TODO what does it contain. Does it have metabolic pathways?
E. Coli Whole Cell Model by Covert Lab Mass fraction summary plot analysis by 
Ciro Santilli 37 Created 2024-12-04 Updated 2025-07-16
Ciro Santilli 37 Created 2024-12-04 Updated 2025-07-16Let's look into a sample plot,
out/manual/plotOut/svg_plots/massFractionSummary.svg, and try to understand as much as we can about what it means and how it was generated.This plot contains how much of each type of mass is present in all cells. Since we simulated just one cell, it will be the same as the results for that cell.
We can see that all of them grow more or less linearly, perhaps as the start of an exponential. We can see that all of them grow more or less linearly, perhaps as the start of an exponential. We can see that all of them grow more or less linearly, perhaps as the start of an exponential.which must correspond to the different
By grepping the title "Cell mass fractions" in the source code, we see the files:
models/ecoli/analysis/cohort/massFractionSummary.py
models/ecoli/analysis/multigen/massFractionSummary.py
models/ecoli/analysis/variant/massFractionSummary.pymassFractionSummary plots throughout different levels of the hierarchy.By reading
models/ecoli/analysis/variant/massFractionSummary.py a little bit, we see that:- the plotting is done with Matplotlib, hurray
- it is reading its data from files under
./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Mass/, more precisely./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Mass/columns/<column-name>/data. They are binary files however.Looking at the source forwholecell/io/tablereader.pyshows that those are just a standard NumPy serialization mechanism. Maybe they should have used the Hierarchical Data Format instead.We can also take this opportunity to try and find where the data is coming from.Massfrom the./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Mass/looks like an ID, so wegrepthat and we reachmodels/ecoli/listeners/mass.py.From this we understand that all data that is to be saved from a simulation must be coming from listeners: likely nothing, or not much, is dumped by default, because otherwise it would take up too much disk space. You have to explicitly say what it is that you want to save via a listener that acts on each time step.
More plot types will be explored at time series run variant, where we will contrast two runs with different growth mediums.
All publicly funded research and teaching materials should be free by Ciro Santilli 37 Created 2024-12-04 Updated 2025-07-16
Ciro Santilli 37 Created 2024-12-04 Updated 2025-07-16Superset of force public university teachers to publish their teaching material with an open license.
One particularly obscene case Ciro Santilli encountered was: all DVSA materials should be free.
The embryonic cell lineage of the nematode Caenorhabditis elegans by Ciro Santilli 37 Created 2024-12-04 Updated 2025-07-16
Ciro Santilli 37 Created 2024-12-04 Updated 2025-07-16Presumably John's 2002 Nobel Prize in Physiology and Medicine paper.
Hobert Lab just uploaded a print and that's it: www.hobertlab.org/wp-content/uploads/2013/03/Sulston_embryonic_lineage_1983.pdf. Hero.
Monumental 55 page beast, presumably the culmination of many years of work.
www.linkedin.com/in/jeff-dean-8b212555/ Joined Google in 1999.
Cute dynamic duo: www.newyorker.com/magazine/2018/12/10/the-friendship-that-made-google-huge They were at Google in 2000 at least.
Good mentions at The man who loved numbers, notably youtu.be/PqP2c5xNaTU?t=349 where Bela Bollobas, friend of Littlewood, talks about their collaboration.
Some good mentions of their dynamic duo status at The Race for the Double Helix. Their chemistry and love are palpable during their joint interviews.
Very clearly, Francis is the charismatic one, and James is the nerd.
Enrico Fermi's father.
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