= E. Coli Whole Cell Model by Covert Lab
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https://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 https://github.com/CovertLab/WholeCellEcoliRelease/discussions/23[rationale on GitHub discussion], and they confirmed as expected that it is to:
* to prevent their <academic publishing>[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 :-)
Oh well.
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 software>[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.
Everything in this section refers to version https://github.com/CovertLab/WholeCellEcoliRelease/tree/7e4cc9e57de76752df0f4e32eca95fb653ea64e4[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.