Ciro Santilli @cirosantilli 37

GoDaddy Updated 2025-07-16

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Graduate course of the University of Oxford Updated 2025-07-16

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Mathematical, Physical and Life Sciences division of the University of Oxford Updated 2025-07-16

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www.mpls.ox.ac.uk/

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Strong CP problem Updated 2025-07-16

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Very low frequency Updated 2025-07-16

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Notably used for communication with submarines, so in particular crucial as part of sending an attack signal to that branch of the nuclear triad.

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E. Coli Whole Cell Model by Covert Lab / Install and first run Updated 2025-07-16

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At 7e4cc9e57de76752df0f4e32eca95fb653ea64e4 you basically need to use the Docker image on Ubuntu 21.04 due to pip breaking changes... (not their fault). Perhaps pyenv would solve things, but who has the patience for that?!?!

The Docker setup from README does just work. The image download is a bit tedius, as it requires you to create a GitHub API key as described in the README, but there must be reasons for that.

Once the image is downloaded, you really want to run is from the root of the source tree:

sudo docker run --name=wcm -it -v "$(pwd):/wcEcoli" docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full

This mounts the host source under /wcEcoli, so you can easily edit and view output images from your host. Once inside Docker we can compile, run the simulation, and analyze results with:

make clean compile &&
python runscripts/manual/runFitter.py &&
python runscripts/manual/runSim.py &&
python runscripts/manual/analysisVariant.py &&
python runscripts/manual/analysisCohort.py &&
python runscripts/manual/analysisMultigen.py &&
python runscripts/manual/analysisSingle.py

The meaning of each of the analysis commands is described at Section "Output overview".

As a Docker refresher, after you stop the container, e.g. by restarting your computer or running sudo docker stop wcm, you can get back into it with:

sudo docker start wcm
sudo docker run -it wcm bash

runscripts/manual/runFitter.py takes about 15 minutes, and it generates files such as reconstruction/ecoli/dataclasses/process/two_component_system.py (related) which is required to run the simulation, it is basically a part of the build.

runSim.py does the main simulation, progress output contains lines of type:

Time (s)  Dry mass     Dry mass      Protein          RNA    Small mol     Expected
              (fg)  fold change  fold change  fold change  fold change  fold change
========  ========  ===========  ===========  ===========  ===========  ===========
    0.00    403.09        1.000        1.000        1.000        1.000        1.000
    0.20    403.18        1.000        1.000        1.000        1.000        1.000

and then it ended on the Lenovo ThinkPad P51 (2017) at:

 2569.18    783.09        1.943        1.910        2.005        1.950        1.963

Simulation finished:
 - Length: 0:42:49
 - Runtime: 0:09:13

when the cell had almost doubled, and presumably divided in 42 minutes of simulated time, which could make sense compared to the 20 under optimal conditions.

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Ionizing and non-ionizing radiation Updated 2025-07-16

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Ray Sidney Updated 2025-07-16

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www.linkedin.com/in/ray-sidney-380b126b/

Said to be the 5th Google employee, and Eileen Gu's father: gossipnextdoor.com/meet-ray-sidney-eileen-guus-alleged-dad/

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RISC-V priviledged ISA Updated 2025-07-16

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Snap (package manager) Updated 2025-07-16

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merlijn.sebrechts.be/blog/2020-08-02-why-one-snap-store/ has some very good comments on how snap is more closed than Flatpak.

Snap's permission system is extremely annoying, notably restricting access to home files. They need a popup that says "permission required by app, accept?" urgently!!!