Real hardware is for newbs. Real hardware is for newbs.
Tested on Ubuntu 23.10 we approximately follow instructions from: docs.zephyrproject.org/3.4.0/develop/getting_started/index.html stopping before the "Flash the sample" section, as we don't flash QEMU. We just run it.
sudo apt install --no-install-recommends git cmake ninja-build gperf \
ccache dfu-util device-tree-compiler wget \
python3-dev python3-pip python3-setuptools python3-tk python3-wheel xz-utils file \
make gcc gcc-multilib g++-multilib libsdl2-dev libmagic1
python3 -m venv ~/zephyrproject/.venv
source ~/zephyrproject/.venv/bin/activate
pip install west
west init ~/zephyrproject
cd ~/zephyrproject
west update
west zephyr-export
cd ~
wget https://github.com/zephyrproject-rtos/sdk-ng/releases/download/v0.16.1/zephyr-sdk-0.16.1_linux-x86_64.tar.xz
tar xvf zephyr-sdk-0.16.1_linux-x86_64.tar.xz
cd zephyr-sdk-0.16.1
./setup.shThe installation procedure install all compiler toolchains for us, so we can then basically compile for any target. It also fetches the latest Git source code of Zephyr under:
~/zephyrproject/zephyrThe "most default" blinky hello world example which blinks an LED is a bit useless for us because QEMU doesn't have LEDs, so instead we are going to use one of the UART examples which will print characters we can see on QEMU stdout.
Let's start with the hello world example on an x86 target:and it outputs:The
cd ~/zephyrproject/zephyr
west build -b qemu_x86 samples/hello_world -t runHello World! qemu_x86qemu_x64 on the output comes from the CONFIG_BOARD macro github.com/zephyrproject-rtos/zephyr/blob/c15ff103001899ba0321b2c38013d1008584edc0/samples/hello_world/src/main.c#L11#include <zephyr/kernel.h>
int main(void)
{
printk("Hello World! %s\n", CONFIG_BOARD);
return 0;
}The
qemu_x86 board is documented at: docs.zephyrproject.org/3.4.0/boards/x86/qemu_x86/doc/index.htmlYou can also first
cd into the directory that you want to build in to avoid typing samples/hello_world all the time:cd ~/zephyrproject/zephyr/samples/hello_world
zephyr west build -b qemu_x86 -t runYou can also build and run separately with:
west build -b qemu_x86
west build -t runAnother important option is:But note that it does not modify your
west build -t menuconfigprj.conf automatically for you.Let's try on another target:and same output, but on a completely different board! The
rm -rf build
zephyr west build -b qemu_cortex_a53 -t runqemu_cortex_a53 board is documented at: docs.zephyrproject.org/3.4.0/boards/arm64/qemu_cortex_a53/doc/index.htmlThe list of all examples can be seen under:which for example contains:
ls ~/zephyrproject/zephyr/sampleszephyrproject/zephyr/samples/hello_worldSo run another sample simply select it, e.g. to run
zephyrproject/zephyr/samples/synchronization:west build -b qemu_cortex_a53 samples/synchronization -t run E. Coli Whole Cell Model by Covert Lab by 
Ciro Santilli 35 Updated 2025-04-24 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-04-24 +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.
The fact that this foundation has a bunch of paid, closed, certification courses makes Ciro Santilli not respect them at all. They should be making open access content instead!
E. Coli Whole Cell Model by Covert Lab Condition by Ciro Santilli 35 Updated 2025-04-24 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-04-24 +Created 1970-01-01reconstruction/ecoli/flat/condition/nutrient/minimal.tsvcontains the nutrients in a minimal environment in which the cell survives:If we compare that to"molecule id" "lower bound (units.mmol / units.g / units.h)" "upper bound (units.mmol / units.g / units.h)" "ADP[c]" 3.15 3.15 "PI[c]" 3.15 3.15 "PROTON[c]" 3.15 3.15 "GLC[p]" NaN 20 "OXYGEN-MOLECULE[p]" NaN NaN "AMMONIUM[c]" NaN NaN "PI[p]" NaN NaN "K+[p]" NaN NaN "SULFATE[p]" NaN NaN "FE+2[p]" NaN NaN "CA+2[p]" NaN NaN "CL-[p]" NaN NaN "CO+2[p]" NaN NaN "MG+2[p]" NaN NaN "MN+2[p]" NaN NaN "NI+2[p]" NaN NaN "ZN+2[p]" NaN NaN "WATER[p]" NaN NaN "CARBON-DIOXIDE[p]" NaN NaN "CPD0-1958[p]" NaN NaN "L-SELENOCYSTEINE[c]" NaN NaN "GLC-D-LACTONE[c]" NaN NaN "CYTOSINE[c]" NaN NaNreconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv, we see that it adds the 20 amino acids on top of the minimal condition:so we guess that"L-ALPHA-ALANINE[p]" NaN NaN "ARG[p]" NaN NaN "ASN[p]" NaN NaN "L-ASPARTATE[p]" NaN NaN "CYS[p]" NaN NaN "GLT[p]" NaN NaN "GLN[p]" NaN NaN "GLY[p]" NaN NaN "HIS[p]" NaN NaN "ILE[p]" NaN NaN "LEU[p]" NaN NaN "LYS[p]" NaN NaN "MET[p]" NaN NaN "PHE[p]" NaN NaN "PRO[p]" NaN NaN "SER[p]" NaN NaN "THR[p]" NaN NaN "TRP[p]" NaN NaN "TYR[p]" NaN NaN "L-SELENOCYSTEINE[c]" NaN NaN "VAL[p]" NaN NaNNaNin theupper moundlikely means infinite.We can try to understand the less obvious ones:ADP: TODOPI: TODOPROTON[c]: presumably a measure of pHGLC[p]: glucose, this can be seen by comparingminimal.tsvwithminimal_no_glucose.tsvAMMONIUM: ammonium. This appears to be the primary source of nitrogen atoms for producing amino acids.CYTOSINE[c]: hmmm, why is external cytosine needed? Weird.
reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/contains sequences of conditions for each time. For example:reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000000_basal.tsvcontains:which means just using"time (units.s)" "nutrients" 0 "minimal"reconstruction/ecoli/flat/condition/nutrient/minimal.tsvuntil infinity. That is the default one used byrunSim.py, as can be seen from./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Environment/attributes/nutrientTimeSeriesLabelwhich contains just000000_basal.reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000001_cut_glucose.tsvis more interesting and contains:so we see that this will shift the conditions half-way to a condition that will eventually kill the bacteria because it will run out of glucose and thus energy!"time (units.s)" "nutrients" 0 "minimal" 1200 "minimal_no_glucose"
Timeseries can be selected with--variant nutrientTimeSeries X Y, see also: run variants.We can use that variant with:VARIANT="condition" FIRST_VARIANT_INDEX=1 LAST_VARIANT_INDEX=1 python runscripts/manual/runSim.pyreconstruction/ecoli/flat/condition/condition_defs.tsvcontains lines of form:"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"]conditionrefers to entries inreconstruction/ecoli/flat/condition/condition_defs.tsvnutrientsrefers to entries underreconstruction/ecoli/flat/condition/nutrient/, e.g.reconstruction/ecoli/flat/condition/nutrient/minimal.tsvorreconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsvgenotype perturbations: there aren't any in the file, but this suggests that genotype modifications can also be incorporated heredoubling time: TODO experimental data? Because this should be a simulation output, right? Or do they cheat and fix doubling by time?active TFs: this suggests that they are cheating transcription factors here, as those would ideally be functions of other more basic inputs
E. Coli Whole Cell Model by Covert Lab Default run variant by Ciro Santilli 35 Updated 2025-04-24 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-04-24 +Created 1970-01-01The default run variant, if you don't pass any options, just has the minimal growth conditions set. What this means can be seen at condition.
Notably, this implies a growth medium that includes glucose and salt. It also includes oxygen, which is not strictly required, but greatly benefits cell growth, and is of course easier to have than not have as it is part of the atmosphere!
But the medium does not include amino acids, which the bacteria will have to produce by itself.
First let's discuss the argument against abortion. Most people would save the life of an infant over that of an animal, even if the animal is more intelligent. The only unbiased reason to do this is that given nutrients, the baby will develop into a more intelligent lifeform in the future. Thus wanting to save a "clump of cells" isn't as irrational as it may seem.
But our hypothetical above assumes that both the baby and the animal want to live. By not killing themselves, all conscious creatures have implicitly expressed their desire to continue living, and most people agree that that is to be respected, at least for humans. Which is why killing a person painlessly while they're unconscious is still considered wrong. But this desire does not apply to fetuses before the third trimester, which have never been conscious. This is the moral argument for abortion. There is also the obvious utilitarian argument for it.
What if a resource is limited within a region? For example, water? by 
Libertarianism FAQ 0 1970-01-01
Libertarianism FAQ 0 1970-01-01Today, shipping costs are so low (eg., $0.50 per kg for US-China shipments) that for most goods, the market is global.
But what if the main water supply in a region is owned by a single entity, and they charge exorbitant prices? Unlike food, bringing in water from faraway regions would be too expensive. Of course, people moving out would result in the entity going out of business and selling the water supply to someone more rational, but due to various reasons, moving out isn't always easy.
Here's the true solution. Currently, the water supply in most countries is owned by the government. Upon transition to libertarianism, the water supply in each region would simply be an entity with ownership distributed among the residents. If some of them sell their shares of the water supply to a company that then jacks up the prices, they'll have to move out, but that is simply them facing the consequences of risking putting their water supply in another's hands.
What if the water supply was sold by the government to a private entity currently subject to regulations? Would a libertarian transition remove those regulations? Note that this situation is caused by having to transition from big government to libertarianism. If a libertarian society arose naturally, rights to natural resources would be distributed among the community via the principle of homesteading. And as before, anyone selling their rights must be moving or have another source ready, othewise accept the potential consequences.
To fix the issues caused by a non-libertarian government, non-libertarian measured may be needed. The government had no right to the water, nor to sell it to the private entity. It may need to be taken back.
E. Coli Whole Cell Model by Covert Lab Publications by Ciro Santilli 35 Updated 2025-04-24 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-04-24 +Created 1970-01-01Unfortunately, due to lack of one page to rule them all, the on-Git tree publication list is meager, some of the most relevant ones seems to be:
- 2021 open access review paper: journals.asm.org/doi/full/10.1128/ecosalplus.ESP-0001-2020 "The E. coli Whole-Cell Modeling Project". They should just past that stuff in a README :-) The article mentions that it is a follow up to the previous M. genitalium whole cell model by Covert lab. Only 43% of known genes modelled at this point however, a shame.
- 2020 under Science paywall: www.science.org/doi/10.1126/science.aav3751 "Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation"
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