Working remotely is hard if you don't already highly master the software and enterprise systems used.
Also you don't feel people's love as strongly, and usefulness is built on love, see also Steve Jobs's Pixar office space design philosophy.
But please, give workers a small silent office so that we can concentrate instead of a silly open space, and create an internal social network so people can see what others are doing.
Remote working is much better if the majority of the team also does it, otherwise you will get excluded. Maybe after VR...
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.
When debugging complex software, make sure to keep notes of every interesting find you make in a note file, as you extract it from the integrated development environment or debugger.
Especially if your memory sucks like Ciro's.
This is incredibly helpful in fully understanding and then solving complex bugs.
The most important program ever written!!!
Ciro Santilli claims to be one of them.
www.quora.com/Why-do-successful-geeky-white-men-have-Asian-wives-This-seems-to-be-the-norm-in-Silicon-Valley suggests it is just an statistical inevitability.
Ciro Santilli's joke version of the Chinese Four Treasures of the Study!In the past, Ciro used to use file managers, which would be the fourth tresure. But he stopped doing so for years due to his cd alias... so it became three. He actually had exactly three windows open when he was checking if there was anything else he could not open hand of.
- web browser
- Text editor
- terminal. Though to be honest, circa 2022, Ciro learned of the ctrl + click to open file (including with file.c:123 line syntax) ability of Visual Studio Code (likely present in other IDEs), and he was starting considering dumping the terminal altogether if some implementation gets it really really right. The main thing is that it can't be a tinny little bar at the bottom, it has to be full window and super easily toggleable!
The three Treasures of the Programmer
. Featuring: Gvim, tmux running in GNOME terminal, and Chromium browser on Ubuntu 22.04. The minimized windows are for demonstration purposes, Cirism mandates that all windows shall be maximized at all times. Splits withing a single program are permitted however.Bought May 2024 to be my clean crypto-only computer. Searched for cheapest 1 TB disk 16 GB RAM not too old on Amazon with Ubuntu certification, and that was it at £479.00.
Some reviews:
OPSEC: will run only cryptocurrency wallets and nothing else. Will connect to Internet, but never ever to a non clean USB flash drive.
Bootstrap OPSEC:It must have taken about one week running full time to sync the Monero blockchain which at the time was at about 3.1M blocks! I checked on system explorer, and CPU and internet usage was never maxed out, suggesting simply slow network. But the computer still overheated quite a bit and froze a few times.
- turn on from factory, start Windows 11 Home 23H2 build 22631.2715, connect to home Wifi during setup process. Considered skipping WiFi, but I'll want to download the Ubuntu ISO later on anyways answers.microsoft.com/en-us/windows/forum/all/bypass-lets-connect-you-to-a-network/2ce188f6-1b28-45a0-97d2-bfccfa3c9188. Don't sign in to online Windows account, and turn off all spyware requests.
- on preinstalled Edge browser, download Ubuntu 24.04 ISO from ubuntu.com, check sha256 with
Get-FileHashon powershell even though that is pointless security.stackexchange.com/questions/1687/does-hashing-a-file-from-an-unsigned-website-give-a-false-sense-of-security, download balenaEtcher portable from etcher.balena.io/ (currently recommended burner at ubuntu.com/download/desktop#how-to-install) from etc, and burn Ubuntu into a SanDisk Ultra Flair 64 GB - install Ubuntu from USB flash. No internet connection initially, default everything.
- notice that Ubuntu 24.04 is too broken, install Ubuntu 22.04.4 on the previously used USB from Ubuntu, and then install 22.04 instead... minimal installation, encrypted ZFS
- Ubuntu 24.04 "The application files has closed unexpectedly". This likely terminated uncompression of the bz2 halfway, and led to a corrupted monerod...
- askubuntu.com/questions/15520/how-can-i-tell-ubuntu-to-do-nothing-when-i-close-my-laptop-lid fix the eternal laptop lid issue without GUI solution...
- copy view only wallet private key by takinga picture of the QR code with Android cell phone. This gives it to the CIA immediately, but that's fine as we're going to publish it publicly.
Aaron, Ciro Santilli will complete your quest to make eduction free. Just legally this time, with the and with the Creative Commons license you helped to create.
Ciro likes how The Internet's Own Boy (2014) explains how Aaron felt like high school was bullshit, and that he could learn whatever he wanted from books, which is one of Ciro's key feelings.
Huge interest overlap with Ciro Santilli, e.g. he's into
- molecular biology in general: I should have loved biology by James Somers
- JCVI-syn3.0: www.newyorker.com/magazine/2022/03/07/a-journey-to-the-center-of-our-cells
- cryo-EM: www.newyorker.com/magazine/2022/03/07/a-journey-to-the-center-of-our-cells
- David Goodsell: www.newyorker.com/magazine/2022/03/07/a-journey-to-the-center-of-our-cells
- History of Google: www.newyorker.com/magazine/2018/12/10/the-friendship-that-made-google-huge
github.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.This resonates a lot with Ciro Santilli's ideas!
- physics and the illusion of life
- physics education needs more focus on understanding experiments and their history:
- Education is broken
- molecular biology feels like systems programming
I've never come across a subject so fractal in its complexity. It reminds me of computing that way.
E. Coli Whole Cell Model by Covert Lab Install and first run by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16At 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 Pinned article: 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 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. Web editor. 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.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. 
- 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