!!! Survivorship bias alert !!!
quoteinvestigator.com/2018/05/07/overcome/
If you want to do something, but you are afraid to do it, then that is likely what you should do.
www.goodreads.com/quotes/50458-whatever-you-re-meant-to-do-do-it-now-the-conditions Doris Lessing:
Whatever you're meant to do, do it now. The conditions are always impossible.
For example, when Ciro Santilli was deciding what to do in university, he wanted mostly to do pure physics.
But because he was afraid he was going to die poor and unemployed because of that, he picked engineering instead.
That was a mistake.
His family was not even poor. He was young and did not have a family to support. His father even told him: "do whatever the fuck you want, we support your decision".
But he was a coward.
It was also in part because a physicist uncle which he respected suggested that as an engineer Ciro might be able to make useful contributions to tooling required by physics. When Roberto Salmeron died in 2020, Ciro's friends shared this 2013 video interview with the late professor, where he explains he first went to the University of São Paulo to study engineering (like Ciro), but then fell for his passion for physics (like Ciro?), his first task being to build a Geiger counter, thus explaining the likely origin of the uncle's theory. But who knows, maybe he was right. Maybe Ciro's OurBigBook.com will become huge and help a lot of people, and it might not have had Ciro not done engineering and learnt programming. Destiny operates in weird ways sometimes.
Furthermore, while in University, Ciro learnt about the molecular Sciences Course of the University of São Paulo, a fantastic sounding full time course that any student could transfer to called that teaches various natural sciences topics which Ciro loves (Mathematics, Physics, Chemistry, Biology) and which students from the entire university can apply to transfer to only after joining the university, with the guarantee that they can go back to their original courses if they didn't adapt to the new course.
But did Ciro do it? Nope, he remained an even larger coward.
Had he studied more sciences, he might have been happier, and might have had greater achievements later in life, in particular when he went to École Polytechnique.
Similar thoughts crossed his mind when he started his campaign for freedom of speech in China, but this time he had learnt the lesson, and went for it, and it felt very good.
If you have a day job, but also have a dream, and want to keep the day job for a reason, try to reserve the time of the day that your brain works best before or after work for your dream: do one cool thing every day.
Companies can help you grow because you see real problems from within them, but their end goal is to consume you as much as possible. Don't let that happen. Invest part of what you gain, in yourself. www.outsideonline.com/outdoor-adventure/paradox-going-outside/ The Paradox of Going Outside by James Somers (2012) puts it incredibly well:
I work, for instance, as a Web developer. It's a very good job. Our office is a block south of Union Square, a 12-minute commute from my apartment. We're served breakfast every morning. Our kitchen is stocked with "provisions" of organic beef jerky, coconut water, craft beers, chips, and two restaurant-class espresso machines. We have two ping pong tables and buckets of 3-star ping pong balls. (A new office manager bought "1-stars" once and some of the guys protested by crushing them.) We work on 4-cored Apple Mac computers with dual monitors. We have an unmolested hour for lunch, 10-minute breaks in the morning and afternoon, and a "do not disturb" policy past the working hours. We even have a specific email address where employees can ask for free things: genuine maple syrup, hot chocolate, a $900 chair, a new keyboard. Most of the programmers make six figures, and many of those have only three or four years of experience.It's impossible to say so without sounding like the spokesperson for Entitlement itself but working there is still sort of soul-crushing. It's soul-crushing in the way that any job that doesn't command your full passionate attention must be. What happens is that I will be in my chair in the early afternoon and I will accidentally step out of myself and all I'll see is time passing, nine-hour parcels of healthy consciousness forever being packed away as the user experience of clerical workers or consumers or whoever gets marginally better; and I'll end up thinking that this enterprise of mine is not so much creative but bureaucratic, that what I've gotten good at is reading the instruction manuals of other people, finding my way around their insignificant warrens. And in those moments the whole business will seem to me like kind of a tragic waste.
Other quotes:
- is a phrase Sergey Brin uses. The Google Story claims he picked that up from academia, and quotes this from a september 2003 talk in an Israeli elite high school.
