Ciro Santilli @cirosantilli 37

This suggests that it is not a video bug then, seems that it is not waking up at all? Gotta try to SSH into it. OK. I did SSH into it, and that was fine, so it is just the video that won't start.

PM: suspend exit

bugs.launchpad.net/ubuntu/+source/linux/+bug/1949977 is another possible bug, based on kernel version. I'm running 5.13, which is one of the failing versions on the report. Can't find any interesting dmesg though.

In another crash:

journalctl -o short-precise -k -b -1

had the following interesting lines:

nvidia-modeset: WARNING: GPU:0: Lost display notification (0:0x00000000); continuing.
[24307.640014] NVRM: GPU at PCI:0000:01:00: GPU-18af74bb-7c72-ff70-e447-87d48378ea20
[24307.640018] NVRM: Xid (PCI:0000:01:00): 79, pid=8828, GPU has fallen off the bus.
[24307.640021] NVRM: GPU 0000:01:00.0: GPU has fallen off the bus.
[24328.054022] nvidia-modeset: ERROR: GPU:0: The requested configuration of display devices (LGD (DP-4)) is not supported on this GPU.
[repeats several more times]
[24328.056767] nvidia-modeset: ERROR: GPU:0: The requested configuration of display devices (LGD (DP-4)) is not supported on this GPU.
[24328.056951] nvidia-modeset: ERROR: GPU:0: Failed to query display engine channel state: 0x0000927c:0:0:0x0000000f
[24328.056955] nvidia-modeset: ERROR: GPU:0: Failed to query display engine channel state: 0x0000927c:1:0:0x0000000f
[24328.056959] nvidia-modeset: ERROR: GPU:0: Failed to query display engine channel state: 0x0000927c:2:0:0x0000000f
[24328.056962] nvidia-modeset: ERROR: GPU:0: Failed to query display engine channel state: 0x0000927c:3:0:0x0000000f
[24328.056983] nvidia-modeset: ERROR: GPU:0: DP-4: Failed to disable DisplayPort audio stream-0
[24328.056992] nvidia-modeset: ERROR: GPU:0: Failed to query display engine channel state: 0x0000947d:0:0:0x0000000f

and there was a corresponding /var/crash/_usr_sbin_gdm3.0.crash.

Related "GPU has fallen off the bus": askubuntu.com/questions/868321/gpu-has-fallen-off-the-bus-nvidia

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Sequelize example by

Ciro Santilli 37 Updated 2025-07-16

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To run examples on a specific database:

./index.js or ./index.js l: SQLite
./index.js p: PostgreSQL. You must manually create a database called tmp and ensure that peer authentication works for it

All examples can be tested on all databases with:

cd sequelize
./test

Overview 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. in AS or WHERE clauses, not just in UPDATE.
- stackoverflow.com/questions/54898994/bulkupdate-in-sequelize-orm/69044138#69044138
- stackoverflow.com/questions/55646233/updating-with-calculated-values-in-sequelize
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: true which does SQLite INSERT OR IGNORE INTO or PostgreSQL ON CONFLICT DO NOTHING. Closely related Upsert versions:
- Upsert
  - nodejs/sequelize/upsert.js: .upsert selects the conflict column automatically by unique columns. Both SQLite and PostgreSQL do INSERT INTO ON CONFLICT. PostgreSQL uses RETURNING, which was added too recently to SQLite: www.sqlite.org/lang_returning.html
    At nodejs/sequelize/composite_index.js we have a .upsert test with a composite index. Works just fine as you'd expect with a composite ON CONFLICT. Well done.
  - 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

nodejs/sequelize/inc.js: demonstrate the increment method. 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: true thing 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/one_to_many_custom_column_name.js:
    stackoverflow.com/questions/43025861/sequelize-association-is-referencing-to-wrong-foreignkey-column-name
    stackoverflow.com/questions/49818406/sequelize-targetkey-not-working/59953948#59953948
- 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:
    github.com/sequelize/sequelize/issues/4553
    stackoverflow.com/questions/66984410/why-the-sequelize-include-order-does-not-work
  - 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:
    stackoverflow.com/questions/22958683/how-to-implement-many-to-many-association-in-sequelize/67973948#67973948
    stackoverflow.com/questions/30308217/sequelize-find-by-association-through-manually-defined-join-table/69899876#69899876
  - nodejs/sequelize/many_to_many_same_model.js: association between a model and itself: users can follow other users. Related:
    stackoverflow.com/questions/43152180/node-sequelize-followering-following-relationship
    stackoverflow.com/questions/27065154/how-to-get-all-children-or-parents-in-a-many-to-many-association-if-one-model-re/72951602#72951602
    github.com/sequelize/sequelize/issues/8263
  - nodejs/sequelize/many_to_many_same_model_super.js
    nodejs/sequelize/find_duplicates.js: stackoverflow.com/questions/71235548/how-to-find-all-rows-that-have-certain-columns-duplicated-in-sequelize/71235550#71235550
  - 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 hasMany with 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

