Subdepartment of the Department of Physics of the University of Oxford Updated 2025-07-16
E. Coli Whole Cell Model by Covert Lab Output overview Updated 2025-07-16
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 Plots are also available in SVG and PDF formats, e.g.:
out/ withfind -name '*.png'The output directory has a hierarchical structure of type:where:
./out/manual/wildtype_000000/000000/generation_000000/000000/wildtype_000000: variant conditions.wildtypeis a human readable label, and000000is an index amongst the possiblewildtypeconditions. 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'snp.random.seedgenereation_000000: this will increase with generations if we simulate multiple cells, which is supported by the model000000: 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.pdfEach of thoes four levels of
plotOut is generated by a different one of the analysis scripts:./out/manual/plotOut: generated bypython 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 bypython runscripts/manual/analysisCohort.py --variant_index 0. TODO not sure how to differentiate between two different labels e.g.wildtype_000000andsomethingElse_000000. If-vis 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 bypython runscripts/manual/analysisMultigen.py --variant_index 0 --seed 0./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut: generated bypython runscripts/manual/analysisSingle.py --variant_index 0 --seed 0 --generation 0 --daughter 0. Contains information about a single specific cell.
Mainframe computer Updated 2025-07-16
Mao Zedong Updated 2025-07-16
Maser Updated 2025-07-16
Principles of the Optical Maser by Bell Labs
. Source. Date: 1963. Netflix Updated 2025-07-16
Tritium Updated 2025-07-16
College puffer jacket Updated 2025-07-16
E.g.: thecollegestore.co.uk/products/ladies-oxford-college-puffer-jacket?variant=40590030864549 Black with 5 rows, on left chest "colege name", logo, "Oxford", and right chest optional initials (or sometimes other identifiers/nicknames) to help distinguish from all the other people's identical clothes.
This has a whitelabel version: www.workweargiant.co.uk/product/result-urban-holkham-down-feel-jacket/, the name appears to be "Holkham Down Feel Jacket".
If you look 20 and wear one of those, it's almost an ID, you can get anywhere that does not require a key card, porters won't look at you twice!
- www.oxfordstudent.com/2019/03/25/in-opposition-to-stash/ In opposition to stash by Morgan Jones (2019), basically because university is your last chance to wear what you want on many professions.
Educational charitable organization Updated 2025-07-16
In this section we list charitable organizations that support education or research:
- elifesciences.org/labs by eLife
- www.digital-science.com/investment/catalyst-grant/ by Shuttleworth Foundation.
- en.wikipedia.org/wiki/PLOS
- www.chanzuckerberg.com/ Zuck has already invested in education previously:
- openuk.uk/
- Sir Peter Lampl, Education Endowment Foundation and Sutton Trust
- Jacobs Foundation, by German-Swiss coffee mogul Klaus Johann Jacobs
- joint-research-centre.ec.europa.eu/what-open-education_en
- www.non-trivial.org/ "Launch Your Own Impactful Project CHOOSE YOUR CAUSE. GET EXPERT GUIDANCE. FIND A SOLUTION AND MAKE IT HAPPEN."
- by United States Government:
- FY 2024 Education Innovation and Research:
- Education Innovation and Research (EIR) Notices Inviting Applications
- oese.ed.gov/offices/office-of-discretionary-grants-support-services/innovation-early-learning/education-innovation-and-research-eir/fy-2024-competition/
- www.federalregister.gov/documents/2024/05/06/2024-09797/applications-for-new-awards-education-innovation-and-research-eir-program-early-phase-grants
- FY 2024 Education Innovation and Research:
Shooter game Updated 2025-07-16
Ciro's Edict #5 Not work Updated 2025-07-16
Why are there two sexes? Updated 2025-07-16
Year 2 of the mathematics course of the University of Oxford Updated 2025-07-16
Domain Name System Updated 2025-07-16
Jesus Christ Superstar (1973) Updated 2025-07-16
Josephson effect regime Updated 2025-07-16
L Updated 2025-07-16
National Security Agency Updated 2025-07-16
O Updated 2025-07-16
Arrow of time Updated 2025-07-16
There are unlisted articles, also show them or only show them.