Healthy Disregard For The Impossible
- quoteinvestigator.com/2014/05/29/find-love/
Find What You Love and Let It Kill You
- Cute boy things by Caroline Ellison:
if you are a boy with the confidence to advocate for unconventional ideas and take actions based on them you are valid
- How can I be as great by Justine Musk:
rock the boat
- From the 1922 poem Portuguese Sea by famous Portuguese poet Fernando Pessoa, which gets drilled into the head of every Brazilian high school student:He who wants to pass beyond the Bojador
Must go beyond pain.Quem quer passar além do Bojador
Tem que passar além da dor. - Translation of a poem by Muhammad Iqbal TODO date:One is reminded of As iron sharpens iron, so one person sharpens another.
- "NPC life" as a way to refer to a soul crushing job
- twitter.com/0xTenkito/status/1775167216641548732, a cryptocurrency investor says:However there is one thing to lose, if you do safer investments and don't lose everything, then you might be able to retire earlier.
- archive.ph/mlaLK
- twitter.com/0xTenkito/status/1775167216641548732, a cryptocurrency investor says:
Dilbert "A small brain irrationally puts more weight on a small loss than on a huge opportunity" cartoon (2000)
Source. 
Jake Likes Onions "Slowly" cartoon
. Source. This is what trying to reach a dream part time feels like. The cartoon reads: "The tiger pursues its prey. Slowly. The human pursues its life goals. Slowly. Very slowly.".Excerpt from the documentary film "Steve Jobs: Secrets of Life" (1994)
Source. When you grow up you tend to get told that the world is the way it is and your life is just to live your life inside the world. Try not to bash into the walls too much. Try to have a nice family life, have fun, save a little money. That's a very limited life. Life can be much broader once you discover one simple fact: Everything around you that you call life was made up by people that were no smarter than you. And you can change it, you can influence it... Once you learn that, you'll never be the same again.
Of course, survivorship bias alert!
What Would You Do If Money Were No Object by Alan Watts
. Source. Sample transcription: genius.com/Alan-watts-what-if-money-was-no-object-annotated:What do you desire? What makes you itch? What sort of a situation would you like?Let's suppose, I do this often in vocational guidance of students, they come to me and say, well, "we're getting out of college and we have the faintest idea what we want to do". So I always ask the question, "what would you like to do if money were no object? How would you really enjoy spending your life?"Well, it's so amazing as a result of our kind of educational system, crowds of students say well, we'd like to be painters, we'd like to be poets, we'd like to be writers, but as everybody knows you can't earn any money that way. Or another person says well, I'd like to live an out-of-doors life and ride horses. I said you want to teach in a riding school?Let's go through with it. What do you want to do? When we finally got down to something, which the individual says he really wants to do, I will say to him, you do that and forget the money, because, if you say that getting the money is the most important thing, you will spend your life completely wasting your time. You'll be doing things you don't like doing in order to go on living, that is to go on doing things you don't like doing, which is stupid. Better to have a short life that is full of what you like doing than a long life spent in a miserable way.And after all, if you do really like what you're doing, it doesn't matter what it is, you can eventually turn it - you could eventually become a master of it. It's the only way to become a master of something, to be really with it. And then you'll be able to get a good fee for whatever it is. So don't worry too much. That's everybody is - somebody is interested in everything, anything you can be interested in, you will find others will.But it's absolutely stupid to spend your time doing things you don't like, in order to go on spending things you don't like, doing things you don't like and to teach our children to follow in the same track. See what we are doing, is we're bringing up children and educating to live the same sort of lives we are living. In order that they may justify themselves and find satisfaction in life by bringing up their children to bring up their children to do the same thing, so it's all retch and no vomit. It never gets there. And so, therefore, it's so important to consider this question: What do I desire?
Keep Chargin' from a Show of Hands by Victor Wooten (1996)
Source. That's the way I live my life, I give it my all. I think that a person should really make up his mind what he wants to do, and when did made up, he cannot fail at it. The basic rule to sucess I think, is when the going gets tough, that is a positive signal to keep chargin'.
Charles Bukowski is one of the most hardcore don't be a pussy people ever. It's almost scary. Far beyond Ciro level.
thebestamericanpoetry.typepad.com/the_best_american_poetry/2008/11/the-laughing-he.html
your life is your life
don't let it be clubbed into dank submission.
be on the watch.
there are ways out.
there is light somewhere.
it may not be much light but
it beats the darkness.
be on the watch.
the gods will offer you chances.
know them.
take them.
you can't beat death but
you can beat death in life, sometimes.
and the more often you learn to do it,
the more light there will be.
your life is your life.
know it while you have it.
you are marvelous
the Gods wait to delight
in you.
www.goodreads.com/quotes/39207-if-you-re-going-to-try-go-all-the-way-otherwise
If you're going to try, go all the way. Otherwise, don't even start. This could mean losing girlfriends, wives, relatives and maybe even your mind. It could mean not eating for three or four days. It could mean freezing on a park bench. It could mean jail. It could mean derision. It could mean mockery--isolation. Isolation is the gift. All the others are a test of your endurance, of how much you really want to do it. And, you'll do it, despite rejection and the worst odds. And it will be better than anything else you can imagine. If you're going to try, go all the way. There is no other feeling like that. You will be alone with the Gods, and the nights will flame with fire. You will ride life straight to perfect laughter. It's the only good fight there is.
I have one of two choices - stay in the post office and go crazy... or stay out here and play at writer and starve. I have decided to starve.
Bukowski kissing his typewriter.
Like Ciro Santilli and his computer!All adults are bored scene from an Edward Teller, An Early Time
. Source. Up to the time that I met Klug ([a mathematiciam]), I was sure that all grown ups were people to be pitied. They had to work, they were tired, they were bored with what they were doing. I heard both my parents often complain. Klug was the first man whom I met who most obviously enoyed what he was doing.
Most definitions tend to be bilinear forms.
We use the unqualified generally refers to the dot product of Real coordinate spaces, which is a positive definite symmetric bilinear form. Other important examples include:The rest of this section is about the case.
- the complex dot product, which is not strictly symmetric nor linear, but it is positive definite
- Minkowski inner product, sometimes called" "Minkowski dot product is not positive definite
The positive definite part of the definition likely comes in because we are so familiar with metric spaces, which requires a positive norm in the norm induced by an inner product.
The default Euclidean space definition, we use the matrix representation of a symmetric bilinear form as the identity matrix, e.g. in :so that:
Our WIP script: wikipedia/import-categories.sh.
Related:
- opendata.stackexchange.com/questions/1533/download-wikipedia-articles-from-a-specific-category
- webapps.stackexchange.com/questions/16359/is-there-a-way-to-download-a-list-of-all-wikipedia-categories/172480#172480
- stackoverflow.com/questions/40119322/how-to-download-all-pages-inside-a-category-in-wikipedia
- category tree on Stack Overflow
- stackoverflow.com/questions/17432254/wikipedia-category-hierarchy-from-dumps/77313490#77313490 Canon but no good answers.
- stackoverflow.com/questions/12227134/how-to-fetch-category-tree-of-wiki
- stackoverflow.com/questions/21782410/finding-subcategories-of-a-wikipedia-category-using-category-and-categorylinks-t. Actually explains it: stackoverflow.com/questions/21782410/finding-subcategories-of-a-wikipedia-category-using-category-and-categorylinks-t/21798259#21798259
- stackoverflow.com/questions/27279649/how-to-build-wikipedia-category-hierarchy
- mdkzaman.com/knowledge-graph-from-wikipedia-category-hierarchy/
Consider:
Let's observe them in MySQL:outputs:
mysql enwiki -e "select page_id, page_namespace, page_title, page_is_redirect from page where page_namespace in (0, 14) and page_title in ('Computer_storage_devices', 'Computer_data_storage')"+----------+----------------+--------------------------+------------------+
| page_id | page_namespace | page_title | page_is_redirect |
+----------+----------------+--------------------------+------------------+
| 5300 | 0 | Computer_data_storage | 0 |
| 42371130 | 0 | Computer_storage_devices | 1 |
| 711721 | 14 | Computer_data_storage | 0 |
| 895945 | 14 | Computer_storage_devices | 0 |
