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: 0:09:13TODO compare with actual datasetes.
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.
Interesting AtomSea & EMBII uploads by 
Ciro Santilli 35 Updated 2025-04-16 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-04-16 +Created 1970-01-01tx e3e37ed5c1de2631c147bd39429e42ff634e95b7d72423bc32d6c6b9d8eef8ee (2014-07-01):
For my first official Journal entry I've decided to archive some old poetry. Here are a few of the computational poems I've created using cyphers.
Shiemaa&Vincent.jpgMessage:TODO identify Shiemaa and Vincent.
"Even if we tried to do it on purpose, never would have we succeeded." My beloved Vincent.
tx 36d0d77acd760f0aa549b6b314f0c1e9690baa6bcc2d0f07ea9f3167f4a5ec99, block 318836 (2014-09-03)Cost: ~0.002 BTC ~ $0.77 at the time.
Several other interesting uploads were also made around block 318836 (September 2014):
RedRaven.jpgbitfossil.org/e17b83234402d85f3a18207eec11bc5c4397f88aa880aae4fb7d15802806a971/index.htmEarth3Archive.jpgbitfossil.org/ae8d3b46b934bedc363e11abe8c8607171994470957c286274f699a0b3a9bbd7/index.htmSkyEarth5Archive.jpgbitfossil.org/ae8d3b46b934bedc363e11abe8c8607171994470957c286274f699a0b3a9bbd7/index.htm
BikeLady.jpgBike Lady by Allen Lee Vandever. tx 2c4b9497af8c0c0eb9383357b40c3de33dba0b4f481099a32719f2b9036da8e7, block 319927 (2014-09-10)
This seems to be a novel work uploaded by its creator artist Allen Vandever according to EMBII.[ref].
Arecibo_message.svgArecibo message on tx c6d2e535cd2ba4659e954a61198c66fd98c60f6475cf8ff92a404f3fe3a16c4b, block 337874 (2015-01-07)
An "artificially" colored visualization of the Arecibo message ripped from Wikipedia: en.wikipedia.org/wiki/File:Arecibo_message.svg (with attribution).
The cool thing about this image is that it highlights the striking parallels between the encoding of the Arecibo message with crypto graffiti, because in both cases people were creating undocumented new ways of communicating with strangers on a new medium in those early blockchain days.
The associated message contains the Arecibo message as ASCII 0's and 1's. When properly cut at the newlines, they draw the message as ASCII art, as the original Arecibo encoding intends, here's a version with the 0's replaced by spaces to make it more readabale:
1 1 1 1
1 1 1 1 1
1 1 1 1 1 11 1
1 1 1 1 1 1 1 1 1 1
11
11 1
11 1
1 1 1
11111
11 111 11 11
1 11 1
11 1 11 11 11 1
11111 11111 11111 11111
1 1
1 1
11111 11111
11 11 111 11
1 1 1
11 1 11 111 11 1
11111 11111 11111 11111
1 11 1
11
1 11 1
11111 11 11111
11
1 1 1
1 11 1
11 11 1
11 1 11
11 11
11 1 11
11 11 1
1 1 1
1 11 1
1 11 1
1 1 1
1 1 1
1 11
11 11
1 111 1 11
1 1
1 11111
1 1 111 1 1 11 11
1 111 1 111111
1 111 111 11 111
1 1 111 11
1 1 1 111111
1 1 1 11
1 11 11
111 1
111 1 1 1 1 1 1 1 1
111 1 1 1 1
1 1
11111
111111111
111 111
11 11
11 1 1 11
11 11 11 11
1 1 1 1 1 1
1 1 1 1 1 1
1 1 1 1
1 1 1
1 1
1 1 1
1111 11111 1 1111
He sleeps in a temple.jpg
PIA17563.jpg
. Source. Associated message:
NASA: A purple nebula, in honor of #Prince, who passed away today. Image: Crab #Nebula, as Seen by Herschel and #Hubble Image credit: ESA/Herschel/PACS/MESS Key Programme Supernova Remnant Team; #NASA, ESA and Allison Loll/Jeff Hester (Arizona State University) #PIA17563
Dr_Craig_Wright.jpg
. Source. Associated message:
The image is present e.g. at: www.kitguru.net/channel/jon-martindale/australian-man-claims-he-is-satoshi-nakamoto-bitcoin-creator/ It was inscribed about two months after Craig publicly claimed that he is Satoshi.
