E. Coli Whole Cell Model by Covert Lab Other run variants Updated 2025-04-24 +Created 1970-01-01
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. Mathematical, Physical and Life Sciences division of the University of Oxford Updated 2025-04-24 +Created 1970-01-01
Cool data embedded in the Bitcoin blockchain Incoming links Updated 2025-04-24 +Created 1970-01-01
By Ciro Santilli:
- 2021-04-13 twitter.com/cirosantilli/status/1382067162492366854: main initial announcement on Twitter. twitter.com/mikko, who has 209.9K followers and a Wikipedia page: Mikko Hypponen hearted the tweet s2
- 2023-01-21 twitter.com/cirosantilli/status/1749172304259535063: improvements to the Prayer wars
- 2024-02-07 twitter.com/cirosantilli/status/1755378931446739373: large-ish update with new items and improved organization
- 2024-03-31 twitter.com/cirosantilli/status/1774531934305071295: binwalk discoveries, start poking a bit into ordinal ruleset inscriptions
- 2024-04-04 twitter.com/cirosantilli/status/1775805941885108392: largest text ordinal inscription
By others:
- 2021-04-15 news.ycombinator.com/item?id=26801067 (96 points) on Hacker News. Reached position 16 at one point: archive.ph/L0Fte and led to about 5k views total. Ah, Ciro could watch that Google Analytics realtime view go bling all day long. Narcissism is a bitch.
- 2021 cryptonewmedia.press/tankman-image-on-bitcoin-blockchain/ by user igadjeed
- 2022-01-23 news.ycombinator.com/item?id=30050479 "Abuse and Harassment on the Blockchain", comment-mid thread
- 2022-01-24 www.reddit.com/r/Buttcoin/comments/sbw0se/when_i_heard_about_nfts_i_thought_they_were/hu2uk8g "When I heard about NFTs, I thought they were stupid, but then I watched a video explaining how they work, it really changed my perspective", comment mid-thread
- 2023-02 lots of Twitter backlinks as a result of ordinal ruleset inscriptions:
- 2023-02-03
Video 1. Source. Features Marijuana plant and Rickrolling sections. He seems to be a finance guru. - 2023-02-07 twitter.com/privateid_ntity/status/1622814063331004421
- 2024-01-18 twitter.com/pete_rizzo_/status/1748049913286447355 by Rizzo, The Bitcoin Historian (81k followers, mid-thread)
- 2024-12-29: x.com/lopp/status/1873453363523932630 by Jameson Lopp (492k subscribers)
- ? cloudhiker.net/ A hand curated and categorized list of interesting links by Kevin Woblick. Only allows users to visit a random one per category, so we can't get proof of backlink, this was noticed through Google Analytics.
- 2025-03-18 Bitcoin Burn Addresses: Unveiling the Permanent Losses and Their Underlying Causes
The mention of this project is brief:Announced at:Ciro Santilli maintains a Web page listing arbitrary data embedded in the Bitcoin blockchain. This is the most complete and up-to-date list of arbitrary data we are aware of. However, he does not specifically focus on burn addresses, but on the stored contents.
- 2025-03-28 x.com/punk3606/status/1905295370227155344 quick "this was already discovered" mention on thread x.com/I____felix____I/status/1905291048798106061 where a dude rediscovers Figure "Warren Buffet"
E. Coli Whole Cell Model by Covert Lab Install and first run Updated 2025-04-24 +Created 1970-01-01
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: 0:09:13ELF is specified by the LSB:
The LSB basically links to other standards with minor extensions, in particular:
- Generic (both by SCO):
- System V ABI 4.1 (1997) www.sco.com/developers/devspecs/gabi41.pdf, no 64 bit, although a magic number is reserved for it. Same for core files. This is the first document you should look at when searching for information.
- System V ABI Update DRAFT 17 (2003) www.sco.com/developers/gabi/2003-12-17/contents.html, adds 64 bit. Only updates chapters 4 and 5 of the previous document: the others remain valid and are still referenced.
- Architecture specific (by the processor vendor):
A handy summary can be found at:
man elfNotably used for communication with submarines, so in particular crucial as part of sending an attack signal to that branch of the nuclear triad.
PDF table of contents feature requests: twitter.com/cirosantilli/status/1459844683925008385
Unlisted articles are being shown, click here to show only listed articles.