How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Qiagen QIAquick PCR Purification Kit by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16www.qiagen.com/us/products/discovery-translational-research/dna-rn-a-purification/dna-purification/dna-clean-up/qiaquick-pcr-purification-kit/#orderinginformation (archive)
Manual archive: web.archive.org/web/20190911100243/https://www.qiagen.com/us/resources/download.aspx?id=e0fab087-ea52-4c16-b79f-c224bf760c39&lang=en
Removes PCR byproducts from purified DNA.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Thermo Scientific Nalgene Polysulfone Reusable Bottle Top Filters by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16Key exmaple: d and L amino acids. Enantiomers have identical physico-chemical properties. But their biological roles can be very different, because an enzyme might only be able to act on one of them.
Ciro Santilli managed to port it to Sequelize for PostgreSQL as shown at: github.com/cirosantilli/feathers-chat/tree/sequelize-pg
Includes:
- amphibians
- amniotes, which includes:
- sauropsida: reptiles and birds, which really are reptiles
- mammals
The exact relationships between those clades is not very clear as there's a bunch of extinct species in the middle we are not sure exactly where they go exactly, some hypothesis are listed at: en.wikipedia.org/w/index.php?title=Tetrapod&oldid=1053601110#Temnospondyl_hypothesis_(TH)
She's truly passionate about health research and keeping healthy, almost obsessed by it. Also she's strong willed, and energetic. Good traits for founding 23andMe.
- www.vanityfair.com/style/2014/04/sergey-brin-amanda-rosenberg-affair Fantastic painting of the people.
As www.nytimes.com/2017/11/18/style/anne-wojcicki-23andme-genetics.html puts it well:
The Wojcickis grew into Silicon Valley royalty. It’s the sort of family, Anne jokes, where “you’re only a viable fetus once you have your Ph.D.
Anne Wojcicki interview by Talks at Google (2018)
Source. She's athletic! As mentioned at: www.vanityfair.com/style/2014/04/sergey-brin-amanda-rosenberg-affair. And despite the name, and unlike Sergey, she's completely american as seen from her perfect accent!- youtu.be/pDoALM0q1LA?t=173 coding on garage while they do dishes and burritos
- youtu.be/pDoALM0q1LA?t=331 why she's obsessed with healthcare. Also mentioned at: www.vanityfair.com/style/2014/04/sergey-brin-amanda-rosenberg-affair how she was trying to save Sergei from some of his genetic predispositions
- youtu.be/pDoALM0q1LA?t=571 she really cared about 23andMe, but the public didn't as much as her. She's truly passionate about mining genetic data. Maybe she came a bit early.
- youtu.be/pDoALM0q1LA?t=1038 doc in a box workaround
- foreign keys are capitalized:
- you must give
foreignKeywhen using aliases, otherwise it fails subtely. That would be derived automatically. - stackoverflow.com/questions/41502699/return-flat-object-from-sequelize-with-association can't auto-flatten to reuse the database's
ORDER limitandoffsetdon't work withoutsubQuery: falsewhen doing includes! It is just too buggy. Examples of this can be found e.g. under nodejs/sequelize/many_to_many_same_model.js.- stackoverflow.com/questions/34059081/how-do-i-reference-an-association-when-creating-a-row-in-sequelize-without-assum hard to not duplicate foreign keys values everywhere
- stack traces permanently broken or requiring non-obvious configs:
- does not automatically update fields on hooks: github.com/sequelize/sequelize/issues/8586#issuecomment-422877555
- cannot change columns when other columns have constraints due to the backup table?
- you have to use
.get()forattributealiased fields, why? stackoverflow.com/questions/32649218/how-do-i-select-a-column-using-an-alias/69890944#69890944 .idgets added toSELECTno matter what, breakingGROUP BYunless you do horrible workarounds:- no simple built-in mechanism for transaction retries: Sequelize transaction retries
- impossible to do subqueries in general. Docs just tell you to use literals. This in particular prevents single query deletes with join as done at nodejs/sequelize/raw/many_to_many.js:Also, you can't get query strings either: github.com/sequelize/sequelize/issues/2325
- sequelize.org/master/manual/sub-queries.html: the docs actually just tell you to use literals, lol
- stackoverflow.com/questions/45354001/nodejs-sequelize-delete-with-nested-select-query
- migrations. Generally speaking, anything but the simplest migrations are exceedingly hard to get right, as you have to go very low level when doing migrations. Syntax can be very different from regular DB operations.
- no way to do (non-raw) queries during migrations, e.g. to update fields based on other fields in a complex way?
- github.com/sequelize/cli/issues/862
- stackoverflow.com/questions/18742962/add-data-in-sequelize-migration-script
- stackoverflow.com/questions/38671483/sequelize-migration-update-model-after-updating-column-attributes
- stackoverflow.com/questions/38998397/can-i-use-sequelize-models-in-migration-scripts
- stackoverflow.com/questions/45286429/custom-query-on-sequelize-seeder
queryInterface.sequelize.modelscontains onlySequelizeMeta. Not sure why they have this limitation. - stackoverflow.com/questions/56043246/node-js-sequelize-no-primary-keys-when-migrating/56046101#56046101
- SQLite
changeColumnmigrations do on delete cascades of other tables. SQLite does not have change column statements, so they have to drop and recreate tables, but they don't temporarily remove cascades, so you lose data: stackoverflow.com/questions/62667269/sequelize-js-how-do-we-change-column-type-in-migration/70486686#70486686 - associations require full explicit index construction: stackoverflow.com/questions/39651853/how-to-create-join-table-with-foreign-keys-with-sequelize-or-sequelize-cli
- ability to iterate over a large result without blowing up memory and without using limit + offset (which is inneficient e.g. when looping over recursive queries). This is also known as cursor or streaming interfaces:E.g. the Python SQLite interface supports this just fine: stackoverflow.com/questions/29582736/python3-is-there-a-way-to-iterate-row-by-row-over-a-very-large-sqlite-table-wi
- stack overflow
- stackoverflow.com/questions/28787889/how-can-i-set-up-sequelize-js-to-stream-data-instead-of-a-promise-callback
- stackoverflow.com/questions/43964067/how-to-implement-cursor-pagination-using-sequelize
- stackoverflow.com/questions/57164242/perform-sequelize-findall-in-a-huge-array
- stackoverflow.com/questions/55191891/how-to-loop-through-result-in-sequelize generic loop
- issue tracker
- stack overflow
- empty
attributes: []breaks some nested queries: github.com/sequelize/sequelize/issues/16436 - does not expose a iteration API that supports large arrays?E.g. Python SQLite does: stackoverflow.com/questions/29582736/python3-is-there-a-way-to-iterate-row-by-row-over-a-very-large-sqlite-table-wi
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.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Sequencing 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 External links to this page by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16- 2021-03-25: Oxford Nanopore Technologies retweeted this article, that's awesome!
- 2021: hackaday.com/author/wd5gnr1/ "SEQUENCING DNA FOR METAGENOMICS" by Al Williams (2021). This came after Ciro Santilli self promoted at: stackoverflow.blog/2021/02/03/sequencing-your-dna-with-a-usb-dongle-and-open-source-code/#comment-1411921
Oxford Master Course in Mathematical and Theoretical Physics by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16Microwave only found applications into the 1940s and 1950s, much later than radio, because good enough sources were harder to develop.
One notable development was the cavity magnetron in 1940, which was the basis for the original radar systems of World War II.
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