This is a relatively unusual AtomSea & EMBII upload as it does not have the common toplevel transaction, everything, text + image fits into a single transaction. This is perhaps why the image is relatively low resolution to have a smaller size.
YellowRobot.jpgYellow Robot on tx 67b2facfd8160d4fa11b02829b6387d07537b57a7a24f19b029b2a5ae7b81830, block 450516 (2017-01-29)
Photography by EMBII, original art by TODO.
The associated message reads:This is one of Ciro's favorite AtomSea & EMBII uploads. This is the cutest thing ever, and perfectly encapsules the "medium as an artform" approach to blockchain art. More Chiharu stalking at: ILoveYouMore.jpg.
Chiharu and I found this little yellow robot while exploring Chicago. It will be covered by tar or eventually removed but this tribute will remain. N 41.880778 E -87.629210
At twitter.com/EMBII4U/status/1615389973343268871 EMBII announced that he would be giving off shares of that image on a Bitcoin-based NFT sale system he's making called Sup!?, and in December 2023 gave some shares to Ciro Santilli. Amen.
Other possibly novel EMBII street photography:
- bitfossil.com/f2efd446475ad58a3ea808cc0f05a63c55cece9fced70d84799a1ffce5d307e4/index.htm "I will not Stop until the Finite becomes the Infinite."
Audio:
alien.wavblock 318638 bitfossil.org/a3a24d6ea01ce481a50346818b8977220687f3ba385838fe8894ce61c9718bbc/OneGiantLeapForMankind.mp3at tx 4f5b25fa8021c67235423930580e69121aa0d2c2bb779f75139bf442f8dc7297 EMBII-indexed at 743f3286b00fc96c13db4b16d5aead8a1e059fee9ce775b1761be9be5bdc2501 and then indexed at: 0427ec598df38b7d7dc75721316c0bbdec54de4871e11aff8ea64f3717c07efbThe toplevel index does appear on Bitfossil: bitfossil.org/0427ec598df38b7d7dc75721316c0bbdec54de4871e11aff8ea64f3717c07efb/index.htm but the audio is not there as it was for Spock below, maybe a bug on upload/Bitfossil?Spock_Live_Long_And_Prosper.mp3block 345858 bitfossil.org/1bc87dbff1ff5831287f62ac7cf95579794e4386688479bab66174963f9a4a0c/index.htm. Audio of Mr. Spock saying the Vulcan salute.OuterSpace.mp3block 409471 bitfossil.org/c14c1bd862bab6269052bf0a2cda7a35940d7a2d9c3415d4fb8fb8dcb9394fae/ "Outer Space by embii 4MB Large file storage test Apertus 0.3.5-beta" OMG, I don't want to calculate how much it cost to upload this, it will make me sad.At twitter.com/EMBII4U/status/1655969645927563266 EMBII mentions that this inscription, made by him, is the largest inscription he knows of.TODO song composer/performer?- bitfossil.com/c2b170ff450f4529dfbd784e0cf5cdddaca494e67a243dd846c0a9450a5558af/ (2021-03-13) contains
Seikilos.mid, a MIDI file
Interesting text:
- block 273522 bitfossil.org/70fd289901bae0409f27237506c330588d917716944c6359a8711b0ad6b4ce76/index.htm pi to 1000+ decimal digits:
- bitfossil.org/8522787e7e49f3f3b6a9f9e86bc30336d26a3acbaecc93809d2e8b4bb1c4d611/ "Antarctic Ice Cores Revised 800KYr CO2 Data" evidence for global warming
- bitfossil.org/ffa6893a70bcde9b940df9823e0f597f0b6cff964c78473c77db838655e1aeb5/ en.wikipedia.org/wiki/Laudato_si', global warming related
HTML pages:
- block 335290 bitfossil.org/0166db6053f1969c28de8b1f9a8fa4ec890cc4bdfee7602757993b306bb7f295/ JavaScript animated timer clock counting down until the start of the next year
- block 340379 bitfossil.org/062990d54045a9c316110fb713009d1313b2f64c4b216d66891c7284d6c1ca0e/ links to bitfossil.org/062990d54045a9c316110fb713009d1313b2f64c4b216d66891c7284d6c1ca0e/bong-ball.html and has a working JavaScript Pong
- block 328445
tom-signature.jpgbitfossil.org/daa050bf8ac22752e40412c9265b4533f68ab8e6ed26d2db1eeee6710e7d9e4b/index.htm Unrendered HTML of:Likely an obituary for: Thomas L. Magliozzi. Images show fine though.- www.cartalk.com/content/tom-and-rays-bios-photos-2
- www.cartalk.com/content/rant-and-rave-36 "The New Theory of Learning" which agrees perfectly with backward design
- block 401648 bitfossil.com/31c5e5336512568e4a1deb4bbf0e57c3565c32094c0e1a118c48e7929ab49e35/bong-ball.html another one! This one is full-screen, and does not have JavaScript
alerts :-) - block 401657 bitfossil.org/03cb74f270d498302d4dd9cbe82c090d801c8840ab6cb26b71d862489b981db8/ has a JavaScript Pac-Man
Good animation explaining it: Video "Electron transport chain by HarvardX (2017)".
In x86 systems, there may actually be 2 address translation steps:like this:
- first segmentation
- then paging
(logical) ------------------> (linear) ------------> (physical)
segmentation pagingThe major difference between paging and segmentation is that:
- paging splits RAM into equal sized chunks called pages
- segmentation splits memory into chunks of arbitrary sizes
This is the main advantage of paging, since equal sized chunks make things more manageable by reducing memory fragmentation problems. See also:
Paging came after segmentation historically, and largely replaced it for the implementation of virtual memory in modern OSs.
Paging has become so much more popular that support for segmentation was dropped in x86-64 in 64-bit mode, the main mode of operation for new software, where it only exists in compatibility mode, which emulates IA-32.
Page size extension.
Allows for pages to be 4M (or 2M if PAE is on) in length instead of 4K.
PSE is turned on and off via the
PSE bit of cr4.Peter Cordes mentions that some architectures like MIPS leave paging almost completely in the hands of software: a TLB miss runs an OS-supplied function to walk the page tables, and insert the new mapping into the TLB. In such architectures, the OS can use whatever data structure it wants.
It is quite mind blowing that this is polyphyletic on mammals and birds, what can't parallel evolution achieve??
Phylogenetic tree of the vertebrates
. Source. Highlights how birds should obviously be classified as reptiles.
University of Oxford intellectual property policy by Ciro Santilli 35 Updated 2025-04-16 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-04-16 +Created 1970-01-01For students (who are paying for the university to start with...), they will not claim tutorials linked to courses. But a tutorial that shows university laboratories, it is unclear: www.ox.ac.uk/students/academic/guidance/intellectual-property (archive) This likely includes graduate students, who are also not paid by the university.
For faculty, the university owns everything it seems, to be confirmed.
The closest site of the University of California to San Francisco. Berkeley, California is a small town on the East of the San Francisco Bay.
Brother of andrew the Apostle, called by Jesus in fishers of men. Born Simon, but Jesus renamed him to Peter, thus the weird "Simon called Peter" way he is referred to as in some versions of the Bible.
Organization developing trapped ion quantum computer by Ciro Santilli 35 Updated 2025-04-16 +Created 1970-01-01
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