This can be used to detect if a given species of microorganism is present in a sample, and is therefore a widely used diagnostics technique to see if someone is infected with a virus.
You could of course do full DNA Sequencing to see everything that is there, but since it is as a more generic procedure, sequencing is more expensive and slow.
The alternative is to use a DNA amplification technique.
One big advantage over FreeFem is that it uses plain old Python to describe the problems instead of a domain-specific language. Matplotlib is used for plotting by default, so we get full Python power out of the box!
One downside is that its documentation is a Springer published PDF link.springer.com/content/pdf/10.1007%2F978-3-319-52462-7.pdf which is several years out-of-date (tested with FEnics 2016.2. Newbs. This causes problems e.g.: stackoverflow.com/questions/53730427/fenics-did-not-show-figure-nameerror-name-interactive-is-not-defined/57390687#57390687
system of partial differential equations are mentioned at: link.springer.com/content/pdf/10.1007%2F978-3-319-52462-7.pdf 3.5 "A system of advection–diffusion–reaction equations". You don't need to manually iterate between the equations.
On Ubuntu 20.04 as per fenicsproject.org/download/Before 2020-06, it was failing with:but they seem to have created the Ubuntu 20.04 package as of 2020-06, so it now worked! askubuntu.com/questions/866901/what-can-i-do-if-a-repository-ppa-does-not-have-a-release-file
sudo apt-get install software-properties-common
sudo add-apt-repository ppa:fenics-packages/fenics
sudo apt-get update
sudo apt-get install --no-install-recommends fenics
sudo apt install fenics
python3 -m pip install -u matplotlibE: The repository 'http://ppa.launchpad.net/fenics-packages/fenics/ubuntu focal Release' does not have a Release file. Solving partial differential equations with the Fourier series Updated 2025-05-21 +Created 1970-01-01
See: math.stackexchange.com/questions/579453/real-world-application-of-fourier-series/3729366#3729366 from heat equation solution with Fourier series.
Separation of variables of certain equations like the heat equation and wave equation are solved immediately by calculating the Fourier series of initial conditions!
Ciro's Edict #5 Completely rebrand Cirodown to OurBigBook Updated 2025-05-21 +Created 1970-01-01
The name cirodown should not appear anywhere now, except with very few exceptions, e.g.:
- github.com/cirosantilli/cirodown to github.com/ourbigbook/ourbigbook
- file extension from
.ciroto.bigb - the Node.js NPM package was renamed from
cirodowntoourbibook. - all in-code instances
I have also squatted
OurBigBook on all major social media handles for near future usage, e.g.: twitter.com/ourbigbook and so on.I was going to do this sooner or later, it was inevitable, but the timing was partly triggered due to noticing that English speakers (and likely many other nationalities) are not able to easily read/hear/pronounce "Ciro".
Stuff that is beautiful but useless because it does not make food or houses cheaper.
Or from Ciro Santilli's best random thoughts:
Without technology, one cannot survive. Without art, one cannot live.
But that sure enough has a Jesus semi-precursor, and likely many others: man shall not live by bread alone.
Maybe those are genial. Maybe not. Nostalgia is just too strong to discern. Ciro still goes back to them for rest.
Technique that uses multiple non-ideal qubits (physical qubits) to simulate/produce one perfect qubit (logical).
One is philosophically reminded of classical error correction codes, where we also have multiple input bits per actual information bit.
TODO understand in detail. This appears to be a fundamental technique since all physical systems we can manufacture are imperfect.
Part of the fundamental interest of this technique is due to the quantum threshold theorem.
For example, when PsiQuantum raised 215M in 2020, they announced that they intended to reach 1 million physical qubits, which would achieve between 100 and 300 logical qubits.
Video "Jeremy O'Brien: "Quantum Technologies" by GoogleTechTalks (2014)" youtu.be/7wCBkAQYBZA?t=2778 describes an error correction approach for a photonic quantum computer.
