Drake (robotics software) Updated +Created
The Robotics team at TRI is working hard to close the gap between simulation and reality. For manipulation, one important piece is accurate simulation of rigid-body contact.
Drug traffic Updated +Created
High pressure Updated +Created
Video 1.
Something weird happens when you keep squeezing by Vox (2023)
Source. Sodium becomes liquid when you compress it. Weird.
Klein-Gordon equation Updated +Created
A relativistic version of the Schrödinger equation.
Correctly describes spin 0 particles.
The most memorable version of the equation can be written as shown at Section "Klein-Gordon equation in Einstein notation" with Einstein notation and Planck units:
Has some issues which are solved by the Dirac equation:
Baltimore classification Updated +Created
Emulator Updated +Created
One of the things Ciro Santilli really likes, see: Linux Kernel Module Cheat.
Gvim Updated +Created
Pitch drop experiment Updated +Created
Bruker Corporation Updated +Created
E. Coli genome starting point Updated +Created
The conventional starting point is not at the E. Coli K-12 MG1655 origin of replication.
biocyc.org/ECOLI/NEW-IMAGE?type=EXTRAGENIC-SITE&object=G0-10506 explains:
This site is the origin of replication of the E. coli chromosome. It contains the binding sites for DnaA, which is critical for initiation of replication. Replication proceeds bidirectionally. For historical reasons, the numbering of E. coli's circular chromosome does not start at the origin of replication, but at the origin of transfer during conjugation.
If it is a bit hard to understand what they mean by "origin of transfer" though, as that term is usually associated with the origin of transfer of bacterial conjugation.
Covariant formulation of classical electromagnetism Updated +Created
Lie algebra of Updated +Created
Quantum electrodynamics experiment Updated +Created
Sandia National Laboratories Updated +Created
Square root Updated +Created
E. Coli K-12 MG1655 gene ytdX Updated +Created
E. Coli Whole Cell Model by Covert Lab / Output overview Updated +Created
Run output is placed under out/:
Some of the output data is stored as .cpickle files. To observe those files, you need the original Python classes, and therefore you have to be inside Docker, from the host it won't work.
We can list all the plots that have been produced under out/ with
find -name '*.png'
Plots are also available in SVG and PDF formats, e.g.:
  • PNG: ./out/manual/plotOut/low_res_plots/massFractionSummary.png
  • SVG: ./out/manual/plotOut/svg_plots/massFractionSummary.svg The SVGs write text as polygons, see also: SVG fonts.
  • PDF: ./out/manual/plotOut/massFractionSummary.pdf
The output directory has a hierarchical structure of type:
./out/manual/wildtype_000000/000000/generation_000000/000000/
where:
  • wildtype_000000: variant conditions. wildtype is a human readable label, and 000000 is an index amongst the possible wildtype conditions. For example, we can have different simulations with different nutrients, or different DNA sequences. An example of this is shown at run variants.
  • 000000: initial random seed for the initial cell, likely fed to NumPy's np.random.seed
  • genereation_000000: this will increase with generations if we simulate multiple cells, which is supported by the model
  • 000000: this will presumably contain the cell index within a generation
We also understand that some of the top level directories contain summaries over all cells, e.g. the massFractionSummary.pdf plot exists at several levels of the hierarchy:
./out/manual/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/000000/plotOut/massFractionSummary.pdf
./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut/massFractionSummary.pdf
Each of thoes four levels of plotOut is generated by a different one of the analysis scripts:
  • ./out/manual/plotOut: generated by python runscripts/manual/analysisVariant.py. Contains comparisons of different variant conditions. We confirm this by looking at the results of run variants.
  • ./out/manual/wildtype_000000/plotOut: generated by python runscripts/manual/analysisCohort.py --variant_index 0. TODO not sure how to differentiate between two different labels e.g. wildtype_000000 and somethingElse_000000. If -v is not given, a it just picks the first one alphabetically. TODO not sure how to automatically generate all of those plots without inspecting the directories.
  • ./out/manual/wildtype_000000/000000/plotOut: generated by python runscripts/manual/analysisMultigen.py --variant_index 0 --seed 0
  • ./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut: generated by python runscripts/manual/analysisSingle.py --variant_index 0 --seed 0 --generation 0 --daughter 0. Contains information about a single specific cell.
Knol Updated +Created
Very similar to OurBigBook.com!
People who worked on it:
Video 1.
How to use Google Knol by Hack Learning (2011)
Source. One of the last users of the website for sure! The owner of that YouTube channel is a Mark Barnes:
Video 2.
Jimmy Wales on Google's Knol (2008)
Source.
Replying to a listener phone-in question WNYC radio, mediated by Brian Lehrer.
It was about to launch it seems, and it was not clear at the time that anyone could write content, as opposed to only selected people.
Jimmy then corrects that misinformation. He then clearly states that since there can be multiple versions of each article, including opinion pieces, like OurBigBook.com, Knol would be very different to Wikipedia, more like blogging than encyclopedia.
Video 3.
Google Knol: the future of academic journals? by Doug Belshaw (2010)
Source.
Bibliography:
Education Updated +Created
One of the causes Ciro Santilli care the most about: motivation.
A list of complaints against education: Section "Education is broken".
How to improve education? Simple:

There are unlisted articles, also show them or only show them.