Incoming links: Code drop
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, very meh, asked rationale on GitHub discussion, and they confirmed as expected that it is to:Oh well.
- to prevent their publication ideas from being stolen. Who would steal publication ideas with public proof in an issue tracker without crediting original authors?
- to prevent noise from non collaborators. They do only get like 2 issues as year though, people forget that it is legal to ignore other people :-)
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.Things that are not nice such as:
- Taboola, Outbrain, and other chumbox
- BLOBs
- Europe cookie law
- adhesive inside mobile phones and more generally, planned obsolescence
- Jupyter Notebook
- typographical characters that look like ASCII ones, but are not the ASCII ones, e.g. typographical quotes, em-dash. The non-breaking hyphen is not even whitespace, and by def Why not stick to ASCII when ASCII is good enough?
- excessive encapsulation
- replacement of master and slave terminology from technology
- mailing lists. And to add insult to injury, HTML on mailing list messages instead of plaintext.
- blank lines in code added by people trying to increase clarity, especially when there is already indentation for that. Every blank line must be preceded by a line comment explaining what the following block is about, or removed.
- messaging software that force you to have a mobile phone
- advertisements by telephone/SMS
- "state" such as global variables and object members, long live functional programming?
- mosquitoes, the only intrinsically bad thing about tropical countries
- projects with slow compilation times
- Microsoft Windows
- the 2019 Chinese government
- e-learning websites that only allows verified teachers to write content. Cowards who can't handle ranking algorithms.
- domain-specific language
- a build system without an out-of-tree option
- non-linear Git history: stackoverflow.com/questions/20348629/what-are-advantages-of-keeping-linear-history-in-git
- visual programming languages like Scratch. Waste of time. Text programming languages are already equally as visual due to indentation:Just make good serious gamedev libraries and integrated development environments for those real languages instead.
if x == 0: x = 1 - software that prevents you from running as root. Let me fucking shoot myself in the foot if I want to. It is better than having to deal with your hand holding bullshit, which is done in a different way for every project. E.g.: stackoverflow.com/questions/17466017/how-to-solve-you-must-not-be-root-to-run-crosstool-ng-when-using-ct-ng/53099177#53099177
- Medium
- luxury goods
- euphemism
- closed access academic journals are evil
- websites without OAuth
- shower room without a window to the exterior (mould!!!)
- single programs with their interface split across multiple windows, e.g. GIMP, ZynAddSubFX
- graphical user interfaces
- logograms
- infinitesimals. Just use limit instead, please
- country
- knowledge olympiads
- programming languages without a decent dominating package system
- closed source offline software used by millions
- exams
- security through obscurities
- dots in Gmail address
- things in websites that look like links, and behave like links, but don't let you middle click to open them on a separate tab
- K-pop
- numerical computing language
- fiscal paradises
- when the front-end of an website changes an important permanent state, but the URL does not change
- splash screens: you should show boot messages so that people will know what to Google for when things fail. Do you think computer newbies will be afraid and have nightmares?
- milk chocolate: why would you eat that instead of dark chocolate if you are older than 10?
- to talk about something without giving the real name to not scare off the audience
- mathematical symbol that looks like a Greek letter but isn't. Or perhaps mathematical notation in general
- when more than two people gather to play a board game or video game, and two or more people start chatting on and on about random subjects rather than concentrating on the game
- watching television while eating. Same for reading, or doing basically anything else but eat. The only acceptable activity is talking relaxedly, not about work.
- noises coming out of your bicycle. It is so hard to find where they come to fix them!!!
- code drop
- private cars as opposed to public transport. As a cyclist, you can just see the effect that large roads have on nearby areas, it just destroys nature.
- closed standards
- double consonants that make no difference to sound. Dilema? Dilemma? Dillema? Dillemma? Please!
- social media websites that show stuff from people you don't follow when you don't explicitly want that, including things which are not ads, just random suggestions. Twitter starting being like that cirac a 2022. Facebook got worse around that time. It is a constant fight against those stupid websites.
- socks with short legs that don't protect your ankle/lower calf from cold/scratches/dirt, e.g. liner socks
- Presta valves. Why would such a flimsy tech have become so popular compared to the infinitely superior Schrader!
GPU accelerated, simulates the Craig's minimized M. genitalium, JCVI-syn3A at a particle basis of some kind.
Lab head is the cutest-looking lady ever: chemistry.illinois.edu/zan, Zaida (Zan) Luthey-Schulten.
- 2022 paper: www.cell.com/cell/fulltext/S0092-8674(21)01488-4 Fundamental behaviors emerge from simulations of a living minimal cell by Thornburg et al. (2022) published on Cell
- faculty.scs.illinois.edu/schulten/lm/ actual source code. No Version control and non-code drop release, openess and best practices haven't reached such far obscure reaches of academia yet. One day.
- blogs.nvidia.com/blog/2022/01/20/living-cell-simulation/ Nvidia announcement. That's how they do business, it is quite interesting how they highlight this kind of research.
- catalog.ngc.nvidia.com/orgs/hpc/containers/lattice-microbes has a container
Conveyor belt 2D top down mining like Factorio, but with more emphasis on tower defense/real-time strategy, PvP looks a lot like StarCraft or Age of Empires.
As of pre alpha 135, the most annoying thing is that you can't easily start a campaign scenario from fresh, if you lose you have to start from wave 1 but with everything already half built as you left it. This gives you a huge advantage...
It is also annoying that you have to manually rebuild everything that was destroyed afer each attack, unless you have some unit that you can only unlock later on...
mindustry-unofficial.fandom.com/wiki/Future_Content#New_Google_Play_Listing suggests freemium features being considered, but they are mostly minor or plaform specific. There seems to be no server list by default however, making the Steam multiplayer freemium valuable.
www.youtube.com/watch?v=o5ThSECaAwA suggests code drop is used.
It is a bit annoying that you have to unlock the tech tree little by little in campaign, but it does serve as a reasonable introduction to the general order of development. Games with progression state are boring, except when there is permadeath. But custom play scenarios have everything unlocked immediately, much better.
It is very cool that you can copy chunks of buildings as macros, and save them for later.
The game runs very well it feels like.
The logic blocks are particularly interesting, and allow you to program a block yourself.