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Raspberry Pi Pico W UART by

Ciro Santilli 37 Updated 2025-07-16

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You can connect form an Ubuntu 22.04 host as:

screen /dev/ttyACM0 115200

When in screen, 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

but be aware of: Raspberry Pi Pico W freezes a few seconds after after screen disconnects from UART.

Other options:

ampy run command, which solves How to run a MicroPython script from a file on the Raspberry Pi Pico W from the command line?

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Superconducting qubits are good because superconductivity is macroscopic by

Ciro Santilli 37 Updated 2025-07-16

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Superconducting 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.

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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 37 Updated 2025-07-16

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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!

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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it / PCR by

Ciro Santilli 37 Updated 2025-07-16

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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:

94˚C for 30 seconds
60˚C for 30 seconds
72˚C for 45 seconds

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 --- 1492R

Code 1.

PCR diagram

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

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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it / Protocols used by

Ciro Santilli 37 Updated 2025-07-16

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Protocols are the biologist term for "recipe".

I found that a lot of biology comes down to this: get the right recipe, follow it well even though you don't understand all the proprietary details, and pray.

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Nick Leeson and the Fall of the House of Barings by Adam Curtis (1996) by

Ciro Santilli 37 Updated 2025-07-16

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Microwave transmission by

Ciro Santilli 37 Updated 2025-07-16

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lujakob/nestjs-realworld-example-app SQLite port by

Ciro Santilli 37 Updated 2025-07-16

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Tried a quick port to SQLite to get rid of annoying local databases for development, but failed, at c1c2cc4e448b279ff083272df1ac50d20c3304fa

npm install sqlite3 --save-dev

and

{
  "type": "sqlite",
  "database": "db.sqlite3",
  "entities": ["src/**/**.entity{.ts,.js}"],
  "synchronize": true
}

then:

npm start

fails with:

DataTypeNotSupportedError: Data type "timestamp" in "ArticleEntity.created" is not supported by "sqlite" database.

Attempt to hack it:

--- a/src/article/article.entity.ts
+++ b/src/article/article.entity.ts
@@ -20,10 +20,10 @@ export class ArticleEntity {
   @Column({default: ''})
   body: string;

-  @Column({ type: 'timestamp', default: () => "CURRENT_TIMESTAMP"})
+  @Column({ default: () => "CURRENT_TIMESTAMP"})
   created: Date;

-  @Column({ type: 'timestamp', default: () => "CURRENT_TIMESTAMP"})
+  @Column({ default: () => "CURRENT_TIMESTAMP"})
   updated: Date;

and after that it seems to run.

I can signup and login, terrible error reporting as usual, make sure to use long enough usernames/passwords.

However, article creation fails with:

Unhandled Rejection (TypeError): Cannot read property 'slug' of undefined

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Fluorescent lamp by

Ciro Santilli 37 Updated 2025-07-16

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ELF Hello World Tutorial / SHN_ABS by

Ciro Santilli 37 Updated 2025-07-16

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hello_world_len points to the special st_shndx == SHN_ABS == 0xF1FF.

0xF1FF is chosen so as to not conflict with other sections.

st_value == 0xD == 13 which is the value we have stored there on the assembly: the length of the string Hello World!.

This means that relocation will not affect this value: it is a constant.

This is small optimization that our assembler does for us and which has ELF support.

If we had used the address of hello_world_len anywhere, the assembler would not have been able to mark it as SHN_ABS, and the linker would have extra relocation work on it later.

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Mineralogy by

Ciro Santilli 37 Updated 2025-07-16

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E. Coli K-12 MG1655 gene thrC by

Ciro Santilli 37 Updated 2025-07-16

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Part of E. Coli K-12 MG1655 operon thrLABC.

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E. Coli K-12 MG1655 gene ytdX by

Ciro Santilli 37 Updated 2025-07-16

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