Cool data embedded in the Bitcoin blockchain / Encrypted data Updated 2025-07-16
View more
Transactions such as tx fe37c7eee73be5fda91068dbe0eb74a68495a3fc7185712b8417032db7fc9c5e (2015-01-15) starting with
U2FsdGVkX1/4iSjLxQ5epo8eRSCOQLGgAsn1CucGii27k8ZyC7Jz6wxhYcevVmxi
6Q4ZFN04WDN0UhKqYardgQf26oeBMURupduDd0ZozxlgMrBkFOCaARqU7RABVWDO
/ruPUcOY0VC8p4lrMNqSdqvN7y6OWwOSH3c0duumZfFNZs9+BbtKCxtaqR5+RkUI
are Base64 encoded. Running them through base64 -d leads to starting output bytes Salted__ which as mentioned at security.stackexchange.com/questions/124312/decrypting-binary-code-from-a-base64-string is OpenSSL encrypted data. So hwerever we see the start:
U2FsdGVkX1/
we might as well give up. That string appears 26 times in our data currently, between 6c091e6152b83ec0df8d0d87c7c5f3da72a3328ed3a5d91768ba0ab899c16b9d (2014-09-28) and 84189c82995db355e92e37f8cfe8a9274e9a5d157f1f1658067672e707469a09 (2019-07-06)
The following via cryptograffiti.info get marked by file as "openssl enc'd data with salted password, Base64 encoded":
  • ad3d8a0a5d57114b1780341cb5104284f029bb01b1b3558f7c7b9ce51eb67e18
  • 1cd0c631f444d664601468f644b70e0166019a54d8678de51310139b6c8b2bd7
  • ccc3fb2c9cb1c640b76645a8658693066fd63433ab17c318691ad5bd62601c0e
  • e6eb0cb8268a9b3d012d2957b32d4b28ccc3317593f54f4bfe4b387326588bd2
  • c40e322b198b715accc4a67fad244ed131b8cef0785070e06d10d56c4ab389f2
  • 37a261ac6dbf59e3c9673a22028bcdbdd08926a9d32134ab8fba0897f6dcd196
  • f1aa516fe00ec2156f16fcb9da422f6cbcd141e8e58c895d8bc37b4ad2fd714e
  • 7faf29c7dd7d9cc6d099c262f7ec7edd7fc768276482ad66ceefdd814f1d38ab
  • 69cac244051661cc0b8b08905af5ab312a1282b68c932e5d1e3c46ad47ff0f7a
  • 1773c39f844951b7169dc34aa0c72aa7b43cae6a103ed1223527ef0f4deec2a9
  • b1d4bf3fc46e63c995ad4299f3576340077bc810dfa5c502d1c068460d54bc98
  • a52625837741902e1dd24de3dbd3b948d6e0907ad3fc957c13cdf53fa2c3b9ac
  • 4ca742813eaccef009e24e92150dda06540c2ac81782f1569b1ebb3179a413d2
  • 6c3bab5fc6e6352c62a16ab0f47394845aa41a2c0b25e1a1073a4aeac150e03d
  • 20b8feef3d293a0dd79e3c169fceb1217465502a523acbab903a7eb0cd183709
  • b7863215b99567bc9e71155b13f3c5f26d15eac52493ee2e834129460ffd2aec
  • 2c8961a64bb11d5855790085f51007273467f7ef862137215c9f1d958dcb6c57
  • bed542957bdd8f644a4fcd671a8c66a5cc5d6168f9fa60d37177703e77558eee
  • 3e45af9d828754d5a38c86636a070610f6e828482718c4a597d272d41a3e31fa
  • a13af4817e85cacce3cfb445001e2fb2f56cdc30f78348fd2580bf8f4c84dc55
  • 87a10f6bc65a08067b2544e46be00d4af62c0cfed3ae0b165d5eedaff09d81da
  • ef55826befabbe9dcd44d87fc385d600dd4c4cba3346cde53d8c591960e9b4dc
  • 5d30f63131dcf2b4d001b4ab530e18cc6ff8ffd16cade055ff4587a59b84e420
  • 8a75514829b6e30b9fea434eef77b1589ff3f4bdfc0056bd087efbfb8314eb59
  • e2be1062c9d43cc6ed43de6f7a40c728d2d92ed0325abde24ff3300cf3ae136a
  • 8fe5c2679237e36c74fda04bb083f732c4afdd06af81121b1d7b4d5bd677135f
  • 7f099f094d8d51105d8655253d45ebddf1c88b9e138c302a65d2878a237e620c
  • 0fc4b3a305e2a7faa2e7d9c2f23d23d626e9e75f1f2a37133f283334b314645b
  • 933b321e7b7144ed5e4e1750f944be9ed10293633d9b288bf05febdeb9dc40a3
  • 6215486bc024dea7991b142e50e111c4063e1db4a867514612b8e794b8ef5635
