"Breaking the Code" is a play written by Hugh Whitemore that premiered in 1986. The work centers on the life of British mathematician and logician Alan Turing, who is best known for his contributions to computer science and for breaking the German Enigma code during World War II.
The conventional starting point is not at the E. Coli K-12 MG1655 origin of replication.
biocyc.org/ECOLI/NEW-IMAGE?type=EXTRAGENIC-SITE&object=G0-10506 explains:If it is a bit hard to understand what they mean by "origin of transfer" though, as that term is usually associated with the origin of transfer of bacterial conjugation.
This site is the origin of replication of the E. coli chromosome. It contains the binding sites for DnaA, which is critical for initiation of replication. Replication proceeds bidirectionally. For historical reasons, the numbering of E. coli's circular chromosome does not start at the origin of replication, but at the origin of transfer during conjugation.
E. Coli Whole Cell Model by Covert Lab by 
Ciro Santilli 37 Updated 2025-07-14 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-14 +Created 1970-01-01github.com/CovertLab/WholeCellEcoliRelease is a whole cell simulation model created by Covert Lab and other collaborators.
The project is written in Python, hurray!
But according to te README, it seems to be the use a code drop model with on-request access to master. Ciro Santilli asked at rationale on GitHub discussion, and they confirmed as expected that it is to:
- to prevent their publication ideas from being stolen. Who would steal publication ideas with public proof in an issue tracker without crediting original authors? Academia is broken. Academia should be the most open form of knowledge sharing. But instead we get this silly competition for publication points.
- to prevent noise from non-collaborators. But they only get like 2 issues as year on such a meganiche subject... Did you know that you can ignore people, and even block them if they are particularly annoying? Much more likely is that no one will every hear about your project and that it will die with its last graduate student slave.
The project is a followup to the earlier M. genitalium whole cell model by Covert lab which modelled Mycoplasma genitalium. E. Coli has 8x more genes (500 vs 4k), but it the undisputed bacterial model organism and as such has been studied much more thoroughly. It also reproduces faster than Mycoplasma (20 minutes vs a few hours), which is a huge advantages for validation/exploratory experiments.
The project has a partial dependency on the proprietary optimization software CPLEX which is freeware, for students, not sure what it is used for exactly, from the comment in the
requirements.txt the dependency is only partial.This project makes Ciro Santilli think of the E. Coli as an optimization problem. Given such external nutrient/temperature condition, which DNA sequence makes the cell grow the fastest? Balancing metabolites feels like designing a Factorio speedrun.
There is one major thing missing thing in the current model: promoters/transcription factor interactions are not modelled due to lack/low quality of experimental data: github.com/CovertLab/WholeCellEcoliRelease/issues/21. They just have a magic direct "transcription factor to gene" relationship, encoded at reconstruction/ecoli/flat/foldChanges.tsv in terms of type "if this is present, such protein is expressed 10x more". Transcription units are not implemented at all it appears.
Everything in this section refers to version 7e4cc9e57de76752df0f4e32eca95fb653ea64e4, the code drop from November 2020, and was tested on Ubuntu 21.04 with a docker install of
docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full with image id 502c3e604265, unless otherwise noted."Breaking the Code" is a 1996 television film directed by Norman Stone, based on the life of the British mathematician and logician Alan Turing. The film is primarily focused on Turing's brilliant contributions to the field of mathematics, particularly during World War II when he played a crucial role in breaking the German Enigma code.
"Codebreaker" is a biographical film that explores the life and contributions of Alan Turing, a British mathematician, logician, and computer scientist who is best known for his work during World War II in breaking the German Enigma code. The film highlights Turing's pivotal role in the development of modern computing and his contributions to cryptography, as well as his struggles with societal acceptance due to his sexuality.
"Cryptonomicon" is a science fiction novel written by American author Neal Stephenson, published in 1999. The book is notable for its intricate plot and the way it intertwines themes of cryptography, computer science, and World War II history.
An Introduction to QED and QCD by Jeff Forshaw (1997) by Ciro Santilli 37 Updated 2025-07-14 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-14 +Created 1970-01-01www.hep.man.ac.uk/u/forshaw/NorthWest/QED.pdf web.archive.org/web/20200824083133/http://www.hep.man.ac.uk/u/forshaw/NorthWest/QED.pdf
These seem very direct and not ultra advanced, good read.
The Statue of Alan Turing at Bletchley Park, located in the UK, is a tribute to the renowned mathematician and computer scientist who played a pivotal role in breaking the Enigma code during World War II. Turing's work at Bletchley Park is considered a significant factor in the Allied victory, as it provided crucial intelligence about German military operations. The statue was unveiled in 2019 and depicts Turing seated on a bench, deep in thought.
"The Innovators: How a Group of Hackers, Geniuses, and Geeks Created the Digital Revolution" is a book written by Walter Isaacson, published in 2014. The book explores the history of the digital revolution and profiles the key figures and teams of innovators who contributed to the development of computers, software, and the internet. Isaacson emphasizes the collaborative nature of innovation, highlighting how many breakthroughs emerged from group efforts rather than individual genius alone.
An Introduction To Quantum Field Theory by Peskin and Schroeder (1995) by Ciro Santilli 37 Updated 2025-07-14 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-14 +Created 1970-01-01Unfortunately, this approach bores Ciro Santilli to death. Or perhaps is too just advanced for him to appreciate. Either of those.
800+ pages.
7 Wonders is a popular card drafting and civilization-building board game designed by Antoine Bauza. First published in 2010, the game can accommodate 3 to 7 players and typically takes about 30 to 45 minutes to play. In 7 Wonders, players assume the roles of leaders of ancient civilizations and aim to build their cities and develop their societies over three ages.
"Cabiria" can refer to a couple of different things depending on the context: 1. **Film**: "Cabiria" is a silent film directed by Giovanni Pastrone, released in 1914. It is notable for its epic scale and is considered one of the earliest examples of Italian cinema. The film is set in ancient times and follows the story of a young girl named Cabiria who is kidnapped and taken to Carthage.
E. Coli Whole Cell Model by Covert Lab Install and first run by Ciro Santilli 37 Updated 2025-07-14 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-14 +Created 1970-01-01At 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"Once Upon a Time... The Discoverers" (original French title: "Il était une fois... les Découvreurs") is an animated educational series that is part of the "Once Upon a Time..." franchise, created by Albert Barillé. This particular series, which aired in 1994, focuses on the history of exploration and the lives of famous explorers throughout various periods.
"The Siege of Syracuse" is a historical drama film that was released in 2018. The movie is set during the time of the ancient Roman Republic following the Siege of Syracuse in 212 BC, which was part of the Second Punic War. The story primarily focuses on the conflict between the Roman forces, led by General Marcus Claudius Marcellus, and the defenders of Syracuse, who were under the command of the renowned mathematician and inventor Archimedes.
E. Coli Whole Cell Model by Covert Lab Other run variants by Ciro Santilli 37 Updated 2025-07-14 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-14 +Created 1970-01-01Besides 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. Pinned article: ourbigbook/introduction-to-the-ourbigbook-project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 2. You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website.
Figure 3. Visual Studio Code extension installation.
Figure 5. . You can also edit articles on the Web editor without installing anything locally. Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact