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.
Multiomics Updated 2025-07-16
Integrating multiple omics, comes quite close to whole cell simulation.
Not the usual bullshit you were expecting from the philosophy of Science, right?
Some notable quoters:
Ron Maimon Updated 2025-07-26
Ron is mostly known for simultaneously:
Ron seems to share a few philosophies which Ciro greatly agrees with as part of Cirism, which together with his knowledge of physics, make Ciro greatly respect Ron. Such philosophies include:
However he also subscribes to some theories which Ciro Santilli considers conspiracy theories, e.g. his ideas about the Boston Marathon bombing that got him banned from Quora (a ban which Ciro strongly opposes due to freedom of speech concerns!), but the physics might be sound, Ciro Santilli does not know enough physics to judge, but it often feels that what he says makes sense.
chat.stackexchange.com/transcript/message/7104585#7104585 mentions that he was at Cornell University and did all but dissertation, but he mentions that he was still self-taught:
Eugene Seidel: On your personal info page you write that you are not a physics Ph.D. but does that mean you were a physics undergrad in college then went to grad school and finished ABD... or are you entirely self taught?
Ron Maimon: ABD. I am self- taught though, I only went to school for accreditation. I had a thesis worth of work at the time I left grad-school,
Eugene Seidel: ok thanks
Ron Maimon: I was just kind of sickened by academic stuff that was going on--- large extra dimensions were popular then.
Eric Walker: Anyway, thanks Ron -- I'll get back to you with more questions soon, I'm sure.
Ron Maimon: Also I was at Cornell, my advisor left for Cincinnatti, and I was not in very good standing there (I was kind of a jerk, as I still am). Some friends wanted to start a biotech company called "Gene Network Sciences", and I joined them.
This is corroborated e.g. at: web.archive.org/web/20201226171231/http://pages.physics.cornell.edu/~gtoombes/Student_Index.html (original pages.physics.cornell.edu/~gtoombes/Student_Index.html down as of 2023).
Bibliography:
Backlinks:
Video 1.
Ron Maimon interview with Jeff Meverson (2014)
Source. Ripped from Jeff's "Quoracast": player.fm/series/quoracast-podcast/ron-maimon-truther Ron mentions he was an early-Usenet user. Key points:
Systems biology Updated 2025-07-16
Studies biology from a more global point of view, if putting all little pieces of an organism make up the final biological function.
Whole cell simulation Updated 2025-07-16
Ciro Santilli started taking some notes at: github.com/cirosantilli/awesome-whole-cell-simulation. but they are going to be all migrated here.
It is interesting to note how one talks about single cell analysis, in contrast to whole cell simulation: experimentally it is hard to analyse a single cell. But theoretically, it is hard to simulate a single cell. This mismatch is perhaps the ultimate frontier of molecular biology.
Video 1.
A Computational Whole-Cell Model Predicts Genotype From Phenotype by Markus Covert (2013)
Source.