  • fc0613e11269962d97373b10e310f451fb76c7bb477ba1afb45773c44851e9ed
  • ab51d2c037b4625394c68706da83c26bad751018d2a3e377a51988bd8ee18647
  • 7ca9b337172f4feff67a0ecbfbd76798265e08c6ebe989a319883c695d756247
  • 0f0b477e456dcf286d7262497bcd5b3b6a3ce89f81761c2f59ff702539ab6183
  • a320152fd59426c8853dd781db9d682f89755953b39a653f9e9c9628a5fce7fb
  • e96221da774fb52d24dda1b83b14c99085eb4befac64691722c56eb750562d68
  • a7a5ca68dd340dd42bd5c91e0febe68e5fd2fb993da2992661183eaafe8ad89e
  • 64e9d95e2333cfd155506199c8d926649e63a98dbc83c1221b8dd1580937b942
blockchain.news/news/mysterious-bitcoin-inscriptions-a-puzzle-in-raw-binary-data mentions a huge 9 MB Ordinal ruleset inscription that no-one managed to decode, and so people suspect is encrypted data. Seems to be split across transactions, starting at fed7de7fb75a3fe3c1acbbd8e19a4c540fb368474c8834e4ddb1d5bab764a767
Read the full article
E. Coli K-12 MG1655 promoter Updated 2025-07-16
View more
From this we see that there is a convention of naming promoters as protein name + p, e.g. the first gene in E. Coli K-12 MG1655 promoter thrLp encodes protein thrL.
It is also possible to add numbers after the p, e.g. at biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=PM0-45989 we see that the protein zur has two promoters:
  • zurp6
  • zurp7
TODO why 6 and 7? There don't appear to be 1, 2, etc.
Read the full article
E. Coli Whole Cell Model by Covert Lab / Condition Updated 2025-07-16
View more
  • reconstruction/ecoli/flat/condition/nutrient/minimal.tsv contains the nutrients in a minimal environment in which the cell survives:
    "molecule id" "lower bound (units.mmol / units.g / units.h)" "upper bound (units.mmol / units.g / units.h)"
"ADP[c]" 3.15 3.15
"PI[c]" 3.15 3.15
"PROTON[c]" 3.15 3.15
"GLC[p]" NaN 20
"OXYGEN-MOLECULE[p]" NaN NaN
"AMMONIUM[c]" NaN NaN
"PI[p]" NaN NaN
"K+[p]" NaN NaN
"SULFATE[p]" NaN NaN
"FE+2[p]" NaN NaN
"CA+2[p]" NaN NaN
"CL-[p]" NaN NaN
"CO+2[p]" NaN NaN
"MG+2[p]" NaN NaN
"MN+2[p]" NaN NaN
"NI+2[p]" NaN NaN
"ZN+2[p]" NaN NaN
"WATER[p]" NaN NaN
"CARBON-DIOXIDE[p]" NaN NaN
"CPD0-1958[p]" NaN NaN
"L-SELENOCYSTEINE[c]" NaN NaN
"GLC-D-LACTONE[c]" NaN NaN
"CYTOSINE[c]" NaN NaN
    If we compare that to reconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv, we see that it adds the 20 amino acids on top of the minimal condition:
    "L-ALPHA-ALANINE[p]" NaN NaN
"ARG[p]" NaN NaN
"ASN[p]" NaN NaN
"L-ASPARTATE[p]" NaN NaN
"CYS[p]" NaN NaN
"GLT[p]" NaN NaN
"GLN[p]" NaN NaN
"GLY[p]" NaN NaN
"HIS[p]" NaN NaN
"ILE[p]" NaN NaN
"LEU[p]" NaN NaN
"LYS[p]" NaN NaN
"MET[p]" NaN NaN
"PHE[p]" NaN NaN
"PRO[p]" NaN NaN
"SER[p]" NaN NaN
"THR[p]" NaN NaN
"TRP[p]" NaN NaN
"TYR[p]" NaN NaN
"L-SELENOCYSTEINE[c]" NaN NaN
"VAL[p]" NaN NaN
    so we guess that NaN in the upper mound likely means infinite.
    We can try to understand the less obvious ones:
    • ADP: TODO
    • PI: TODO
    • PROTON[c]: presumably a measure of pH
    • GLC[p]: glucose, this can be seen by comparing minimal.tsv with minimal_no_glucose.tsv
    • AMMONIUM: ammonium. This appears to be the primary source of nitrogen atoms for producing amino acids.
    • CYTOSINE[c]: hmmm, why is external cytosine needed? Weird.
  • reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/ contains sequences of conditions for each time. For example:
    • reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000000_basal.tsv contains:
      "time (units.s)" "nutrients"
0 "minimal"
      which means just using reconstruction/ecoli/flat/condition/nutrient/minimal.tsv until infinity. That is the default one used by runSim.py, as can be seen from ./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Environment/attributes/nutrientTimeSeriesLabel which contains just 000000_basal.
    • reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000001_cut_glucose.tsv is more interesting and contains:
      "time (units.s)" "nutrients"
0 "minimal"
1200 "minimal_no_glucose"
      so we see that this will shift the conditions half-way to a condition that will eventually kill the bacteria because it will run out of glucose and thus energy!
    Timeseries can be selected with --variant nutrientTimeSeries X Y, see also: run variants.
    We can use that variant with:
    VARIANT="condition" FIRST_VARIANT_INDEX=1 LAST_VARIANT_INDEX=1 python runscripts/manual/runSim.py
  • reconstruction/ecoli/flat/condition/condition_defs.tsv contains lines of form:
    "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"]
    • condition refers to entries in reconstruction/ecoli/flat/condition/condition_defs.tsv
    • nutrients refers to entries under reconstruction/ecoli/flat/condition/nutrient/, e.g. reconstruction/ecoli/flat/condition/nutrient/minimal.tsv or reconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv
    • genotype perturbations: there aren't any in the file, but this suggests that genotype modifications can also be incorporated here
    • doubling time: TODO experimental data? Because this should be a simulation output, right? Or do they cheat and fix doubling by time?
    • active TFs: this suggests that they are cheating transcription factors here, as those would ideally be functions of other more basic inputs
Read the full article
E. Coli Whole Cell Model by Covert Lab / Time series run variant Updated 2025-07-16
View more
To modify the nutrients as a function of time, with To select a time series we can use something like:
python runscripts/manual/runSim.py --variant nutrientTimeSeries 25 25
As mentioned in python runscripts/manual/runSim.py --help, nutrientTimeSeries is one of the choices from github.com/CovertLab/WholeCellEcoliRelease/blob/7e4cc9e57de76752df0f4e32eca95fb653ea64e4/models/ecoli/sim/variants/__init__.py#L57
25 25 means to start from index 25 and also end at 25, so running just one simulation. 25 27 would run 25 then 26 and then 27 for example.
The timeseries with index 25 is reconstruction/ecoli/flat/condition/timeseries/000025_cut_aa.tsv and contains
"time (units.s)" "nutrients"
0 "minimal_plus_amino_acids"
1200 "minimal"
so we understand that it starts with extra amino acids in the medium, which benefit the cell, and half way through those are removed at time 1200s = 20 minutes. We would therefore expect the cell to start expressing amino acid production genes exactly at that point.
nutrients likely means condition in that file however, see bug report with 1 1 failing: github.com/CovertLab/WholeCellEcoliRelease/issues/24
When we do this the simulation ends in:
Simulation finished:
 - Length: 0:34:23
 - Runtime: 0:08:03
so we see that the doubling time was faster than the one with minimal conditions of 0:42:49, which makes sense, since during the first 20 minutes the cell had extra amino acid nutrients at its disposal.
The output directory now contains simulation output data under out/manual/nutrientTimeSeries_000025/. Let's run analysis and plots for that:
python runscripts/manual/analysisVariant.py &&
python runscripts/manual/analysisCohort.py --variant 25 &&
python runscripts/manual/analysisMultigen.py --variant 25 &&
python runscripts/manual/analysisSingle.py --variant 25
We can now compare the outputs of this run to the default wildtype_000000 run from Section "Install and first run".
  • out/manual/plotOut/svg_plots/massFractionSummary.svg: because we now have two variants in the same out/ folder, wildtype_000000 and nutrientTimeSeries_000025, we now see a side by side comparision of both on the same graph!
    The run variant where we started with amino acids initially grows faster as expected, because the cell didn't have to make it's own amino acids, so growth is a bit more efficient.
    Then, at 20 minutes, which is about 0.3 hours, we see that the cell starts growing a bit less fast as the slope of the curve decreases a bit, because we removed that free amino acid supply.
    Figure 1.
    Minimal condition vs amino acid cut mass fraction plot
    . Source. From file out/manual/plotOut/svg_plots/massFractionSummary.svg.
The following plots from under out/manual/wildtype_000000/000000/{generation_000000,nutrientTimeSeries_000025}/000000/plotOut/svg_plots have been manually joined side-by-side with:
for f in out/manual/wildtype_000000/000000/generation_000000/000000/plotOut/svg_plots/*; do
  echo $f
  svg_stack.py \
    --direction h \
    out/manual/wildtype_000000/000000/generation_000000/000000/plotOut/svg_plots/$(basename $f) \
    out/manual/nutrientTimeSeries_000025/000000/generation_000000/000000/plotOut/svg_plots/$(basename $f) \
    > tmp/$(basename $f)
done
Figure 2.
Amino acid counts
. Source. aaCounts.svg:
  • default: quantities just increase
  • amino acid cut: there is an abrupt fall at 20 minutes when we cut off external supply, presumably because it takes some time for the cell to start producing its own
Figure 3.
External exchange fluxes of amino acids
. Source. aaExchangeFluxes.svg:
  • default: no exchanges
  • amino acid cut: for all graphs except phenylalanine (PHE), either the cell was intaking the AA (negative flux), and that intake goes to 0 when the supply is cut, or the flux is always 0.
    For PHE however, the flux is at all times, except shortly after the cut. Why? And why there was no excretion on the default conditions?
Figure 4.
Evaluation time
. Source. evaluationTime.svg: this has nothing to do with biology, but it is rather a profile of the program runtime. We can see that the simulation gets slower and slower as time passes, presumably because there are more and more molecules to simulate.
Figure 5.
mRNA count of highly expressed mRNAs
. Source. From file expression_rna_03_high.svg. Each of the entries is a gene using the conventional gene naming convention of xyzW, e.g. here's the BioCyc for the first entry, tufA: biocyc.org/gene?orgid=ECOLI&id=EG11036, which comments
Elongation factor Tu (EF-Tu) is the most abundant protein in E. coli.
and
In E. coli, EF-Tu is encoded by two genes, tufA and tufB
. What they seem to mean is that tufA and tufB are two similar molecules, either of which can make up the EF-Tu of the E. Coli, which is an important part of translation.
Figure 6.
External exchange fluxes
. Source.
mediaExcange.svg: this one is similar to aaExchangeFluxes.svg, but it also tracks other substances. The color version makes it easier to squeeze more substances in a given space, but you lose the shape of curves a bit. The title seems reversed: red must be excretion, since that's where glucose (GLC) is.
The substances are different between the default and amino acid cut graphs, they seem to be the most exchanged substances. On the amino cut graph, first we see the cell intaking most (except phenylalanine, which is excreted for some reason). When we cut amino acids, the uptake of course stops.
Read the full article
ELF Hello World Tutorial / SHT_NULL Updated 2025-07-16
View more
In index 0, SHT_NULL is mandatory. Are there any other uses for it: stackoverflow.com/questions/26812142/what-is-the-use-of-the-sht-null-section-in-elf ?
Read the full article
GitLab cookbook Updated 2025-07-16
View more
Read the full article
gnuplot command line hello world Updated 2025-07-16
View more
CLI hello world:
gnuplot -p -e 'p sin(x)'
Read the full article
Instrumental goal Updated 2025-07-16
Read the full article
Pro of superconducting qubits Updated 2025-07-16
Read the full article
E. Coli K-12 MG1655 gene Updated 2025-07-16
Read the full article
FeathersJS Heroku deployment Updated 2025-07-16
View more
One major step was to port to PostgreSQL as shown at feathers-chat PostgreSQL.
There's also a heroku branch at: github.com/feathersjs/feathers-chat/tree/heroku, but it also seems to use NeDB? So you can have a filesystem in Heroku? Doesn't seem so: stackoverflow.com/questions/42775418/heroku-local-persistent-storage
Read the full article
Git tips / Move your branch on top of newest master Updated 2025-07-16
View more
Before:
5 master
|
4 7 my-feature HEAD
| |
3 6
|/
2
|
1
Action:
git rebase
After:
7 my-feature HEAD
|
6
|
5 master
|
4
|
3
|
2
|
1
Ready to push with linear history!
Read the full article
History of the electromagnetic theory of light Updated 2025-07-16
Read the full article
Inside Job (2010) Updated 2025-07-16
Read the full article
Tachyonic antitelephone Updated 2025-07-16
Read the full article
The Big Short (2015) Updated 2025-07-16
View more
Video 1.
I'm Jacked to the Tits remix by The Big Short (2021)
Source.
Read the full article
MSc course of the University of Oxford Updated 2025-07-16
Read the full article
QMUL Game AI Research Group Updated 2025-07-16
View more
Principal investigator: Simon M. Lucas.
Read the full article
Realworld app written in Express Updated 2025-07-16
View more
gothinkster/realworld implementations based on Express.js.
Read the full article
Category 5 cable Updated 2025-07-16
Read the full article

Unlisted articles are being shown, click here to show only listed articles.