github.com/CovertLab/WholeCellEcoliRelease is a whole cell simulation model created by Covert Lab and other collaborators.
The project is written in Python, hurray!
But according to te README, it seems to be the use a code drop model with on-request access to master. Ciro Santilli asked at rationale on GitHub discussion, and they confirmed as expected that it is to:
- to prevent their publication ideas from being stolen. Who would steal publication ideas with public proof in an issue tracker without crediting original authors? Academia is broken. Academia should be the most open form of knowledge sharing. But instead we get this silly competition for publication points.
- to prevent noise from non-collaborators. But they only get like 2 issues as year on such a meganiche subject... Did you know that you can ignore people, and even block them if they are particularly annoying? Much more likely is that no one will every hear about your project and that it will die with its last graduate student slave.
The project is a followup to the earlier M. genitalium whole cell model by Covert lab which modelled Mycoplasma genitalium. E. Coli has 8x more genes (500 vs 4k), but it the undisputed bacterial model organism and as such has been studied much more thoroughly. It also reproduces faster than Mycoplasma (20 minutes vs a few hours), which is a huge advantages for validation/exploratory experiments.
The project has a partial dependency on the proprietary optimization software CPLEX which is freeware, for students, not sure what it is used for exactly, from the comment in the
requirements.txt the dependency is only partial.This project makes Ciro Santilli think of the E. Coli as an optimization problem. Given such external nutrient/temperature condition, which DNA sequence makes the cell grow the fastest? Balancing metabolites feels like designing a Factorio speedrun.
There is one major thing missing thing in the current model: promoters/transcription factor interactions are not modelled due to lack/low quality of experimental data: github.com/CovertLab/WholeCellEcoliRelease/issues/21. They just have a magic direct "transcription factor to gene" relationship, encoded at reconstruction/ecoli/flat/foldChanges.tsv in terms of type "if this is present, such protein is expressed 10x more". Transcription units are not implemented at all it appears.
Everything in this section refers to version 7e4cc9e57de76752df0f4e32eca95fb653ea64e4, the code drop from November 2020, and was tested on Ubuntu 21.04 with a docker install of
docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full with image id 502c3e604265, unless otherwise noted.Have a look at some interesting examples under nodejs/sequelize/raw/many_to_many.js.
Company co-founded by Scott Hassan, early Google programmer at Stanford University, and Carl Victor Page, Jr., Larry Page's older brother.
The company was sold to Yahoo! in August 2000 for $432m and became Yahoo! Groups. They managed to miraculously dodge the Dot-com bubble, which mostly poppet in 2021. After the acquisition, Yahoo started to redirect them to: groups.yahoo.com as can be seen on the Wayback Machine: web.archive.org/web/20000401000000*/egroups.com The first archive of groups.yahoo.com is from February 2001: web.archive.org/web/20010202055100/http://groups.yahoo.com/ and it unsurprisingly looks basically exactly like eGroups.
eGroups logo
. From the earliest archive of their "about" page: web.archive.org/web/19991004062653/http://www.egroups.com/info/top.html in 1999.Unlike SARS-CoV-2 non-structural protein, these are not needed for test tube reproduction. They must therefore be for host modulation.
Lots of focus on Heroku deployability, which is fantastic: shakacode.gitbooks.io/react-on-rails/content/docs/additional-reading/heroku-deployment.html
Live instance: www.reactrails.com/ with source at: github.com/shakacode/react-webpack-rails-tutorial Not the most advanced web-app (a gothinkster/realworld-level would be ideal). Also has clear dependency description, which is nice.
Trying at github.com/shakacode/react-webpack-rails-tutorial/tree/8e656f97d7a311bbe999ceceb9463b8479fef9e2 on Ubuntu 20.10. Got some failures: github.com/shakacode/react-webpack-rails-tutorial/issues/488 Finally got a version of it working at: github.com/shakacode/react-webpack-rails-tutorial/issues/488#issuecomment-812506821
Oh, and the guy behind that project lives in Hawaii (Ciro Santilli's ideal city to live in), has an Asian-mixed son, and two Kinesis Advantage 2 keyboards as seen at twitter.com/railsonmaui/status/1377515748910755851, Ciro Santilli was jealous of him.
- stackoverflow.com/questions/1206872/go-to-previous-line-in-gdb/46996380#46996380
- stackoverflow.com/questions/1470434/how-does-reverse-debugging-work/53063242#53063242
- stackoverflow.com/questions/3649468/setting-breakpoint-in-gdb-where-the-function-returns/46116927#46116927
- stackoverflow.com/questions/27770896/how-to-debug-a-rare-deadlock/50073993#50073993
- stackoverflow.com/questions/522619/how-to-do-bidirectional-or-reverse-debugging-of-programs/50074106#50074106 link only, marked as duplicate of go to previous line
- softwareengineering.stackexchange.com/questions/181527/why-is-reverse-debugging-rarely-used
Framework built on top of React.
gothinkster/realworld blog example by Ciro Santilli: node Express Sequelize Next.js realworld example app.
Basically what this does is to get server-side rendering just working by React, including hydration, which is a good thing.
Next.js sends the first pre-rendered HTML page along with the JavaScript code. Then, JavaScript page switches just load the API data.
Next.js does this nicely by forcing you to provide page data in a serialized JSON format, even when rendering server-side (e.g. the return value of
getServerSideProps). This way, it is also able to provide either the full HTML, or just the JSON.Some general downsides:
- it does feel like they don't document deployment very well however, especially non-Vercel options, which is the company behind Next.js. I'm unable to find how to use a non Vercel CDN with ISR supposing that is possible.
- Next.js is very opinionated, and like any opinionated library it is sometimes hard to know why something is/isn't happening, and sometimes it is hard/impossible to do what you want with it unless they add support. They have done good progress, but even as of 2022, some aspects just feel so immature, some major-looking use cases are not very well done.
In theory, Next.js could be the "ultimate frontend framework". It does have a lot of development difficulties that need to be ironed out, but the general concepts, and things it tries to integrate, including e.g. webpack, TypeScript, etc. are good. Maybe the question is when will someone put it together with an amazing backend library and dominate and finally put an end to the infinite number of Js Frameworks!
In-tree examples at: github.com/vercel/next.js/tree/canary/examples
In order to offer its amazing features, Next.js is also extremely opinionated, which means that if something wasn't designed to be possible, it basically isn't.
No prerender with custom server? It forces you to write your API with next as well? Or does it mean something else?
TODO can it statically generate pages that are created at runtime? E.g. if I create a new blog post, will it automatically upload a static page? It seems that yes, and that this is exactly what Incremental Static Regeneration means:However, Ciro can't find any mention of how to specify where the pages are uploaded to... this is pat of the non-Vercel deployment problem.
- github.com/vercel/next.js/discussions/25410
- vercel.com/docs/next.js/incremental-static-regeneration
- github.com/vercel/next.js/discussions/17711
- www.reddit.com/r/nextjs/comments/mvvhym/a_complete_guide_to_incremental_static/
- github.com/vercel/next.js/discussions/11552#discussioncomment-115595
- stackoverflow.com/questions/62105756/how-to-use-aws-with-next-js
- github.com/vercel/next.js/discussions/17080
- github.com/vercel/next.js/discussions/16852
Can't ISR prerenter by URL query parameters:
That plus the requirement to have one page per file under
pages/ leads to a lot of useless duplication, because then you are forced to place the URL parameters on the pathnames."Module not found: Can't resolve 'fs'" Hell. The main reason this happens seems to be the that in a higher order component, webpack can't determine if callbacks use the require or not to remove it from frontend code. Fully investigated and solved at:
Overviews:
- www.reddit.com/r/reactjs/comments/8evy5d/what_are_the_downsides_to_nextjs/ 2017 What are the downsides to Next.js?
Examples under python/sklearn
. .venv/bin/activate
pip install sklearn matplotlib seabornIn it, each of the six sides has a clear and simple to understand photon polarization state, either of:
The sphere clearly suggests for example that a rotational or diagonal polarizations are the combination of left/right with the correct phase. This is clearly explained at: Video "Quantum Mechanics 9b - Photon Spin and Schrodinger's Cat II by ViaScience (2013)".
Quantum Computing with Networked Ion traps by NQIT (2018)
Source. The video is a bit useless. But it does show the networked approach proposal a little bit. Universal Quantum's homepage particularly rejects that.The "AI" part is just prerequisite buzzword of the AI boom era for any project and completely bullshit.
According to job postings such as: archive.ph/wip/Fdgsv their center is in Goleta, California, near Santa Barbara. Though Google tends to promote it more as Santa Barbara, see e.g. Daniel's t-shirt at Video "Building a quantum computer with superconducting qubits by Daniel Sank (2019)".
Control of transmon qubits using a cryogenic CMOS integrated circuit (QuantumCasts) by Google (2020)
Source. Fantastic video, good photos of the Google Quantum AI setup!- 2022: $15 million www.orcacomputing.com/blog/orca-computing-completes-15-million-series-a-funding-round
- 2021: $14.5 million for an Innovate UK project
Carl Zeiss, Explained by Asianometry (2021)
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