Qiagen QIAquick PCR Purification Kit by 
Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01www.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.
Thermo Scientific Nalgene Polysulfone Reusable Bottle Top Filters by Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01www.fishersci.no/shop/products/nalgene-polysulfone-reusable-bottle%20-top-filters/10465781 (archive)
This is where we poured the water. It was not large enough for the entire 1L sample, so we had to do it a few times.
VELP Scientifica WIZARD IR Infrared Vortex Mixer by Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01 Biochrom SimpliNano spectrophotometer by Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01Mirror images.
Key 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.
The default feathers-chat app runs on NeDB (local filesystem JSON database).
Ciro Santilli managed to port it to Sequelize for PostgreSQL as shown at: github.com/cirosantilli/feathers-chat/tree/sequelize-pg
E. Coli K-12 MG1655 transcription unit thrL by Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01Contains the gene: e. Coli K-12 MG1655 gene thrL.
Subset of the longer E. Coli K-12 MG1655 transcription unit thrLABC.
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)
But at least it seems rock solid that those three are actually clades.
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.Edit: actually things will likely just work if immediately after making table changes you just instantiate a new sequelize and do any data changes. - 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.
Once we had the amplified 16S DNA, we were almost ready to start sequencing!
- 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 35 Updated 2025-03-28 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-03-28 +Created 1970-01-01At least they have a fucking clear course schedule unlike the undergrad.
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