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.
Big excitement picture at: molecular biology technologies.
For some reason, this is one of the things that makes Ciro Santilli want to puke the most. More than surgery or blood.
One of the sequencers made by Oxford Nanopore Technologies.
The device has had several updates since however, notably of the pore proteins which are present in the critical flow cell consumable.
Official documentation: nanoporetech.com/products/minion (archive)
The following images of the device and its peripherals were taken during the experiment: Section "How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it".
Top view of a closed Oxford Nanopore MinION
. Source. 
Side view of an Oxford Nanopore MinION
. Source. 
Top view of an open Oxford Nanopore MinION
. Source. 
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Why Oxford Nanopore was used instead of Illumina for the sequencing by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16At the time of the experiment, Illumina equipment was cheaper per base pair and dominates the human genome sequencing market, but it required a much higher initial investment for the equipment (TODO how much).
The reusable Nanopore device costs just about 500 dollars, and about 500 dollars (50 unit volume) for the single usage flow cell which can decode up to 30 billion base pairs, which is about 10 human genomes 1x! Note that 1x is basically useless for one of the most important of all applications of sequencing: detection of single-nucleotide polymorphisms, since the error rate would be too high to base clinical decisions on.
Compare that to Illumina which is currently doing about an 1000 dollar human genome at 30x, and a bit less errors per base pair (TODO how much).
Other advantages of the MinION over Illumina which didn't really matter to this particular experiment are:
- portability for e.g. to do analysis on the field near infections outbreaks. Compare that to the smallest Illumina sequencer currently available in 2019, the iSeq 100: Figure 1. "Illumina iSeq 100 DNA sequencer".
- long reads which can be necessary for long repetitive regions, see also: Section "Sequence alignment"
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-pyelftools
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- 2024 www.uktech.news/foodtech/alternative-meat-research-centre-20240829A research centre examining the implementation of alternatives to meat, backed by £38m, will be launched by the University of Leeds.
- 2024 techcrunch.com/2024/08/04/even-after-1-6b-in-vc-money-the-lab-grown-meat-industry-is-facing-massive-issues/ "Even after $1.6B in VC money, the lab-grown meat industry is facing 'massive' issues"
- www.reuters.com/markets/commodities/hoxton-farms-raises-22-million-cultivated-animal-fat-2022-10-20/ Hoxton Farms, cultured animal fat
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