Ciro Santilli @cirosantilli 40

www.gelifesciences.com/en/us/shop/protein-analysis/protein-sample-preparation/protein-enrichment/magrack-6-p-05761 (archive).

www.bidspotter.com/en-us/auction-catalogues/bscsur/catalogue-id-bscsur10011/lot-c6605b41-1a14-40e5-a255-a5c5000866e0 (archive) Cannot exact same product on official website, but here is a similar one: www.fishersci.co.uk/shop/products/lm-26-2uv-transilluminator/12382038 (archive).

PuntSeq is a side project led by a few University of Cambridge PhDs that aims to determine which bacteria are present in the River Cam.

In July 2019, the PuntSeq team got together with the awesome Cambridge Biomakespace, an awesome biology makerspace open to all, to create a two day science outreach activity showing their procedures.

The data collected in this experiment, together with other collection sessions done by the organizers actually led to a publication on eLife: elifesciences.org/articles/61504 "Freshwater monitoring by nanopore sequencing" by Lara Urban et al. (2021), so it is awesome to see that were are actual being part of "real science".

Ciro knows nothing about biology, but since he is very curious about it, he jumped at this opportunity, and decided to document things as well as his limited knowledge would allow.

All participants chipped in some money to help cover the experiment's costs. Ciro suspects that this activity was done partially to help crowdfund the experiment, but it was a worthy investment!

The impressions you get from the experiment as a software engineer will be:

Because Ciro's a software engineer, and he's done enough staring in computers for a lifetime already, and he believes in the power of Git, he didn't pay much attention to this part ;-)

According to the eLife paper, the code appears to have been uploaded to: github.com/d-j-k/puntseq. TODO at least mention the key algorithms used more precisely.

Ciro can however see that it does present interesting problems!

Because it was necessary to wait for 2 days to get our data, the workshop first reused sample data from previous collections done earlier in the year to illustrate the software.

First there is some signal processing/machine learning required to do the base calling, which is not trivial in the Oxford Nanopore, since neighbouring bases can affect the signal of each other. This is mostly handled by Oxford Nanopore itself, or by hardcore programmers in the field however.

After the base calling was done, the data was analyzed using computer programs that match the sequenced 16S sequences to a database of known sequenced species.

This is of course not just a simple direct string matching problem, since like any in experiment, the DNA reads have some errors, so the program has to find the best match even though it is not exact.

The PuntSeq team would later upload the data to well known open databases so that it will be preserved forever! When ready, a link to the data would be uploaded to: www.puntseq.co.uk/data

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".

Lit: fish timber question answer.

On Baidu Baike: baike.baidu.com/item/渔樵问答/336905

The dialog is also known as allegory for an incredibly deep philosophical discussion between an idealized wise woodcutter and a fisherman, e.g. mentioned at: www2.kenyon.edu/Depts/Religion/Fac/Adler/Writings/Fisherman%20and%20Woodcutter.pdf

This song is just too slow for Ciro Santilli to make much out of it.

Bibliography:

Reaches 2 mK^[ref]. youtu.be/upw9nkjawdy?t=487 from Video "Building a quantum computer with superconducting qubits by Daniel Sank (2019)" mentions that 15 mK are widely available.

Used for example in some times of quantum computers, notably superconducting quantum computers. As mentioned at: youtu.be/uPw9nkJAwDY?t=487, in that case we need to go so low to reduce thermal noise.

Ideally can be thought of as a one-way ticket gate that only lets electrons go in one direction with zero resistance! Real devices do have imperfections however, so there is some resistance.

First they were made out of vacuum tubes, but later semiconductor diodes were invented and became much more widespread.