To run examples on a specific database:All examples can be tested on all databases with:
./index.jsor./index.js l: SQLite./index.js p: PostgreSQL. You must manually create a database calledtmpand ensure that peer authentication works for it
cd sequelize
./testOverview of the examples:
- nodejs/sequelize/index.js: a bunch of basic examples
- nodejs/sequelize/update.js: This file is also where we are storing our expression-foo for now, e.g. how to do stuff like
col1 + col2. Such knowledge can however be used basically anywhere else however, e.g. inASorWHEREclauses, not just inUPDATE. - nodejs/sequelize/count.js: a simplified single-table count example. In practice, this will be usually done together with JOIN queries across multiple tables. Answers: stackoverflow.com/questions/22627258/how-does-group-by-works-in-sequelize/69896449#69896449
- nodejs/sequelize/date.js: automatic date typecasts
- nodejs/sequelize/like.js: LIKE
- nodejs/sequelize/camel_case.js: trying to get everything in the database camel cased, columns starting with lowercase, and tables starting with uppercase. The defaults documented on getting started documentation do uppercase foreign keys, and lowercase non-foreign keys. It's a mess.
- nodejs/sequelize/ignore_duplicates.js: ignore query on unique violation with
ignoreDuplicates: truewhich does SQLiteINSERT OR IGNORE INTOor PostgreSQLON CONFLICT DO NOTHING. Closely related Upsert versions:- Upsert
- nodejs/sequelize/upsert.js:
.upsertselects the conflict column automatically by unique columns. Both SQLite and PostgreSQL doINSERT INTO ON CONFLICT. PostgreSQL usesRETURNING, which was added too recently to SQLite: www.sqlite.org/lang_returning.html - nodejs/sequelize/update_on_duplicate.js:
.bulkCreate({}, { updateOnDuplicate: ['col1', col2'] }. Produces queries analogous to.upsert. This method is cool because it can upsert multiple columns at once. But it is annoying that you have to specify all fields to be updated one by one manually. - stackoverflow.com/questions/29063232/how-to-get-the-id-of-an-inserted-or-updated-record-in-sequelize-upsert/72092277#72092277
- stackoverflow.com/questions/55531860/sequelize-bulkcreate-updateonduplicate-for-postgresql
- Upsert
- nodejs/sequelize/inc.js: demonstrate the
incrementmethod. In SQLite, it produces a statement of type:UPDATE `IntegerNames` SET `value`=`value`+ 1,`updatedAt`='2021-11-03 10:23:45.409 +00:00' WHERE `id` = 3 - nodejs/sequelize/sync_alter.js: illustrates
Model.sync({alter: true})to modify a table definition, answers: stackoverflow.com/questions/54898994/bulkupdate-in-sequelize-orm/69044138#69044138 - nodejs/sequelize/truncate_key.js
- nodejs/sequelize/validation.js: is handled by a third-party library: github.com/validatorjs/validator.js. They then add a few extra validators on top of that.The
args: truething is explained at: stackoverflow.com/questions/58522387/unhandled-rejection-sequelizevalidationerror-validation-error-cannot-create-pr/70263032#70263032 - nodejs/sequelize/composite_index.js: stackoverflow.com/questions/34664853/sequelize-composite-unique-constraint
- nodejs/sequelize/indent_log.js: stackoverflow.com/questions/34664853/sequelize-composite-unique-constraint
- association examples:
- nodejs/sequelize/one_to_many.js: basic one-to-many examples.
- nodejs/sequelize/many_to_many.js: basic many-to-many examples, each user can like multiple posts. Answers: stackoverflow.com/questions/22958683/how-to-implement-many-to-many-association-in-sequelize/67973948#67973948
- ORDER BY include:
- nodejs/sequelize/many_to_many_custom_table.js: many-to-many example, but where we craft our own table which can hold extra data. In our case, users can like posts, but likes have a integer weight associated with them. Related threads:
- nodejs/sequelize/many_to_many_same_model.js: association between a model and itself: users can follow other users. Related:
- nodejs/sequelize/many_to_many_same_model_super.js
- nodejs/sequelize/many_to_many_super.js: "Super many to many": sequelize.org/master/manual/advanced-many-to-many.html This should not exist and shows how bad this library is for associations, you need all that boilerplate in order to expose certain relationships that aren't otherwise exposed by a direct
hasManywith implicit join table.
- nested includes to produce queries with multiple JOIN:
- nodejs/sequelize/nested_include.js: find all posts by users that a given user follows. Answers: stackoverflow.com/questions/42632943/sequelize-multiple-where-clause/68018083#68018083
- nodejs/sequelize/nested_include_super.js: like nodejs/sequelize/nested_include.js but with a super many to many. We should move this to nodejs/sequelize/many_to_many_super.js.
- two relationships between two specific tables: we need to use
as:to disambiguate them- nodejs/sequelize/many_to_many_double.js: users can both follow and like posts
- nodejs/sequelize/one_to_many_double.js: posts have the author and a mandatory reviewer
- hooks
- internals:
- nodejs/sequelize/common.js: common utilities used across examples, most notably:
- to easily setup different DBRM
- nodejs/sequelize/min_nocommon.js: to copy paste to Stack Overflow
- nodejs/sequelize/min.js: template for new exapmles in the folder
- nodejs/sequelize/common.js: common utilities used across examples, most notably:
Transaction retries are inevitable, as some sQL isolation levels
Doesn't seem to have any simple built-in mechanism?
Very raw. Easy to understand. Relatively well organiezd. But also very buggy at 3ab8d9f849a1cdf2985a8d123b1893f0fd4e79ab: github.com/Varun-Hegde/Conduit_NodeJS/issues/3, I just can't trust it. There must be several helper libraries that would greatly DRY up the repetitive CRUD. Ciro hates the style :-) 4 space indents, no space after commas, no semicolon. Not based on github.com/gothinkster/node-express-realworld-example-app which is essentially one of the reference implementations, so from scratch apparently, which is a bad sign.
You can connect form an Ubuntu 22.04 host as:When in but be aware of: Raspberry Pi Pico W freezes a few seconds after after screen disconnects from UART.
screen /dev/ttyACM0 115200screen, you can Ctrl + C to kill main.py, and then execution stops and you are left in a Python shell. From there:- Ctrl + D: reboots
- Ctrl + A K: kills the GNU screen window. Execution continues normally
Other options:
- ampy
runcommand, which solves How to run a MicroPython script from a file on the Raspberry Pi Pico W from the command line?
Then there are two appraoches:
- thonny if you like clicking mouse buttons:and select the interpreter as the Pico.
pipx install thonny - ampy if you like things to just run from the CLI: How to run a MicroPython script from a file on the Raspberry Pi Pico W from the command line?
Ubuntu 22.04 build just worked, nice! Much feels much cleaner than the Micro Bit C setup:
sudo apt install cmake gcc-arm-none-eabi libnewlib-arm-none-eabi libstdc++-arm-none-eabi-newlib
git clone https://github.com/raspberrypi/pico-sdk
cd pico-sdk
git checkout 2e6142b15b8a75c1227dd3edbe839193b2bf9041
cd ..
git clone https://github.com/raspberrypi/pico-examples
cd pico-examples
git checkout a7ad17156bf60842ee55c8f86cd39e9cd7427c1d
cd ..
export PICO_SDK_PATH="$(pwd)/pico-sdk"
cd pico-exampes
mkdir build
cd build
# Board selection.
# https://www.raspberrypi.com/documentation/microcontrollers/c_sdk.html also says you can give wifi ID and password here for W.
cmake -DPICO_BOARD=pico_w ..
make -jThen we install the programs just like any other UF2 but plugging it in with BOOTSEL pressed and copying the UF2 over, e.g.:Note that there is a separate example for the W and non W LED, for non-W it is:
cp pico_w/blink/picow_blink.uf2 /media/$USER/RPI-RP2/cp blink/blink.uf2 /media/$USER/RPI-RP2/Also tested the UART over USB example:You can then see the UART messages with:
cp hello_world/usb/hello_usb.uf2 /media/$USER/RPI-RP2/screen /dev/ttyACM0 115200TODO understand the proper debug setup, and a flash setup that doesn't require us to plug out and replug the thing every two seconds. www.electronicshub.org/programming-raspberry-pi-pico-with-swd/ appears to describe it, with SWD to do both debug and flash. To do it, you seem need another board with GPIO, e.g. a Raspberry Pi, the laptop alone is not enough.
Superconducting qubits are good because superconductivity is macroscopic by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16Superconducting qubits are regarded as promising because superconductivity is a macroscopic quantum phenomena of Bose Einstein condensation, and so as a macroscopic phenomena, it is easier to control and observe.
This is mentioned e.g. in this relatively early: physicsworld.com/a/superconducting-quantum-bits/. While most quantum phenomena is observed at the atomic scale, superconducting qubits are micrometer scale, which is huge!
Physicists are comfortable with the use of quantum mechanics to describe atomic and subatomic particles. However, in recent years we have discovered that micron-sized objects that have been produced using standard semiconductor-fabrication techniques – objects that are small on everyday scales but large compared with atoms – can also behave as quantum particles.
Good overgrown section in the middle of Fresnel's biography: en.wikipedia.org/w/index.php?title=Augustin-Jean_Fresnel&oldid=1064236740#Historical_context:_From_Newton_to_Biot.
Particularly cool is to see how Fresnel fully understood that light is somehow polarized, even though he did not know that it was made out of electromagnetism, clear indication of which only came with the Faraday effect in 1845.
spie.org/publications/fg05_p03_maluss_law:
At the beginning of the nineteenth century the only known way to generate polarized light was with a calcite crystal. In 1808, using a calcite crystal, Malus discovered that natural incident light became polarized when it was reflected by a glass surface, and that the light reflected close to an angle of incidence of 57° could be extinguished when viewed through the crystal. He then proposed that natural light consisted of the s- and p-polarizations, which were perpendicular to each other.
Matches the quantum superposition probability proportional to the square law. Poor Étienne-Louis Malus, who died so much before this was found.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Experiment background by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16PuntSeq 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!
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Overview of the experiment by Ciro Santilli 40 Updated 2026-08-21
Ciro Santilli 40 Updated 2026-08-21For those that know biology and just want to do the thing, see: Section "Protocols used".
The PuntSeq team uses an Oxford Nanopore MinION DNA sequencer made by Oxford Nanopore Technologies to sequence the 16S region of bacterial DNA, which is about 1500 nucleotides long.
This kind of "decode everything from the sample to see what species are present approach" is called "metagenomics".
This is how the MinION looks like: Figure 1. "Oxford Nanopore MinION top".
Oxford Nanopore MinION top open
. Source. 
Before sequencing the DNA, we will do a PCR with primers that fit just before and just after the 16S DNA, in well conserved regions expected to be present in all bacteria.
The PCR replicates only the DNA region between our two selected primers a gazillion times so that only those regions will actually get picked up by the sequencing step in practice.
Eukaryotes also have an analogous ribosome part, the 18S region, but the PCR primers are selected for targets around the 16S region which are only present in prokaryotes.
This way, we amplify only the 16S region of bacteria, excluding other parts of bacterial genome, and excluding eukaryotes entirely.
Despite coding such a fundamental piece of RNA, there is still surprisingly variability in the 16S region across different bacteria, and it is those differences will allow us to identify which bacteria are present in the river.
The variability exists because certain base pairs are not fundamental for the function of the 16S region. This variability happens mostly on RNA loops as opposed to stems, i.e. parts of the RNA that don't base pair with other RNA in the RNA secondary structure as shown at: Code 1. "RNA stem-loop structure".
This is how the 16S RNA secondary structure looks like in its full glory: Figure 5. "16S RNA secondary structure".
Since loops don't base pair, they are less crucial in the determination of the secondary structure of the RNA.
The variability is such that it is possible to identify individual species apart if full sequences are known with certainty.
With the experimental limitations of experiment however, we would only be able to obtain family or genus level breakdowns.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Sample collection by Ciro Santilli 40 Updated 2026-08-21
Ciro Santilli 40 Updated 2026-08-21As you would expect, not much secret here, we just dumped a 1 liter glass bottle with a rope attached around the neck in a few different locations of the river, and pulled it out with the rope.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it DNA extraction by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16 How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it PCR by Ciro Santilli 40 Updated 2026-08-21
Ciro Santilli 40 Updated 2026-08-21More 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.
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:
- use a different barcode for samples collected from different locations. This means we
- did PCR separately for each one of them
- for each PCR run, used a different set of primers, each with a different tag
- the primer is still able to attach, and then the tag just gets amplified with the rest of everything!
- sequence them all in one go
- then just from the sequencing output the barcode to determine where each sequence came from!
Input: Bacterial DNA (a little bit)
... --- 27S --- 16S --- 1492R --- ...
|||
|||
vvv
Output: PCR output (a lot of)
Barcode --- 27S --- 16S --- 1492RCode 1.
PCR diagram
. Finally, after purification, we used the Qiagen QIAquick PCR Purification Kit protocol to purify the generated from unwanted PCR byproducts.
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. Web editor. You can also edit articles on the Web editor without installing anything locally.Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact