Ciro Santilli @cirosantilli 35

As claimed on their README, their operation truly appears to be 10x faster than the node-sqlite package!! It is insane!! How can that other package still exist at all?

The only big problem was the lack of ORM, but people are looking into that by adding it to Sequelize:

OpenNMT CLI front-end.

Hello world: askubuntu.com/questions/380847/is-it-possible-to-translate-words-via-terminal/1309774#1309774

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.

www.fishersci.no/shop/products/nalgene-polysulfone-reusable-bottle%20-top-filters/10465781 (archive)

This is where we poured the water. It was not large enough for the entire 1L sample, so we had to do it a few times.

www.knfusa.com/en/laboport/ (archive).

biochromspectros.com/spectrophotometers/simplinano-cat/simplinano-spectrophotometer.html (archive)

Manual: biochromspectros.com/media/wysiwyg/support_page/support-simplinano/Simplinano-UM.pdf (archive)

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:

They are not public in any meaningful modern sense, just like "public universities" in the United Kingdom: are public universities in the UK owned by the Government?.

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!

We then just had to connect the MinION to the computer, and wait for 2 days.

During this time, the DNA would be sucked through the pores.

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.

The first/only way Ciro could find was with ampy: stackoverflow.com/questions/74150782/how-to-run-a-micropython-host-script-file-on-the-raspbery-pi-pico-from-the-host/74150783#74150783 That just worked and it worked perfectly!

TODO: possible with rshell?

Examples at: Raspberry Pi Pico W MicroPython example.

This section is about partial implementations that are only able to read the blocks, ususally coming from Bitcoin Core, to interpret the data: