Example:
- the three most table polymorphs of calcium carbonate polymorphs are:
Last updated 2018 as of 2021, but still just worked.
Gotta run github.com/feathersjs/feathers-chat first: github.com/feathersjs-ecosystem/feathers-chat-react/issues/5, then it worked:and on the other terminal:then visit localhost:3000/ and you can create an account and login, tested on Ubuntu 20.10. Data is stored on persistently.
git clone https://github.com/feathersjs/feathers-chat
cd feathers-chat
git checkout fd729a47c57f9e6170cc1fa23cee0c84a004feb5
npm install
npm startgit clone https://github.com/feathersjs-ecosystem/feathers-chat-react
cd feathers-chat-react
git checkout 36d56cbe80bbd5596f6a108b1de9db343b33dac3
npm install
npm startIf you disable JavaScript on Chromium, it stops working completely. There is a section on how to solve that at: docs.feathersjs.com/cookbook/express/view-engine.html but it does not cover React specifically. Codaisseur/feathersjs-react-redux-ssr might be good to look into.
Allow us to determine with good approximation in a multi-electron atom which electron configuration have more energy. It is a bit like the Aufbau principle, but at a finer resolution.
Note that this is not trivial since there is no explicit solution to the Schrödinger equation for multi-electron atoms like there is for hydrogen.
For example, consider carbon which has electron configuration 1s2 2s2 2p2.
gothinkster/node-express-realworld-example-app by 
Ciro Santilli 37 Updated 2025-07-11 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-11 +Created 1970-01-01Good 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.
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 37 Updated 2025-07-11 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-11 +Created 1970-01-01As 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 Conclusions by Ciro Santilli 37 Updated 2025-07-11 +Created 1970-01-01
Ciro Santilli 37 Updated 2025-07-11 +Created 1970-01-01- against all odds, the experiment worked and we got DNA out of the water, despite a bunch of non-bio newbs actively messing with random parts of the experiment
- PuntSeq and Biomakespace people, and all those tho do scientific outreach, are awesome!
- biology is hard
- creating insanely media rich articles like this is also hard, but the following helped enormously:
- Wikimedia Commons to store large media files out of Git
- Asciidoctor extensions to easily include those media files. The lessons learnt in this article were then an important motivation for Ciro's OurBigBook Markup, to which this article was later migrated.
- Nomacs to give Google Photos photos meaningful names and to edit people's faces out of pictures ;-)
- some scientific Wikipedia pages may or may not have been edited with better pictures during the course of writing this article
Isomers were quite confusing for early chemists, before atomic theory was widely accepted, and people where thinking mostly in terms of proportions of equations, related: Section "Isomers suggest that atoms exist".
Fabry Perot Interferometer by JFC UCL (2016)
Source. Description only, reasonable animations. Considers the case of two nearby beam splitters.Fabry-Perot Introduction by Williams College Physics (2020)
Source. Shows a working device. Confocal optical cavity, one of the mirrors scans back and forward moved by a piezoelectric motor, this is called a "scanning Fabry-Perot interferometer".
Does not produce an interference pattern, only an on/off blob, which is then fed into an oscilloscope for analysis. The oscilloscope shows both the mirror displacement (which is given by a voltage) and the light detector output.
The main FeathersJS hello world demo. Notable missing things...
- instant Heroku deployability: FeathersJS Heroku deployment
- no Front-end web framework which sucks, but there are basically official demos that worked e.g. feathers-chat-react
- FeathersJS signup email verification
NCBI entry: www.ncbi.nlm.nih.gov/gene/945803.
This protein is an enzyme. The UniProt entry clearly shows the chemical reactions that it catalyses. In this case, there are actually two! It can either transforming the metabolite:Also interestingly, we see that both of those reaction require some extra energy to catalyse, one needing adenosine triphosphate and the other nADP+.
TODO: any mention of how much faster it makes the reaction, numerically?
Since this is an enzyme, it would also be interesting to have a quick search for it in the KEGG entry starting from the organism: www.genome.jp/pathway/eco01100+M00022 We type in the search bar "thrA", it gives a long list, but the last entry is our "thrA". Selecting it highlights two pathways in the large graph, so we understand that it catalyzes two different reactions, as suggested by the protein name itself (fused blah blah). We can now hover over:Note that common cofactor are omitted, since we've learnt from the UniProt entry that this reaction uses ATP.
- the edge: it shows all the enzymes that catalyze the given reaction. Both edges actually have multiple enzymes, e.g. the L-Homoserine path is also catalyzed by another enzyme called metL.
- the node: they are the metabolites, e.g. one of the paths contains "L-homoserine" on one node and "L-aspartate 4-semialdehyde"
If we can now click on the L-Homoserine edge, it takes us to: www.genome.jp/entry/eco:b0002+eco:b3940. Under "Pathway" we see an interesting looking pathway "Glycine, serine and threonine metabolism": www.genome.jp/pathway/eco00260+b0002 which contains a small manually selected and extremely clearly named subset of the larger graph!
But looking at the bottom of this subgraph (the UI is not great, can't Ctrl+F and enzyme names not shown, but the selected enzyme is slightly highlighted in red because it is in the URL www.genome.jp/pathway/eco00260+b0002 vs www.genome.jp/pathway/eco00260) we clearly see that thrA, thrB and thrC for a sequence that directly transforms "L-aspartate 4-semialdehyde" into "Homoserine" to "O-Phospho-L-homoserine" and finally tothreonine. This makes it crystal clear that they are not just located adjacently in the genome by chance: they are actually functionally related, and likely controlled by the same transcription factor: when you want one of them, you basically always want the three, because you must be are lacking threonine. TODO find transcription factor!
The UniProt entry also shows an interactive browser of the tertiary structure of the protein. We note that there are currently two sources available: X-ray crystallography and AlphaFold. To be honest, the AlphaFold one looks quite off!!!
By inspecting the FASTA for the entire genome, or by using the NCBI open reading frame tool, we see that this gene lies entirely in its own open reading frame, so it is quite boring
From the FASTA we see that the very first three Codons at position 337 arewhere
ATG CGA GTGATG is the start codon, and CGA GTG should be the first two that actually go into the protein:ecocyc.org/gene?orgid=ECOLI&id=ASPKINIHOMOSERDEHYDROGI-MONOMER mentions that the enzime is most active as protein complex with four copies of the same protein:TODO image?
Aspartate kinase I / homoserine dehydrogenase I comprises a dimer of ThrA dimers. Although the dimeric form is catalytically active, the binding equilibrium dramatically favors the tetrameric form. The aspartate kinase and homoserine dehydrogenase activities of each ThrA monomer are catalyzed by independent domains connected by a linker region.
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