Ciro Santilli @cirosantilli 35

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:

This section is about groups of ordinal ruleset inscription that share a theme and were presumably created by a single entity.

A detailed list of all transactions is kept at: sponsor/budget.js.

Ciro Santilli use the following accounting for this sponsorship calculations.

For significant one time donations, he takes the final money received in one of his cash GBP accounts, then he checks how much that is in dollars on Google at the time of cash out, and then writes that amount down as the final dollar value which is what ultimately counts. This exposes Ciro to USD/GBP fluctuations, but it simplifies accounting for donors which is more important, so it is likely worth it.

For small regular donations, Ciro just tallies it all up in GBP from time to time and converts it all to dollars in one go as it is not worth spending too much time updating those too often.

Ciro Santilli wants to make sure that you get clear highlights of what your donation money is going into!Sponsors also receive the "Ciro's Edit" email newsletter if desired, which contains similar updates to the above, but delivered directly to their inbox.

Mission: to live in a world where you can learn university-level mathematics, physics, chemistry, biology and engineering from perfect free books that anyone can write to get famous.

Live website: ourbigbook.com

Further information and rationale: Section "OurBigBook.com"

The project's mission is one of, or perhaps the most important, life objective of Ciro Santilli. Reproductive goals aside. These two types of goal are incommensurable. This is one of the great challenges of life.

This is ongoing project.

Ciro's goals in advertising this half done project are is partly to obtain some feedback, and partly to give the idea to someone else who might help push it further, be it in this stack or not.

Better editing support is a must, likely WYSIWYG.

But besides that, it is already in broad strokes the best approach Ciro Santilli can come up with to try and reach the mission statement only with technical advances, i.e. without large amounts of money or political influence which Ciro Santilli does not have.

Maybe that website isn't enough of a technical advance to reach its mission. Maybe there is some further not yet imagined technical insight that would push it into viability. Maybe not. But one must try. Only God can know the answer to these questions.

As of 2022, Ciro has spent about 2.5 years full time working on this project. First he spent about 1 year in 2014 on the first iteration: github.com/booktree/booktree, a GitLab fork, but then decided it was not the way to go.

Then around 2021 he put in some more 1.5 year of full time work, now with a possibly overly complicated (or perhaps just insane/immature) Next.js/Sequelize from scratch website stack.

It makes Ciro a bit ashamed to see that "so little user visible stuff was achieved in so much time". It is partly because he and many people underestimate the difficulty of web development. Perhaps there were some bad stack/useless feature choices issues. And a good dose of indulging in studying the natural sciences to bootstrap content and have fun. But really trying is the only way to learn.

Generally, if something is labelled as "e-learning", it's not a good sign, as it implies that it adheres to the "teacher"/"student" separation which Ciro Santilli much despises: E-learning websites must allow students to create learning content.

Others:

A very good information dump!

Currently a redirect page on Wikipedia: en.wikipedia.org/?title=Department_of_Statistics,_University_of_Oxford&redirect=no Newbies!

Why is this not part of the Mathematical Institute of the University of Oxford? Who knows!

More generic PCR information at: Section "Polymerase chain reaction".

Because it is considered the less interesting step, and because it takes quite some time, this step was done by the event organizers between the two event days, so participants did not get to take many photos.

PCR protocols are very standard it seems, all that biologists need to know to reproduce is the time and temperature of each step.

We did 35 cycles of:

This process used a Marshal Scientific MJ Research PTC-200 Thermal Cycler:

We added PCR primers for regions that surround the 16S DNA. The primers are just bought from a vendor, and we used well known regions are called 27F and 1492R. Here is a paper that analyzes other choices: academic.oup.com/femsle/article/221/2/299/630719 (archive) "Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment" by Yuichi Hongoh, Hiroe Yuzawa, Moriya Ohkuma, Toshiaki Kudo (2003)

One cool thing about the PCR is that we can also add a known barcode at the end of each primer as shown at Code 1. "PCR diagram".

This means that we bought a few different versions of our 27F/1492R primers, each with a different small DNA tag attached directly to them in addition to the matching sequence.

This way, we were able to:

Input: Bacterial DNA (a little bit)
... --- 27S --- 16S --- 1492R --- ...

|||
|||
vvv

Output: PCR output (a lot of)
Barcode --- 27S --- 16S --- 1492R

Finally, after purification, we used the Qiagen QIAquick PCR Purification Kit protocol to purify the generated from unwanted PCR byproducts.

The remedy to cowardice, inattention, censorship and amorality.

Due to Ciro Santilli's campaign for freedom of speech in China, Ciro Santilli maintains information on this at mostly at:

Dan Dascalescu's "Web page archiving" comparison table: web.archive.org/web/20130922192354/http://wiki.dandascalescu.com/reviews/online_services/web_page_archiving

tmux for newbs: Section "Terminal multiplexers are CLI desktop environments".

A network interface controller that does more than just the base OSI model protocols, notably in a programmable way.