+----------+----------------+--------------------------+------------------+mysql enwiki -e "select cl_from, cl_to from categorylinks where cl_from in (5300, 711721, 895945, 42371130)"+----------+-----------------------------------------------------------------------+
| cl_from | cl_to |
+----------+-----------------------------------------------------------------------+
| 5300 | All_articles_containing_potentially_dated_statements |
| 5300 | Articles_containing_potentially_dated_statements_from_2009 |
| 5300 | Articles_containing_potentially_dated_statements_from_2011 |
| 5300 | Articles_with_GND_identifiers |
| 5300 | Articles_with_NKC_identifiers |
| 5300 | Articles_with_short_description |
| 5300 | Computer_architecture |
| 5300 | Computer_data_storage |
| 5300 | Short_description_matches_Wikidata |
| 5300 | Use_dmy_dates_from_June_2020 |
| 5300 | Wikipedia_articles_incorporating_text_from_the_Federal_Standard_1037C |
| 711721 | Computer_architecture |
| 711721 | Computer_data |
| 711721 | Computer_hardware_by_type |
| 711721 | Data_storage |
| 895945 | Computer_data_storage |
| 895945 | Computer_peripherals |
| 895945 | Recording_devices |
| 42371130 | Redirects_from_alternative_names |
+----------+-----------------------------------------------------------------------+So we see that
cl_from encodes the parent categories:- parent categories of categories:
- en.wikipedia.org/wiki/Category:Computer_data_storage, which has ID
711721, has parent categories: "Computer hardware by type", "Computer data", "Data storage", "Computer architecture". This matches exactly on the database. These are all encoded on the source code of the page:{{DEFAULTSORT:Storage}} [[Category:Computer hardware by type]] [[Category:Computer data|Storage]] [[Category:Data storage|Computer]] [[Category:Computer architecture]] - en.wikipedia.org/wiki/Category:Computer_storage_devices has parent categories: "Computer data storage", "Recording devices", "Computer peripherals". This matches exactly on the database.
- en.wikipedia.org/wiki/Category:Computer_data_storage, which has ID
- parent categories of pages:
- en.wikipedia.org/wiki/Computer_storage_devices whish is a redirect gets the magic category "Redirects_from_alternative_names", a humongous placeholder with many thousands of pages: en.wikipedia.org/wiki/Category:Redirects_from_alternative_names
- en.wikipedia.org/wiki/Computer_data_storage shows only two categories onthe web UI: "Computer data storage" and "Computer architecture". Both of these are present on the database and at the end of the source code:The others appear to be more magic. Two of them we can guess from the templates:
{{DEFAULTSORT:Computer Data Storage}} [[Category:Computer data storage| ]] [[Category:Computer architecture]]are likely{{short description|Storage of digital data readable by computers}} {{Use dmy dates|date=June 2020}}Use_dmy_dates_from_June_2020andArticles_with_short_descriptionbut the rest is more magic and not necessarily present in-source.
So to find all articls and categories under a given category title, say en.wikipedia.org/wiki/Category:Mathematics we can run:
mariadb enwiki -e "select cl_from, cl_to, page_namespace, page_title from categorylinks inner join page on page_namespace in (0, 14) and cl_from = page_id and cl_to = 'Mathematics'"- stackoverflow.com/questions/600079/how-do-i-clone-a-subdirectory-only-of-a-git-repository/52269934#52269934
- summaries:
- dupes:
- file or directory
- file
- only small files:
dumps.wikimedia.org/enwiki/latest/enwiki-latest-all-titles-in-ns0.gz Characterization:
- contains redirects, e.g. en.wikipedia.org/wiki/"Ampere_North" redirects to en.wikipedia.org/wiki/Ampere_North,_New_Jersey and both are present. Noted in this comment: stackoverflow.com/questions/24474288/how-to-obtain-a-list-of-titles-of-all-wikipedia-articles#comment136016773_24474476
Toy model of matter that exhibits phase transition in dimension 2 and greater. It does not provide numerically exact results by itself, but can serve as a tool to theorize existing and new phase transitions.
As mentioned at: stanford.edu/~jeffjar/statmech/intro4.html some systems which can be seen as modelled by it include:
- the spins direction (up or down) of atoms in a magnet, which can undergo phase transitions depending on temperature as that characterized by the Curie temperature and an externally applied magnetic fieldNeighboring spins like to align, which lowers the total system energy.
- the type of atom at a lattice point in a 2-metal alloy, e.g. Fe-C (e.g. steel). TODO: intuition for the neighbor interaction? What likes to be with what? And aren't different phases in different crystal structures?
Also has some funky relations to renormalization TODO.
Bibliography:
The Ising Model in Python by Mr. P Solver
. Source. The dude is crushing it on a Jupyter Notebook.The hard part then is how to make any predictions from it:
- 2024 www.nature.com/articles/d41586-024-02935-z Fly-brain connectome helps to make predictions about neural activity. Summary of "Connectome-constrained networks predict neural activity across the fly visual system" by J. K. Lappalainen et. al.
2024: www.nature.com/articles/d41586-024-03190-y Largest brain map ever reveals fruit fly's neurons in exquisite detail
As of 2022, it had been almost fully decoded by post mortem connectome extraction with microtome!!! 135k neurons.
- 2021 www.nytimes.com/2021/10/26/science/drosophila-fly-brain-connectome.html Why Scientists Have Spent Years Mapping This Creature’s Brain by New York Times
That article mentions the humongous paper elifesciences.org/articles/66039 elifesciences.org/articles/66039 "A connectome of the Drosophila central complex reveals network motifs suitable for flexible navigation and context-dependent action selection" by a group from Janelia Research Campus. THe paper is so large that it makes eLife hang.
Subtle is the Lord by Abraham Pais (1982) page 85:so it is quite cool to see that organic chemistry is one of the things that pushed atomic theory forward. Because when you start to observe that isomers has different characteristics, despite identical proportions of atoms, this is really hard to explain without talking about the relative positions of the atoms within molecules!
However, it became increasingly difficult in chemical circles to deny the reality of molecules after 1874, the year in which Jacobus Henricus van't Hoff and Joseph Achille Le Bel independently explained the isomerism of certain organic substances in terms of stereochemical properties of carbon compounds.
Ciro Santilli supports full legalization of all drugs, because he feels that it would be better overall for the world to have cheaper drugs and more drug addicts, but way, way less organized crime.
These should be extremely controlled of course, with extremely high taxes that puts their price just below the current illegal market, and a complete ban on any positive advertising.
Ciro believes that maybe the government could even go as far as giving free drugs to drug addicts so they don't have to rob to get a fix.
This is notably considering that drug-led organized crime completely dominates and corrupts the politics of many production and trafficking zones, which are already generally poor fucked up places to start with:Ciro's experiences in Brazil such as mentioned at São Remo, the favela next to USP, although much less extreme than the above, also come to mind.
Drug traffic corrupts everything. It prevents development of honest people. It is a cancer, which we have failed time and time a gain to cure. The only cure is to accept the other less insidious of addiction.
Bibliography:
- How to Fix a Drug Scandal (2020) gives a good sense of the relentlessness of the drug war, and how it affects people who are already poor the most
In the context of tensors , we use raised indices to refer to members of the dual basis vs the underlying basis:The dual basis vectors are defined to "pick the corresponding coordinate" out of elements of V. E.g.:By expanding into the basis, we can put this more succinctly with the Kronecker delta as:
Note that in Einstein notation, the components of a dual vector have lower indices. This works well with the upper case indices of the dual vectors, allowing us to write a dual vector as:
This is the one where French Nobel Prizes come from: en.wikipedia.org/wiki/List_of_École_normale_supérieure_people#Nobel_laureates
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: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.
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.
In the 2010's/2020's, many people got excited about getting children in to electronics with cheap devboards, notably with Raspberry Pi and Arduino.
While there is some potential in that, Ciro Santilli always felt that this is very difficult to do, while also keeping his sacred principle of backward design in mind.
The reason for this is that "everyone" already has much more powerful computers at hand: their laptops/desktops and even mobile phones as of the 2020s. Except perhaps if you are thing specifically about poor countries.
Therefore, the advantage using such devboards for doing something that could useful must come from either:
- their low cost. This would be an important consideration if you were to mass produce your product, but that is not going to be the case for learners, at least initially.
- their portability, and closely linked their ability to act as sensors
- their ability to act as actuators, which is often missing from regular computers
- them having hardware accelerators that are not normally present in regular computers, e.g. FPGAs or AI accelerators. And then the demo project must demonstrate that the project is able to do something significantly faster/cheaper on the devboard than on a desktop computer.
And most important of all: you should not start learning phenomena by reading the from first principles derivation.
Instead, you should see what happens in experiments, and how matches some known formula (which hopefully has been derived from first principles).
Only open the boxes (understand from first principles derivation) if the need is felt!
E.g.:
- you don't need to understand everything about why SQUID devices have their specific I-V curve curve. You have to first of all learn what the I-V curve would be in an experiment!
- you don't need to understand the fine details of how cavity magnetrons work. What you need to understand first is what kind of microwave you get from what kind of input (DC current), and how that compares to other sources of microwaves
- lasers: same
Physics is all about predicting the future. If you can predict the future with an end result, that's already predicting the future, and valid.
This is a pre-requisite of Section "Students must have a flexible choice of what to learn".
If the choice of what to learn depend on a years long dependency graph of other obligations, which currently are the increasingly interlinked:you end up without much choice at all.
- passing the University entry exam
- getting your undergrad degree
- getting your PhD
The lock-in periods must be much more fluid and shorter term than those, otherwise it makes the almost inevitable pivots to success impossible.
This is something that Ciro Santilli has heard from several people at the end of their undergrad/PhD degrees. Some online mentions:
NCBI taxonomy entry: www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145 This links to:
- Interactively browse the sequence on the browser viewer: "Reference genome: Escherichia coli str. K-12 substr. MG1655" which eventually leads to: www.ncbi.nlm.nih.gov/nuccore/556503834?report=graphIf we zoom into the start, we hover over the very first gene/protein: the famous (just kidding) e. Coli K-12 MG1655 gene thrL, at position 190-255.The second one is the much more interesting e. Coli K-12 MG1655 gene thrA.
- Gene list, with a total of 4,629 as of 2021: www.ncbi.nlm.nih.gov/gene/?term=txid511145
20 minutes in optimal conditions, with a crazy multiple start sites mechanism: E. Coli starts DNA replication before the previous one finished.
Otherwise, naively, would take 60-90 minutes just to replicate and segregate the full DNA otherwise. So it starts copying multiple times.
- biology.stackexchange.com/questions/30080/how-can-e-coli-proliferate-so-rapidly
- stochasticscientist.blogspot.co.uk/2012/02/how-e-coli-grows-so-fast.html
- www.ncbi.nlm.nih.gov/pmc/articles/PMC2063475/ Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli by Fossum et al (2007)
github.com/CovertLab/WholeCellEcoliRelease is a whole cell simulation model created by Covert Lab and other collaborators.
The project is written in Python, hurray!
But according to te README, it seems to be the use a code drop model with on-request access to master. Ciro Santilli asked at rationale on GitHub discussion, and they confirmed as expected that it is to:
- to prevent their publication ideas from being stolen. Who would steal publication ideas with public proof in an issue tracker without crediting original authors? Academia is broken. Academia should be the most open form of knowledge sharing. But instead we get this silly competition for publication points.
- to prevent noise from non-collaborators. But they only get like 2 issues as year on such a meganiche subject... Did you know that you can ignore people, and even block them if they are particularly annoying? Much more likely is that no one will every hear about your project and that it will die with its last graduate student slave.
The project is a followup to the earlier M. genitalium whole cell model by Covert lab which modelled Mycoplasma genitalium. E. Coli has 8x more genes (500 vs 4k), but it the undisputed bacterial model organism and as such has been studied much more thoroughly. It also reproduces faster than Mycoplasma (20 minutes vs a few hours), which is a huge advantages for validation/exploratory experiments.
The project has a partial dependency on the proprietary optimization software CPLEX which is freeware, for students, not sure what it is used for exactly, from the comment in the
requirements.txt the dependency is only partial.This project makes Ciro Santilli think of the E. Coli as an optimization problem. Given such external nutrient/temperature condition, which DNA sequence makes the cell grow the fastest? Balancing metabolites feels like designing a Factorio speedrun.
There is one major thing missing thing in the current model: promoters/transcription factor interactions are not modelled due to lack/low quality of experimental data: github.com/CovertLab/WholeCellEcoliRelease/issues/21. They just have a magic direct "transcription factor to gene" relationship, encoded at reconstruction/ecoli/flat/foldChanges.tsv in terms of type "if this is present, such protein is expressed 10x more". Transcription units are not implemented at all it appears.
Everything in this section refers to version 7e4cc9e57de76752df0f4e32eca95fb653ea64e4, the code drop from November 2020, and was tested on Ubuntu 21.04 with a docker install of
docker.pkg.github.com/covertlab/wholecellecolirelease/wcm-full with image id 502c3e604265, unless otherwise noted. There are unlisted articles, also show them or only show them.