKINIHOMOSERDEHYDROGI-MONOMER, which is the ID for thethrAwe care about! This is confirmed incomplexationReactions.tsv.
reconstruction/ecoli/flat/complexationReactions.tsvcontains information about chemical reactions that produce protein complexes:The"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" 1coeffis 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:Fantastic literature summary! Can't find that in database form there however.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.
reconstruction/ecoli/flat/proteinComplexes.tsvcontains 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.tsvcontains 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"
E. Coli Whole Cell Model by Covert Lab Model validation Updated 2025-07-16
TODO compare with actual datasetes.
E. Coli Whole Cell Model by Covert Lab Publications Updated 2025-07-16
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"
E. Coli K-12 MG1655 Updated 2026-10-19
NCBI taxonomy entry: www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145 This links to:
- Interactively browse the sequence on the browser viewer: "Reference genome: Escherichia coli str. K-12 substr. MG1655" which eventually leads to: www.ncbi.nlm.nih.gov/nuccore/556503834?report=graphIf we zoom into the start, we hover over the very first gene/protein: the famous (just kidding) e. Coli K-12 MG1655 gene thrL, at position 190-255.The second one is the much more interesting e. Coli K-12 MG1655 gene thrA.
- Gene list, with a total of 4,629 as of 2021: www.ncbi.nlm.nih.gov/gene/?term=txid511145
AlphaGo Updated 2025-07-16
AlphaZero Updated 2025-07-16
Generalization of AlphaGo Zero that plays Go, chess and shogi.
- www.science.org/doi/10.1126/science.aar6404 A general reinforcement learning algorithm that masters chess, shogi, and Go through self-play by Silver et al. (2018), published without source code
- www.quora.com/Is-there-an-Open-Source-version-of-AlphaZero-specifically-the-generic-game-learning-tool-distinct-from-AlphaGo
www.quora.com/Which-chess-engine-would-be-stronger-Alpha-Zero-or-Stockfish-12/answer/Felix-Zaslavskiy explains that it beat Stockfish 8. But then Stockfish was developed further and would start to beat it. We know this because although AlphaZero was closed source, they released the trained artificial neural network, so it was possible to replay AlphaZero at its particular stage of training.
Flatpak Updated 2025-07-16
Snap (package manager) Updated 2025-07-16
merlijn.sebrechts.be/blog/2020-08-02-why-one-snap-store/ has some very good comments on how
snap is more closed than Flatpak. CPT symmetry Updated 2025-09-17
Strong CP problem Updated 2025-07-16
Undergraduate course of the University of Oxford Updated 2025-07-16
Graduate course of the University of Oxford Updated 2025-07-16
Cool data embedded in the Bitcoin blockchain cryptograffiti.info Updated 2025-07-16
twitter.com/cryptograffiti (marked as joined March 2014)
At some point it stopped using Bitcoin mainline and moved to Bitcoin Cash instead: www.newsbtc.com/news/bitcoin/cryptograffiti-rejects-bitcoin-core-bch-now-available-payment-method/ and therefore became useless. Existing indexes seem to have been broken as well.
Also, based on the timing of Figure "Erich Erstu", this service may be responsible for a large part of the raw JPEG images present in the blockchain from block 416527 (2016) onwards. This is also suggested by the comments at Figure "Tank Man".
A Quantitative Analysis of the Impact of Arbitrary Blockchain Content on Bitcoin gives the interesting insight that all its transactions seem to return change/fees to one or two given addresses, thus making it very easy to list all their uploads if they were consistent! So all we need are some starting points, which we have mostly due to ASCII mentions of the site on known inscriptions, all of which have a few common spent addresses at the very end:so we just have to solve get all Bitcoin transactions from and to a given address and we are done. Blockchair shows about 800 entries as of February 2024, between 4f94f97eb156b8563a213bb292314a0bd9c95b39afc521fc5965d050daab2a78 (2014-03-02) and ac5f4ea03597b43a72fb8ab42bd5384629f87f4f4abc534f38b8c15148ccaf9f (2017-10-12): blockchair.com/bitcoin/outputs?s=time(desc)&q=recipient(1MVpQJA7FtcDrwKC6zATkZvZcxqma4JixS)
- 4c903a377addab7c1e35a685d3dabc664199e406374b1e5ce2fc59e78fb5b754: 1MVpQJA7FtcDrwKC6zATkZvZcxqma4JixS
- 87aad85c6cd75a516789f364637d243c668e3424d031ae510e43c6edfe6ed206: 1MVpQJA7FtcDrwKC6zATkZvZcxqma4JixS
- c206e8fff656f07b27dac831ef9b956792bae4e76a2cb43f14f49f0298bf2c2f: 1MVpQJA7FtcDrwKC6zATkZvZcxqma4JixS
- ca4f11131eca6b4d61daf707a470cfccd1ef3d80a6f8b70f1f07616b451ca64e: 1MVpQJA7FtcDrwKC6zATkZvZcxqma4JixS
Other related transactions:
- tx 87aad85c6cd75a516789f364637d243c668e3424d031ae510e43c6edfe6ed206 block 474652 (2017-07-07) via cryptograffiti.info the default pandoc markdown pandoc.org/try markdown tutorial string! First, unseen in our ASCII dumps due to UTF-8 encoding::followed by:
Unicode test: `Ä Ö Õ Ü ä ö õ ü`.And if ends with:An h1 header ============ Paragraphs are separated by a blank line.Uploaded from http://cryptograffiti.info to demonstrate Markdown rendering.
TODO understand what these are:
- ae92dc4c31943955ad6e3e45a4eb0067f488fdd9aecca65c946460dd2a85488d
- 3020dbd7c850bf8c19ebacf670a2830fe50999a8b2560a202af21d536760eea4
- d65384a21cb1c327cc42416a0b1e2a78ad0296cb7a15312bdcd67ef169ecb309
- a3e3100d2b9a86e310430945c001df97a70626220a9e151208aecbb613f1f152
- a9c82ebc47fabd1eed7eeea7760d0a3c99288af3c3a17e396ec790fc280698a2
- 92bfd5c0fb0f24efa6ca568c4475f44e94dfc8d0d4d5da04dfafc6261bf17f45
- 73c22adb21b93f9220d00d2614a50350824be95b8ea966349e6f35fe5ac5537b
- 099c0fd06d18953c886121ff143ea0a20d0baf29999f424fa1ac707a81cf4987
- 3ad6677303fb6f700a4f2f977fe86e5324e0ddb0d3b33a649e513d7e88904e85
- 31a2ddaf4b146e021246e1f82e28121f5c9c8729620978309004515c7e559910
- adaae897fd286aefb64a69e88a53e9af17ee98611ea595c3c92d038f3274d723
- d8bf48e9ad3de62c695ff34a96e340912bd62e0a0282b94da6386b837c31a30d
Cool data embedded in the Bitcoin blockchain Early AtomSea & EMBII uploads Updated 2026-05-27
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/root/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 at bitfossil.org/?object=1GSt59J2LxjmEshSbkDwZ2Sj4kFCcaw4WD and it reads:followed by:The bug message is definitely a reference to the previous non-visible bugged upload bitfossil.org/root/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!!! In 2026 EMBII comments that it was coincidentally inscribed on NeptuneMonk in his birthday, a early contributor, so he gifted it to him.[ref]
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.
WeAreStarStuff.jpgThe 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/root/fac0b9a4f90414710b806fd286e020aea2404498946845ef3783f305dd4cd3a7 (2024-01-13) contains a cropped version with only AtomSea persent.
HugPuddle.jpgThe 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 are two undecoded ones TODO investigate:
Then Nelson-Mandela.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.
tx 56768b30dec33bd284223d85c23087975e2360b3391d20d505aa59a5675e5379 (2013-12-13, on bitfossil.org):
Dear Aliens,Hey.Sincerely,
EMBII & AtomSea
tx 415c702759893c63b3a57a7d196b014e51b2a33d2396c74b8e71acfaff6b9360 (2013-12-14) contains a poem by 13th century Persian poet Rumi (TODO find bitfossil.org toplevel), starting with:Reproduced e.g. at: www.abuddhistlibrary.com/Buddhism/H%20-%20World%20Religions%20and%20Poetry/World%20Religions/Islam/Teachers/Rumi/My%20dear%20friend/Rumi%20-%20my%20dear%20friend.htm
My dear friend
never lose hope
when the Beloved
sends you away.
bitfossil.org/root/73ca50321147bac9010bec43d63f7f76857fe9ede240cc89710e28723fdb242f/ (2013-12-14) has message:and links to 3 .txt files
MULTIFILE SUPPORT TEST
1.txt, 2.txt, 3.txt containing single characters 1, 2, and 3.
CompressedLogo.png
. Source.2013-12-20. Message:Possibly www.linkedin.com/in/colby-nelson-59b538207/.
Colby Nelson and myself burnt the midnight oils designing the APERTUS imagery last night....Thanks Colby for all your help.
Contains an Apertus logo which is used on bitfossil.org/root/ itself, presumably they were designing that logo.
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