How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it DNA extraction Updated 2025-07-16
How Ciro Santilli manages to write so much Updated 2025-07-16
- Suck at your job:
- Have bad memory so you have to take notes: Ciro Santilli's bad old event memory
- Be a compulsive knowledge hoarder: Ciro Santilli's knowledge hoarding
- Seek glory over money: Ciro Santilli's selfish desires
- Try to make a carrier out of it: OurBigBook.com
- Be born compassionate: Ciro Santilli's self perceived compassionate personality
- He doesn't actually write that much, but when he does he focuses on higher impact stuff, see remarks about "He doesn't like to refresh the homepage looking for easy reputation" on Section "Ciro Santilli's Stack Overflow contributions"
- Contribute in a place where it is super easy for people to give you upvotes if they like your stuff. This way, you will see the uploads, and that will motivate you to re-read your content and make it more perfect with additions and corrections.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Experiment background Updated 2025-07-16
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:
- OMG, this is so labour intensive, why haven't they automated this
- OMG, this is frightening, all the 8 hours of work I've just done are present in that tiny plastic tube
- Amazing! Look at that apparatus! And the bio people are like: I've used this a million times, it's cheap and every lab has one, just work faster and don't break you piece of junk!
Personal knowledge instance Updated 2025-07-16
SQL RECURSIVE prevent infinite recursion Updated 2025-07-16
Example under: nodejs/sequelize/raw/tree.js
SQL SERIALIZABLE isolation level Updated 2025-07-16
Aberration (astronomy) Updated 2025-07-16
Finite special general linear group Updated 2025-07-16
Just like for the finite general linear group, the definition of special also works for finite fields, where 1 is the multiplicative identity!
Note that the definition of orthogonal group may not have such a clear finite analogue on the other hand.
Mathematics illustration software Updated 2025-07-16
Survey by Ciro Santilli: math.stackexchange.com/questions/1985/software-for-drawing-geometry-diagrams/3938216#3938216
Many plotting software can be used to create mathematics illustrations. They just tend to have more data-oriented rather than explanatory-oriented output.
SPARQL tutorial Updated 2025-07-16
In this tutorial, we will use the Jena SPARQL hello world as a starting point. Tested on Apache Jena 4.10.0.
Basic query on rdf/vcard.ttl RDF Turtle data to find the person with full name "John Smith":Output:
sparql --data=rdf/vcard.ttl --query=<( printf '%s\n' 'SELECT ?x WHERE { ?x <http://www.w3.org/2001/vcard-rdf/3.0#FN> "John Smith" }')---------------------------------
| x |
=================================
| <http://somewhere/JohnSmith/> |
---------------------------------To avoid writing Output:
http://www.w3.org/2001/vcard-rdf/3.0# a billion times as queries grow larger, we can use the PREFIX syntax:sparql --data=rdf/vcard.ttl --query=<( printf '%s\n' '
PREFIX vc: <http://www.w3.org/2001/vcard-rdf/3.0#>
SELECT ?x
WHERE { ?x vc:FN "John Smith" }
')---------------------------------
| x |
=================================
| <http://somewhere/JohnSmith/> |
---------------------------------Bibliography:
- UniProt contains some amazing examples runnable on their servers: sparql.uniprot.org/.well-known/sparql-examples/
First block not mined by Satoshi Updated 2025-07-16
Mathy Magic: The Gathering thoughts Updated 2025-07-16
In 2019, a paper proved that MTG is Turing complete with a legacy legal deck. Live demo with some hand waving: Video "I Built a COMPUTER in Magic: The Gathering by Because Science (2019)". As Ciro Santilli comments at: github.com/cirosantilli/cirosantilli.github.io/issues/42 this was an interest addition to the previous "indefinite infinite loop" e.g. as found in a Four Horsemen combo deck
Spectral line Updated 2025-07-16
A single line in the emission spectrum.
So precise, so discrete, which makes no sense in classical mechanics!
Has been the leading motivation of the development of quantum mechanics, all the way from the:
- Schrödinger equation: major lines predicted, including Zeeman effect, but not finer line splits like fine structure
- Dirac equation: explains fine structure 2p spin split due to electron spin/orbit interactions, but not Lamb shift
- quantum electrodynamics: explains Lamb shift
- hyperfine structure: due to electron/nucleus spin interactions, offers a window into nuclear spin
Apple Inc. person Updated 2025-07-16
Asian fetish Updated 2025-07-16
Whenever Ciro's wife starts with "the Asian fetish talk", Ciro reminds her of her own claimed "tall person fetish", and they call it quits.
Asian fetish is much more than sex. It is about the culture, the history, the language. It is the same fetish that makes great mathematicians an Artists do what they do.
When Ciro Santilli was at École Polytechnique, he had to do a presentation for his stupid English courses that all students were forced to take, no matter how good their English was.
The topic was likely something like "pick a country", and Ciro was delighted when he managed to pick "China", after it had gone around a table with many many people before him.
The PowerPoint presentation Ciro made over the weekend was so amazing (and making it was actually fun to make, Ciro actually remembers it a bit!), drawing partly from stuff his wife then girlfriend showed him, that at the end the one of the other students asked him if he had lived in China.
It is a shame Ciro couldn't find the presentation when he wrote this line many many years later. Anything that is not in a BLOB-free monorepo, will disappear, heed my words. But he's certain about two things which it contained:
en.wikipedia.org/wiki/Asian_fetish#History_of_originssubservient, passive, mysterious are understandable. But Hyper-sexual and villainous? OMG have these people never seen real Asians?
en.wikipedia.org/wiki/Asian_fetish#Pornography:
In the United States, women of East and Southeast Asian descent are sometimes stereotyped as subservient, passive, mysterious, villainous in nature, and hyper-sexual.
en.wikipedia.org/wiki/Asian_fetish#Pornography:
Open source standard cell library Updated 2025-07-16
Open source ones:
- www.quora.com/Are-there-good-open-source-standard-cell-libraries-to-learn-IC-synthesis-with-EDA-tools/answer/Ciro-Santilli Are there good open source standard cell libraries to learn IC synthesis with EDA tools?
Pivot (strategy) Updated 2025-07-16
Applications of the Fourier series Updated 2025-07-16
How to value startup shares Updated 2025-07-16
SQL TRIGGER Updated 2025-07-16
In particular, everything that happens in a trigger happens as if it were in a transaction. This way, you can do less explicit transactions when you use triggers. It is a bit like the advantages of SQL CASCADE.
DBMS:
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