Program Raspberry Pi Pico W with MicroPython code from the command line Updated 2025-07-16
Program the Raspberry Pi Pico W with MicroPython from Thonny Updated 2025-07-16
Raspberry Pi Pico W MicroPython example Updated 2025-07-27
An upstream repo at: github.com/raspberrypi/pico-micropython-examples
Some generic Micropython examples most of which work on this board can be found at: Section "MicroPython example".
The examples can be run as described at Program Raspberry Pi Pico W with MicroPython.
- rpi-pico-w/upython/led_on.py: turn on-board LED on and leave it on forever. Useful to quickly check that you are still able to update the firmware.
- rpi-pico-w/upython/led_off.py: turn on-board LED off and leave it off forever
- rpi-pico-w/upython/pwm.py: pulse width modulation. Using the same circuit as the rpi-pico-w/upython/blink_gpio.py, you will now see the external LED go from dark to bright continuously and then back
Double bond Updated 2025-07-16
Triple bond Updated 2025-07-16
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Pre-sequencing preparation Updated 2026-08-21
One cool thing we did in this procedure was to use magnetic separation with magnetic beads to further concentrate the DNA: Figure 1. "GE MagRack 6 pipetting.".
The beads are coated to stick to the DNA, which allows us to easily extract the DNA from the rest of the solution. This is cool, but bio people are borderline obsessed by those beads! Go figure!
Then we prepared the DNA for sequencing with the Oxford Nanopore specific part: Oxford Nanopore SQK-LSK109 Ligation Sequencing Kit.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Using the Oxford Nanopore Updated 2026-08-21
With all this ready, we opened the Nanopore flow cell, which is the 500 dollar consumable piece that goes in the sequencer.
We then had to pipette the final golden Eppendorf into the flow cell. My anxiety levels were going through the roof: Figure 4. "Oxford nanopore MinION flow cell pipette loading.".
At this point bio people start telling lab horror stories of expensive solutions being spilled and people having to recover them from fridge walls, or of how people threw away golden Eppendorfs and had to pick them out of trash bins with hundreds of others looking exactly the same etc. (but also how some discoveries were made like this). This reminded Ciro of: youtu.be/89UNPdNtOoE?t=919 Alfred Maddock's plutonium spill horror story.
Luckily this time, it worked out!
As can be seen from Video 1. "Oxford Nanopore MinION software channels pannel on Mac." the software tells us which pores are still working.
Pores go bad sooner or later randomly, until there are none left, at which point we can stop the process and throw the flow cell away.
48 hours was expected to be a reasonable time until all pores went bad, and so we called it a day, and waited for an email from the PuntSeq team telling us how things went.
We reached a yield of 16 billion base pairs out of the 30Gbp nominal maximum, which the bio people said was not bad.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Qiagen DNeasy PowerWater Kit Updated 2026-08-21
www.qiagen.com/gb/products/discovery-and-translational-research/dna-rna-purification/dna-purification/microbial-dna/dneasy-powerwater-kit (archive) Here is its documentation: www.qiagen.com/gb/resources/download.aspx?id=bb731482-874b-4241-8cf4-c15054e3a4bf&lang=en (archive).
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Qiagen QIAquick PCR Purification Kit Updated 2025-07-16
www.qiagen.com/us/products/discovery-translational-research/dna-rn-a-purification/dna-purification/dna-clean-up/qiaquick-pcr-purification-kit/#orderinginformation (archive)
Manual archive: web.archive.org/web/20190911100243/https://www.qiagen.com/us/resources/download.aspx?id=e0fab087-ea52-4c16-b79f-c224bf760c39&lang=en
Removes PCR byproducts from purified DNA.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Oxford Nanopore SQK-LSK109 Ligation Sequencing Kit Updated 2025-07-16
Repairs the ends of DNA, and also attaches an adapter protein to the DNA that makes them go through the pores of e.g. an Oxford Nanopore MinION.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it PCR verification with gel electrophoresis Updated 2026-08-21
For this reason, it is wise to verify that certain steps are correct whenever possible.
Gel electrophoresis separates molecules by their charge-to-mass ratio. It is one of those ultra common lab procedures!
Since we know that we amplified the 16S regions which we know the rough size of (there might be a bit of variability across species, but not that much), we were expecting to see a big band at that size.
And that is exactly what we saw!
First we had to prepare the gel, put the gel comb, and pipette the samples into wells present in the gel:
To see the DNA, we added ethidium bromide to the samples, which is a substance that that both binds to DNA and is fluorescent.
Because it interacts heavily with DNA, ethidium bromide is a mutagen, and the biology people sure did treat the dedicated electrophoresis bench area with respect! Figure 4. "Gel electrophoresis dedicated bench area to prevent ethidium bromide contamination.".
Gel electrophoresis dedicated waste bin for centrifuge tubes and pipette tips contaminated with ethidium bromide.
Source. The UV transilluminator we used to shoot UV light into the gel was the Fisher Scientific UVP LM-26E Benchtop 2UV Transilluminator. The fluorescent substance then emitted a light we can see.
As barely seen at Figure 8. "Fischer Scientific UVP LM-26E Benchtop 2UV Transilluminator illuminated gel." due to bad photo quality due to lack of light, there is one strong green line, which compared to the ladder matches our expected 16S length. What we saw it with the naked eyes was very clear however.
At 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"
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