Ciro Santilli @cirosantilli 37

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.

Keep the example/theory ratio high, very, very high.

For natural sciences, add as many reproducible experiment images/videos/descriptions as you can.

Tell students to:

Praise those that do this very highly, and give them better grades if you have that superpower.

This is part of a larger concept Ciro Santilli holds dear: don't just consume, but also produce.

Whatever you do, even if it is playing video games: if you manage to produce related content that will interest other people, and possibly allow you to get paid, it will much much fun to do that thing.

If you give a course in a classroom, you reach 10 people (the others were sleeping).

If you make a perfect course online, and answer questions online, you reach 10 thousand.

Not doing things online is a waste of time.

You are a highly trained professional, and your time is extremely valuable.

Even if it takes twice as long to create the material than giving course, you are still more efficient by a factor of 500.

It is as if there were 500 little copies of you working full time. It is a superpower.

en.wikipedia.org/wiki/Help:Footnotes#Footnotes:_using_a_source_more_than_once gives the following method:

Definition, anywhere on article, likely ideally as the first usage:

And then you can use it later on as:which automatically expands the exact same thing, or using the shortcut:

To cite multiple pages of a book: en.wikipedia.org/wiki/Wikipedia:Citing_sources#Citing_multiple_pages_of_the_same_source, the best method is to define and use the reference without adding the p or location in cite as:Do not set the page in cite, otherwise it shows up on the references. Instead we use the {{rp}} template. And then use the reference with the {{r}} template as:or for multiple pages:

Circa 2023, the feed is an unbearable list of stupid suggestions, never-ending idiotic memes, and you just end up missing posts you actually care about from people you actually follow.

uk.vwr.com/store/product/8306728/microcentrifuges-ventilated-refrigerated-micro-star-17-17r (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:

Interesting website, hosts mostly:

What's the point of this website vs GitHub? www.reddit.com/r/MLQuestions/comments/ylf4be/whats_the_deal_with_hugging_faces_popularity/

This section is about games initially designed for humans, but which ended up being used in AI development as well, e.g.:

Allow us to determine with good approximation in a multi-electron atom which electron configuration have more energy. It is a bit like the Aufbau principle, but at a finer resolution.

Note that this is not trivial since there is no explicit solution to the Schrödinger equation for multi-electron atoms like there is for hydrogen.

For example, consider carbon which has electron configuration 1s2 2s2 2p2.

If we were to populate the 3 p-orbitals with two electrons with spins either up or down, which has more energy? E.g. of the following two:

This was the pre-Internet precursor of wikis. This program was likely venerable, shame it predates Ciro Santilli's era.

But the thing was much more bloated it seems, and also included visual programming elements, and WYSISYG UI creation.

They put a lot of emphasis into base calling. E.g.:

The normal navigation to them was paywalled, but the static files are served without login checks if you know their URL. One way to go about it is to search by prefix on the Wayback Machine: web.archive.org/web/*/https://www2.physics.ox.ac.uk/sites/default/files/contentblock/2011/06/03/*

The last handbooks we can find are 2020/2021, they might have move to a new more properly paywalled location after that year.

Cool tool that allows you to graphically visualize page view counts of specific pages. It offers somewhat similar insights to Google Trends.

Homepage: pageviews.wmcloud.org/

Documentation: meta.wikimedia.org/wiki/Pageviews_Analysis#Massviews

The homepage shows views of selected pages, e.g. when Google had their 25th birthday: pageviews.wmcloud.org/?project=en.wikipedia.org&platform=all-access&agent=user&redirects=0&start=2023-09-11&end=2023-10-01&pages=Cat|Dog|Larry_Page Larry Page briefly beat "Cat" and "Dog".

/topviews shows the most viewed pages for a given month: pageviews.wmcloud.org/topviews/?project=en.wikipedia.org&platform=all-access&date=2023-08&excludes= It is extremelly epic that XXX: Return of Xander Cage, a 2017 film, is on the top ten of the August 2023 month. The page was around 8th place on a Google search for "xxx": archive.ph/wip/giRY8 at the time. XXXX (beer) was also on the top 20, followed by Sex on 21.

The growing number of parameters of the Standard Model is one big source of worry for early 21st century physics, much like the growing number of particles was a worry in the beginning of the 20th (but that one was solved by 2020).

List: en.wikipedia.org/w/index.php?title=Standard_Model&oldid=1042518939#Construction_of_the_Standard_Model_Lagrangian

The by far dominating DNA sequencing company of the late 2000's and 2010's due to having the smallest cost per base pair.

Illumina actually bought their 2010's dominating technology from a Cambridge company called Solexa.

To understand how Illumina's technology works basically, watch this video: Video 1. "Illumina Sequencing by Synthesis by Illumina (2016)".

The key innovation of this method is the Bridge amplification step, which produces a large amount of identical DNA strands.

Crop 20 pixels from the bottom of the image: