This contains the C. elegans connectome.
The browseable thing is this massive interactive PDF: wormwiring.org/papers/Interactive-Diagram.pdf. It lists neurons from the C. elegans cell lineage using the standard cell names, and how they connect to each other. Some make a surprising ammount of connections.
TODO what does it contain. Does it have metabolic pathways?
Mass fraction summary plot analysis by 
Ciro Santilli 35 Updated 2025-04-18 +Created 2024-12-04
Ciro Santilli 35 Updated 2025-04-18 +Created 2024-12-04Let'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 35 Updated 2025-04-18 +Created 2024-12-04
Ciro Santilli 35 Updated 2025-04-18 +Created 2024-12-04Superset 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 35 Updated 2025-04-18 +Created 2024-12-04
Ciro Santilli 35 Updated 2025-04-18 +Created 2024-12-04Presumably 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.
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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.
Pinned article: ourbigbook/introduction-to-the-ourbigbook-project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 2. You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website.
Figure 3. Visual Studio Code extension installation.
Figure 5. . You can also edit articles on the Web editor without installing anything locally. Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact