Fermion Updated 2025-07-16
Permanent private hall Updated 2025-07-16
Similar to a college, but led by religious denomination leaders rather than fellows.
Aragonite Updated 2025-07-16
Boson Updated 2025-07-16
In this section we document the outcomes of more detailed inspection of both the communication mechanisms (JavaScript, JAR, swf) and HTML that might help to better fingerprint the websites.
But by looking at the URLs of the screenshots they provided from other websites we can easily uncover all others that had screenshots, except for the Johnny Carson one, which is just generically named. E.g. the image for the Chinese one is www.reuters.com/investigates/special-report/assets/usa-spies-iran/screencap-activegaminginfo.com.jpg?v=192516290922 which leads us to domain activegaminginfo.com.
Oleg Shakirov later discovered that the Carson one had its domain written right on the screenshot, as part of a watermark present on the original website itself. Therefore the URLs of all the websites were in one way or another essentially given on the article.
The full list of domains from screenshots is:
Vaterite Updated 2025-07-16
AppImage Updated 2025-07-16
CPT symmetry Updated 2025-09-17
Crow intelligence experiment Updated 2025-07-16
Video 1.
Causal understanding of water displacement by a crow by PLOS Media (2014)
Source.
webpack/template Updated 2025-07-16
../webpack/template contains a reasonable starter template.
This will produce, under dist/ the following minimized files:
You can also run this test with the development server on localhost:9000:
npm start
which uses unminimized outptus, and automatically push reloads the page whenever you change any of the input files!
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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