Bibliography:
Quick facts:
- Nationalities: Italian and Brazilian
- Grew up in: Brazil
- Relationship status 2017-: married
- Given name pronunciation: take your pick from Ciro Santilli's given name
- Chinese name: 三西猴, means "three western monkeys". Phonetic approximation to SANtilli CIRO. More info at: Ciro Santilli's Chinese name. Semi-unintentionally reminds Chinese people of Sun Wukong (孙悟空). This association is further slightly strengthened by the phonetic choice of 三 San, which Ciro later noticed matches the middle character of Tang Sanzang (唐三藏), the monk in Journey to the West. The given name 西猴 was given by Ciro Santilli's wife, then recent girlfriend, as a semi-joke, and he took it up because the best way to take a joke is to play along with the joker. 三 was chosen by Ciro himself.
- laptop: high end Lenovo ThinkPad
- distro: latest Ubuntu release
- Vim or Emacs: vi/vim. But for The Love, will someone please make an open source C++ integrated development environment that actually just works?
- tabs or spaces: spaces
- Mailing list or Git(Hub|Lab): Git(Hub|Lab), with passion, see Section "Mailing list"
- system or unit tests: system
- programming languages: Python and C++. He'll learn Rust and Haskell once he's rich. As of the 2020s, Rust was picking up some serious steam, so Ciro might end up eating his own words there.
- musical instruments to listen: Chinese Guqin and electric Jazz-fusion guitar
- metric or imperial: metric, for The Love. Science? Standardization? 21st century anyone?
- QWERTY or Dvorak: QWERTY, alas
- birth name: Ciro Duran Santilli
Other people with the same name are listed at Section "Ciro Santilli's homonyms".
19th century illustration of the Journey to the West protagonist Sun Wukong
. Source. Sun Wukong (孙悟空) is a playful and obscenely powerful monkey Journey to the West. He protects Buddhist monk Tang Sanzang, and likes eating fruit, just like Ciro. Oh, and Goku from Dragon Ball is based on him. His japanese name is "Sun Wukong" (same Chinese characters with different Japanese pronunciation) for the love. His given name "Wukong" means literally "the one who mastered the void", which is clearly a Dharma name and fucking awesome in multiple ways. This is another sad instance of a Chinese thing better known in the West as Japanese.
It is worth noting however that although Wukong is extremely charming, Ciro's favorite novel of the Four Great Classic Novels is Water Margin. Journey to the West is just a monster of the week for kids, but Water Margin is a fight for justice saga. Sorry Wukong!
Ciro Santilli playing with a pipette at the University of Cambridge circa 2017
. The photo was taken in an open event organized by the awesome Cambridge Synthetic Biology outreach group, more or less the same people who organize: www.meetup.com/Cambridge-Synthetic-Biology-Meetup/ and who helped organize Section "How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it".
Taking part in such activities is what Ciro tries to do to overcome his lifelong regret of not having done more experimental stuff at university. Would he have had the patience to handle all the bullshit of the physical word without going back to the informational sciences? Maybe, maybe not. But now he will probably never know?!
Notice the orange high visibility cycling jersey under the lab coat, from someone who had just ridden in from work as fast as possible as part of his "lunch break". It is more fun when it is hard.
Scribe Jean Miélot, 15th century
. Ciro Santilli fantasizes that he would have make a good scribe in the middle ages, partly due to his self diagnosed graphomania, but also appreciation for foreign languages, and his mild obsession with the natural sciences.
OurBigBook.com is Ciro's view of a modern day scriptorium, except that now the illuminations are YouTube videos.
Chill and eat your bread in peace comes to mind. A scribe, in a library, reading and writing the entire day in peace and quiet. The life!
The job of a Internet-age scribe is basically that of making knowledge more open, legally extracting it from closed copyrighted sources, and explaining your understanding of it to the wider world under Creative Commons licenses on the web. And in the process of greater openness, given a well organized system, we are able combine the knowledge of many different people, and thus make things more understandable than any single/few creator closed source source could ever achieve.
Ciro Santilli waving hello in infrared.
More info at: Figure "Ciro Santilli waving hello in infrared".The weird one, not directly coded in the genetic code.
Sequence and organization of the human mitochondrial genome by Sanger et al. (1981) Updated 2025-05-21 +Created 1970-01-01
There are unlisted articles, also show them or only show them.