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".

Moodle instance of the Mathematical Institute of the University of Oxford.

Has a mixture of open access and closed access. But at least it can have open access unlike the in-house systems such as Canvas where everything is necessarily paywalled!

Sometimes things appear open but don't show any meaningful content if you are not logged in, which is annoying.

But at least it gives a clear public course list, thing that certain departments (cough Department of Physics of the University of Oxford cough).

The organization is a bit crap, when you expand e.g. C Michaelmas term it shows nothing, just a search.

The way to go is via the year year categories e.g. "Year 2022-23": courses.maths.ox.ac.uk/course/index.php?categoryid=734. Term splitting is annoying, but one can stand it.

There seems to be no way to list all versions of a single course across multiple years besides just doing a search e.g.

This job announcement from 2022 gives a good idea about their tech stack: web.archive.org/web/20220920114810/https://oxfordionics.bamboohr.com/jobs/view.php?id=32&source=aWQ9MTA%3D. Notably, they use ARTIQ.

Funding:

Funding:

This is apparently where past exam papers can be found. Paywalled of course.

The paywall is stupid however, as they seem to provide past papers upon request, e.g.

This adds to the mess of having a different location for material per department. Presumably this exists because the central university authority wants to centralize examinations to have better control over degree requirements. If only they would also do the same for all materials and end the mess.

As seen from explicit scalar form of the Maxwell's equations, this expands to 8 equations, so the question arises if the system is over-determined because it only has 6 functions to be determined.

As explained on the Wikipedia page however, this is not the case, because if the first two equations hold for the initial condition, then the othe six equations imply that they also hold for all time, so they can be essentially omitted.

It is also worth noting that the first two equations don't involve time derivatives. Therefore, they can be seen as spacial constraints.

TODO: the electric field and magnetic field can be expressed in terms of the electric potential and magnetic vector potential. So then we only need 4 variables?

Bibliography:

Base JavaScript library that implements the OurBigBook Markup. Use by both:

Stack Exchange solves to a good extent the use cases:points of view. It is a big open question if we can actually substantially improve it.

Major shortcoming are mentioned at idiotic Stack Overflow policies:

Bibliography:

Education has become an expensive bureaucratic exercise, completely dissociated from reality and usefulness.

It completely rejects what the individual wants to achieve, and instead attempts to mass homogenize and test people through endless hours of boredom.

And the only goals it achieves are testing student's resilience to stress, and facilitating the finding of sexual partners. True learning is completely absent.

Teachers only teach because they have to do it to get paid, not for passion. Their only true incentive is co-authoring papers.

We reject this bullshit.

Education is meant to help us, the students, achieve our goals through passionate learning.

And, we, the students, are individuals, with different goals and capabilities.

The way we protest is to publish the knowledge from University for free, on the Internet, so that anyone can access it.

And we do this is a law-abiding way, without copyright infringement, so that no one can legally take it down.

We come to our courses just for the useless roll calls. But we already know all the subject better than the "teacher" on the very first day.

And we are already more famous than the "teacher" online, and through the Internet have already taught more way way more people than they ever will.

The effect of this is to demoralize the entire school system at all levels, until only one conclusion is possible: implosion.

And from the ashes of the old system, we will build a new one, which does only what matters with absolute efficiency: help the individual students achieve their goals.

A system in which the only reason why university exist will be to allow the most knowledgeable students to access million dollar laboratory equipment, and to pay the most prolific content creators so they can continue content creating.

No more useless courses. No more useless tests. Only passion, usefulness and focus.

See: docs.ourbigbook.com/#ourbigbook-web-user-manual

If Ciro Santilli were to write a book about quantum mechanics as of 2020 (before OurBigBook.com went live), he would upload an OurBigBook Markup website to GitHub Pages.

But there is one major problem with that: the entry barrier for new contributors is very large.

If they submit a pull request, Ciro has to review it, otherwise, no one will ever see it.

Our amazing website would allow the reader to add his own example of, say, The uncertainty principle, whenever they wants, under the appropriate section.

Then, people who want to learn more about it, would click on the "defined tag" by the article, and our amazing analytics would point them to the best such articles.