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. 
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 runDefault mathematics typesetting used in OurBigBook Markup.
Key issues:
- github.com/KaTeX/KaTeX/issues/2228
newcommanddid not support optional arguments
Their crash system does not have an amazing user interface.
Tested on Ubuntu 21.10.
After something crashes, look under
/var/crash for a crash file, which helps to determine which package to report under on Launchpad.E.g. a file
/var/crash/_usr_sbin_gdm3.0.crash makes you want to file the bug under gdm at: bugs.launchpad.net/ubuntu/+source/gdm/+filebugThen, while reporting the bug, you want to give the developpers access to that Ubuntu's crash report system has already uploaded the
.crash file. But you can't publicly upload it because it contains memory dumps and could contain secret information. The way to do it is to look at the ID under:sudo cat /var/crash/_usr_sbin_gdm3.0.uploaded.crash for you, so you just have to confirm it and give the ID on the ticket.You can view a list of all your uploaded errors at:and each of those contain a link to:which you yourself cannot see.
xdg-open https://errors.ubuntu.com/user/$(sudo cat /var/lib/whoopsie/whoopsie-id)https://errors.ubuntu.com/oops/<.uloaded error id>askubuntu.com/questions/434431/how-can-i-read-a-crash-file-from-var-crash asks how to read the
.crash files.Running:splits it up into a few files, but does not make any major improvements.
sudo apport-unpack /var/crash/_usr_sbin_gdm3.0.crash /tmp/appapport-retracesudo apt install apport-retrace
sudo chmod 666 /var/crash/_usr_sbin_gdm3.0.crash
apport-retrace -g /var/crash/_usr_sbin_gdm3.0.crashTried:but then
echo "deb http://ddebs.ubuntu.com $(lsb_release -cs) main restricted universe multiverse" | sudo tee -a /etc/apt/sources.list.d/ddebs.list
echo -e "deb http://ddebs.ubuntu.com $(lsb_release -cs)-updates main restricted universe multiverse\ndeb http://ddebs.ubuntu.com $(lsb_release -cs)-proposed main restricted universe multiverse" | sudo tee -a /etc/apt/sources.list.d/ddebs.list
sudo apt install ubuntu-dbgsym-keyringsudo apt update fails with:E: The repository 'http://ddebs.ubuntu.com impish-security Release' does not have a Release file.Please refer to Video "Linus Torvalds saying "Nvidia Fuck You" (2012)".
Does not happen every time, only some times. Can't figure out why. Usually happens when has suspended for a longer time.
bugs.launchpad.net/ubuntu/+source/nvidia-graphics-drivers-470/+bug/1946303 sounds like a likely report, Nvidia driver version 470, but can't find those error messages anywhere. The last line of:once was:which is when sleep starts.
journalctl -o short-precise -k -b -1PM: suspend entry (deep)This suggests that it is not a video bug then, seems that it is not waking up at all? Gotta try to SSH into it. OK. I did SSH into it, and that was fine, so it is just the video that won't start.
PM: suspend exitbugs.launchpad.net/ubuntu/+source/linux/+bug/1949977 is another possible bug, based on kernel version. I'm running 5.13, which is one of the failing versions on the report. Can't find any interesting dmesg though.
In another crash:had the following interesting lines:and there was a corresponding
journalctl -o short-precise -k -b -1nvidia-modeset: WARNING: GPU:0: Lost display notification (0:0x00000000); continuing.
[24307.640014] NVRM: GPU at PCI:0000:01:00: GPU-18af74bb-7c72-ff70-e447-87d48378ea20
[24307.640018] NVRM: Xid (PCI:0000:01:00): 79, pid=8828, GPU has fallen off the bus.
[24307.640021] NVRM: GPU 0000:01:00.0: GPU has fallen off the bus.
[24328.054022] nvidia-modeset: ERROR: GPU:0: The requested configuration of display devices (LGD (DP-4)) is not supported on this GPU.
[repeats several more times]
[24328.056767] nvidia-modeset: ERROR: GPU:0: The requested configuration of display devices (LGD (DP-4)) is not supported on this GPU.
[24328.056951] nvidia-modeset: ERROR: GPU:0: Failed to query display engine channel state: 0x0000927c:0:0:0x0000000f
[24328.056955] nvidia-modeset: ERROR: GPU:0: Failed to query display engine channel state: 0x0000927c:1:0:0x0000000f
[24328.056959] nvidia-modeset: ERROR: GPU:0: Failed to query display engine channel state: 0x0000927c:2:0:0x0000000f
[24328.056962] nvidia-modeset: ERROR: GPU:0: Failed to query display engine channel state: 0x0000927c:3:0:0x0000000f
[24328.056983] nvidia-modeset: ERROR: GPU:0: DP-4: Failed to disable DisplayPort audio stream-0
[24328.056992] nvidia-modeset: ERROR: GPU:0: Failed to query display engine channel state: 0x0000947d:0:0:0x0000000f/var/crash/_usr_sbin_gdm3.0.crash.Related "GPU has fallen off the bus": askubuntu.com/questions/868321/gpu-has-fallen-off-the-bus-nvidia
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.
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