Published as: arxiv.org/pdf/2304.03442.pdf Generative Agents: Interactive Simulacra of Human Behavior by Park et al.
A multi-scenario demo.
The second protein to have its structure determined, after myoglobin, by X-ray crystallography, in 1965.
Breaks up peptidoglycan present in the bacterial cell wall, which is thicker in Gram-positive bacteria, which is what this enzyme seems to target.
Part of the inate immune system.
reconstruction/ecoli/flat/condition/nutrient/minimal.tsvcontains the nutrients in a minimal environment in which the cell survives:If we compare that to"molecule id" "lower bound (units.mmol / units.g / units.h)" "upper bound (units.mmol / units.g / units.h)" "ADP[c]" 3.15 3.15 "PI[c]" 3.15 3.15 "PROTON[c]" 3.15 3.15 "GLC[p]" NaN 20 "OXYGEN-MOLECULE[p]" NaN NaN "AMMONIUM[c]" NaN NaN "PI[p]" NaN NaN "K+[p]" NaN NaN "SULFATE[p]" NaN NaN "FE+2[p]" NaN NaN "CA+2[p]" NaN NaN "CL-[p]" NaN NaN "CO+2[p]" NaN NaN "MG+2[p]" NaN NaN "MN+2[p]" NaN NaN "NI+2[p]" NaN NaN "ZN+2[p]" NaN NaN "WATER[p]" NaN NaN "CARBON-DIOXIDE[p]" NaN NaN "CPD0-1958[p]" NaN NaN "L-SELENOCYSTEINE[c]" NaN NaN "GLC-D-LACTONE[c]" NaN NaN "CYTOSINE[c]" NaN NaNreconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv, we see that it adds the 20 amino acids on top of the minimal condition:so we guess that"L-ALPHA-ALANINE[p]" NaN NaN "ARG[p]" NaN NaN "ASN[p]" NaN NaN "L-ASPARTATE[p]" NaN NaN "CYS[p]" NaN NaN "GLT[p]" NaN NaN "GLN[p]" NaN NaN "GLY[p]" NaN NaN "HIS[p]" NaN NaN "ILE[p]" NaN NaN "LEU[p]" NaN NaN "LYS[p]" NaN NaN "MET[p]" NaN NaN "PHE[p]" NaN NaN "PRO[p]" NaN NaN "SER[p]" NaN NaN "THR[p]" NaN NaN "TRP[p]" NaN NaN "TYR[p]" NaN NaN "L-SELENOCYSTEINE[c]" NaN NaN "VAL[p]" NaN NaNNaNin theupper moundlikely means infinite.We can try to understand the less obvious ones:ADP: TODOPI: TODOPROTON[c]: presumably a measure of pHGLC[p]: glucose, this can be seen by comparingminimal.tsvwithminimal_no_glucose.tsvAMMONIUM: ammonium. This appears to be the primary source of nitrogen atoms for producing amino acids.CYTOSINE[c]: hmmm, why is external cytosine needed? Weird.
reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/contains sequences of conditions for each time. For example:reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000000_basal.tsvcontains:which means just using"time (units.s)" "nutrients" 0 "minimal"reconstruction/ecoli/flat/condition/nutrient/minimal.tsvuntil infinity. That is the default one used byrunSim.py, as can be seen from./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Environment/attributes/nutrientTimeSeriesLabelwhich contains just000000_basal.reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000001_cut_glucose.tsvis more interesting and contains:so we see that this will shift the conditions half-way to a condition that will eventually kill the bacteria because it will run out of glucose and thus energy!"time (units.s)" "nutrients" 0 "minimal" 1200 "minimal_no_glucose"
Timeseries can be selected with--variant nutrientTimeSeries X Y, see also: run variants.We can use that variant with:VARIANT="condition" FIRST_VARIANT_INDEX=1 LAST_VARIANT_INDEX=1 python runscripts/manual/runSim.pyreconstruction/ecoli/flat/condition/condition_defs.tsvcontains lines of form:"condition" "nutrients" "genotype perturbations" "doubling time (units.min)" "active TFs" "basal" "minimal" {} 44.0 [] "no_oxygen" "minimal_minus_oxygen" {} 100.0 [] "with_aa" "minimal_plus_amino_acids" {} 25.0 ["CPLX-125", "MONOMER0-162", "CPLX0-7671", "CPLX0-228", "MONOMER0-155"]conditionrefers to entries inreconstruction/ecoli/flat/condition/condition_defs.tsvnutrientsrefers to entries underreconstruction/ecoli/flat/condition/nutrient/, e.g.reconstruction/ecoli/flat/condition/nutrient/minimal.tsvorreconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsvgenotype perturbations: there aren't any in the file, but this suggests that genotype modifications can also be incorporated heredoubling time: TODO experimental data? Because this should be a simulation output, right? Or do they cheat and fix doubling by time?active TFs: this suggests that they are cheating transcription factors here, as those would ideally be functions of other more basic inputs
Ciro Santilli used to use file managers in the past.
But he finally converted to a shell
cd aliases that auto-ls: github.com/cirosantilli/dotfiles/blob/a51bcc324f0cff0eddd4c3bb8654ec223a0adb7b/home/.bashrc#L1058 Structure of Hen Egg-White Lysozyme: A Three-dimensional Fourier Synthesis at 2 Å Resolution (1965) by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16www.nature.com/articles/206757a0 on Nature 181, 662-666. Paywalled as of 2022. Has some nice pictures in it.
The people who work on this will go straight to heaven, no questions asked.
In this example, posts have tags. When a post is deleted, we check to see if there are now any empty tags, and now we want to delete any empty tags that the post deletion may have created.
If we are creating and deleting posts concurrently, a naive implementation might wrongly delete the tags of a newly created post.
This could be due to a concurrency issue of the following types.
Failure case 1:which would result in the new post incorrectly not having the
- thread 2: delete old post
- thread 2: find all tags with 0 posts. Finds
tag0from the deleted old post which is now empty. - thread 1: create new post, which we want to have tag
tag0 - thread 1: try to create a new tag
tag0, but don't because it already exists, this is done using SQLite'sINSERT OR IGNORE INTOor PostgreSQL'sINSERT ... ON CONFLICT DO NOTHING - thread 1: assign
tag0to the new post by adding an entry to the join table - thread 2: delete all tags with 0 posts. It still sees from its previous search that
tag0is empty, and deletes it, which then cascades into the join table
tag0.Failure case 2:which leads to a foreign key failure, because the tag does not exist anymore when the assignment happens.
- thread 2: delete old post
- thread 2: find all tags with 0 posts
- thread 1: create new post
- thread 1: try to create a new tag
tag0, but don't because it already exists - thread 2: delete all tags with 0 posts. It still sees from its previous search that
tag0is empty, and deletes it - thread 1: assign
tag0to the new post
Failure case 3:which leads to a foreign key failure, because the tag does not exist anymore when the assignment happens.
- thread 2: delete old post
- thread 1: create new post, which we want to have tag
tag0 - thread 1: try to create a new tag
tag0, and succeed because it wasn't present - thread 2: find all tags with 0 posts, finds the tag that was just created
- thread 2: delete all tags with 0 posts, deleting the new tag
- thread 1: assign
tag0to the new post
Sample executions:All executions use 2 threads.
node --unhandled-rejections=strict ./parallel_create_delete_empty_tag.js p 9 1000 'READ COMMITTED': PostgreSQL, 9 tags, DELETE/CREATE thetag0test tag 1000 times, useREAD COMMITTEDExecution often fails, although not always. The failure is always:because the:error: insert or update on table "PostTag" violates foreign key constraint "PostTag_tagId_fkey"tries to insert a tag that was deleted in the other thread, as it didn't have any corresponding posts, so this is the foreign key failure.INSERT INTO "PostTag"node --unhandled-rejections=strict ./parallel_create_delete_empty_tag.js p 9 1000 'READ COMMITTED' 'FOR UPDATE': do aSELECT ... FOR UPDATEbefore trying toINSERT.This is likely correct and the fastest correct method according to our quick benchmarking, about 20% faster thanREPEATABLE READ.node --unhandled-rejections=strict ./parallel_create_delete_empty_tag.js p 9 1000 'REPEATABLE READ': repeatable readWe've never observed any failures with this level. This should likely fix the foreign key issue according to the PostgreSQL docs, since:- the
DELETE "Post"commit cannot start to be seen only in the middle of the thread 1 transaction - and then if DELETE happened, the thread 1 transaction will detect it, ROLLBACK, and re-run. TODO how does it detect the need rollback? Is it because of the foreign key? It is very hard to be sure about this kind of thing, just can't find the information. Related: postgreSQL serialization failure.
