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E. Coli Whole Cell Model by Covert Lab by

Ciro Santilli 37 Updated 2025-07-16

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.

Eigenvalues and eigenvectors by

Ciro Santilli 37 Updated 2025-07-16

Applications of eigenvalues and eigenvectors by

Ciro Santilli 37 Updated 2025-07-16

Eigendecomposition of a real symmetric matrix by

Ciro Santilli 37 Updated 2025-07-16

The general result from eigendecomposition of a matrix:

M = Q D Q^{- 1}

becomes:

M = O D O^{T}

(2)

where

O

is an orthogonal matrix, and therefore has

O^{- 1} = O^{T}

Dense and sparse matrices by

Ciro Santilli 37 Updated 2025-07-16

A good definition is that the sparse matrix has non-zero entries proportional the number of rows. Therefore this is Big O notation less than something that has

N^{2}

non zero entries. Of course, this only makes sense when generalizing to larger and larger matrices, otherwise we could take the constant of proportionality very high for one specific matrix.

Of course, this only makes sense when generalizing to larger and larger matrices, otherwise we could take the constant of proportionality very high for one specific matrix.

Symmetric matrix by

Ciro Santilli 37 Updated 2025-07-16

A matrix that equals its transpose:

M = M^{T}

Can represent a symmetric bilinear form as shown at matrix representation of a symmetric bilinear form, or a quadratic form.

Skew-symmetric matrix by

Ciro Santilli 37 Updated 2025-07-16

WTF is a skew? "Antisymmetric" is just such a better name! And it also appears in other definitions such as antisymmetric multilinear map.

Academic publishing is broken by

Ciro Santilli 37 Updated 2025-07-16

experimentalhistory.substack.com/p/the-rise-and-fall-of-peer-review The rise and fall of peer review by Adam Mastroianni (2022)

One of the most beautiful things is how they paywall even public domain works. E.g. here: www.nature.com/articles/119558a0 was published in 1927, and is therefore in the public domain as of 2023. But it is of course just paywalled as usual throughout 2023. There is zero incentive for them to open anything up.

Video 1.

What they don't tell you about academic publishing by Andy Stapleton (2021)

Source.

Video 2.

The publishing scandal happening right now by Andy Stapleton (2023)

Source. TOOD get the name of the academic who quit.

Change of basis between symmetric matrices by

Ciro Santilli 37 Updated 2025-07-16

When we have a symmetric matrix, a change of basis keeps symmetry iff it is done by an orthogonal matrix, in which case:

N = BM B^{- 1} = OM O^{T}

Tensor product by

Ciro Santilli 37 Updated 2025-07-16

First public announcement of Bitoin by

Ciro Santilli 37 Updated 2025-07-16

www.metzdowd.com/pipermail/cryptography/2008-October/014810.html

bit gold by

Ciro Santilli 37 Updated 2025-07-16

Scalar (mathematics) by

Ciro Santilli 37 Updated 2025-07-16

A member of the underlying field of a vector space. E.g. in

R^{3}

, the underlying field is

R

, and a scalar is a member of

R

, i.e. a real number.

Raised and lowered indices by

Ciro Santilli 37 Updated 2025-07-16

TODO what is the point of them? Why not just sum over every index that appears twice, regardless of where it is, as mentioned at: www.maths.cam.ac.uk/postgrad/part-iii/files/misc/index-notation.pdf.

Vectors with the index on top such as

x^{i}

are the "regular vectors", they are called covariant vectors.

Those in indices on bottom are called contravariant vectors.

It is possible to change between them by Raising and lowering indices.

The values are different only when the metric signature matrix is different from the identity matrix.

Raising and lowering indices by

Ciro Santilli 37 Updated 2025-07-16

d'Alembert operator in Einstein notation by

Ciro Santilli 37 Updated 2025-07-16

Given the function

ψ

ψ : R^{4} \to C

the operator can be written in Planck units as:

\partial_{i} \partial^{i} ψ (x_{0}, x_{1}, x_{2}, x_{3}) - m^{2} ψ (x_{0}, x_{1}, x_{2}, x_{3}) = 0

(2)

often written without function arguments as:

\partial_{i} \partial^{i} ψ

(3)

Note how this looks just like the Laplacian in Einstein notation, since the d'Alembert operator is just a generalization of the laplace operator to Minkowski space.

Symmetry by

Ciro Santilli 37 Updated 2025-07-16

Directly modelled by group.

For continuous symmetries, see: Lie group.

Important discrete mathematical group by

Ciro Santilli 37 Updated 2025-07-16

The direct product of two cyclic groups of coprime order is another cyclic group by

Ciro Santilli 37 Updated 2025-07-16

You just map the value (1, 1)

C_{m} \times C_{n}

to the value 1 of

C_{mn}

, and it works out. E.g. for

C_{2} \times C_{3}

, the group generated by of (1, 1) is:

0 = (0, 0)
1 = (1, 1)
2 = (0, 2)
3 = (1, 0)
4 = (0, 1)
5 = (1, 2)
6 = (0, 0) = 0