- the
node --unhandled-rejections=strict ./parallel_create_delete_empty_tag.js p 9 1000 'SERIALIZABLE': serializablenode --unhandled-rejections=strict ./parallel_create_delete_empty_tag.js p 9 1000 'NONE': magic value, don't use any transaction. Can blow up of course, since even less restrictions thanREAD COMMITTED
Some theoretical notes:
stackoverflow.com/questions/10935850/when-to-use-select-for-update from SELECT FOR UPDATE also talks about a similar example, and has relevant answers.
How MRI Works Part 1 by thePIRL (2018)
Source. - youtu.be/TQegSF4ZiIQ?t=326 the magnet is normally always on for the entire lifetime of the equipment!
- youtu.be/TQegSF4ZiIQ?t=465 usage of non-ionizing radiation (only radio frequencies) means that it is very safe to use. The only dangerous part is the magnetic field interacting with metallic objects.
Tomorrow's World gave audiences a true world first as Dr Peter Mansfield of the University of Nottingham demonstrated the first full body prototype device for Magnetic resonance imaging (MRI), allowing us to see inside the human body without the use of X-rays.
Ollama is a highly automated open source wrapper that makes it very easy to run multiple Open weight LLM models either on CPU or GPU.
Its README alone is of great value, serving as a fantastic list of the most popular Open weight LLM models in existence.
Install with:
curl https://ollama.ai/install.sh | shOn P14s it runs on CPU and generates a few tokens per second, which is quite usable for a quick interactive play.
As mentioned at github.com/jmorganca/ollama/blob/0174665d0e7dcdd8c60390ab2dd07155ef84eb3f/docs/faq.md the downloads to under The file:gives a the exact model name and parameters.
/usr/share/ollama/.ollama/models/ and ncdu tells me:--- /usr/share/ollama ----------------------------------
3.6 GiB [###########################] /.ollama
4.0 KiB [ ] .bashrc
4.0 KiB [ ] .profile
4.0 KiB [ ] .bash_logout/usr/share/ollama/.ollama/models/manifests/hf.co/mlabonne/Meta-Llama-3.1-8B-Instruct-abliterated-GGUF/Q2_KWe can also do it non-interactively with:which gave me:but note that there is a random seed that affects each run by default. ollama-expect is an attempt to make the output deterministic.
/bin/time ollama run llama2 'What is quantum field theory?'0.13user 0.17system 2:06.32elapsed 0%CPU (0avgtext+0avgdata 17280maxresident)k
0inputs+0outputs (0major+2203minor)pagefaults 0swapsSome other quick benchmarks from Amazon EC2 GPU on a g4nd.xlarge instance which had an Nvidia Tesla T4:and on Nvidia A10G in an g5.xlarge instance:
0.07user 0.05system 0:16.91elapsed 0%CPU (0avgtext+0avgdata 16896maxresident)k
0inputs+0outputs (0major+1960minor)pagefaults 0swaps0.03user 0.05system 0:09.59elapsed 0%CPU (0avgtext+0avgdata 17312maxresident)k
8inputs+0outputs (1major+1934minor)pagefaults 0swapsIt tends to babble quite a lot by default, but eventually decides to stop.
A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis (1958) by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16 nodejs/sequelize/raw/parallel_select_and_update_deterministic.js by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16This example contains a deterministic demo of when postgreSQL serialization failures may happen.
Tested on PostgreSQL 13.5.
Pinned article: 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 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. Web editor. 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.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. 
- 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