Sequence alignment is trying to match a DNA or amino acid sequence, even though the sequences might not be exactly the same, otherwise it would be a straight up string-search algorithm.
This is fundamental in bioinformatics for two reasons:
- when you sequence the DNA of a new species, you can guess what each protein does by comparing it with similar proteins in other species that you have already studied
- when doing DNA sequencing, and specially short-read DNA sequencing, you generally need to align the reads to reference genomes to know where you are inside the entire genome, and then be able to spot mutations, notably single-nucleotide polymorphisms
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.
This website used to allow embedding text messages with OP_RETURN, here's an archive from 2015: web.archive.org/web/20150718052659/http://eternitywall.it/
As of January 2024, it seems to read-only mode, where it simply indexes matching transactions that were made via other means: web.archive.org/web/20230929075331/https://eternitywall.it/
A Reddit announcement from July 2015: www.reddit.com/r/Bitcoin/comments/3dxy9f/eternity_wall_messages_lasting_forever/
There were 3191 hits for the search term:in our data starting with tx a3b3af21514bd79a4cbcac9916a8514636a72d813539192214542fd85247082e (2015-06-24):up to the last entry on tx 28820bc14cf2cfda58ecbc9ac6df3f41a1cb90f4246543f01ba42a5e9dac3cf8 (2023-06-15)no doubt initials of 4 Chinesepeople. A blood brother oath comes to mind, akin to the Oath of the Peach Garden. Will these four be the ones to take down the evil dictator Xi Jinping?
git grep '\bEW 'EW Eternity wall is live
EW May our friendship endure, signed by hg, kty, wjj, and xyz.
The very first message gives away the name of what we assume is a web-based upload system, "EW" being its advertisement signature added to every message.
Running shows that the messages are encoded with OP_RETURN:
bitcoin-cli:bitcoin-core.cli getrawtransaction a3b3af21514bd79a4cbcac9916a8514636a72d813539192214542fd85247082e true "vout": [
{
"value": 0.00000000,
"n": 0,
"scriptPubKey": {
"asm": "OP_RETURN 455720457465726e6974792077616c6c206973206c697665For now we are going to keep this site porn-free and only link to prevent bad things from happening, as it might violate GitHub porn policy depending on how it is hosted, and Google may dislike it. Video "What is more obscene: sex or war? scene from The People vs. Larry Flynt".
If illegal porn were to ever be found, we would be unable to acknowledge that, and would just have to silently remove it. Of course, the reproducible nature of Bitcoin Inscription Indexer means that anyone who regenerates the data would immediately see such entries in the diff.
Another issue is that it can be quite hard to determine if porn is legal or illegal, e.g. it can be hard to distinguish legal an illegal ages or revenge vs consensual porn, especially at the low resolutions that you may expect to find embedded in the blockchain. We are generally going to be quite strict about this, and in case of uncertainty on porn legality we will censor first.
OK the list:
- tx 4c903a377addab7c1e35a685d3dabc664199e406374b1e5ce2fc59e78fb5b754 (2016-07-09) contains an animated GIF of a woman pole dancing. She is seen from behind, in revealing blue clothes that show her buttocks. Reproduced at: twitter.com/cirosantilli/status/1755378949117370668. The file contains the following strings embedded into it:and:
This GIF file was assembled with GIF Construction Set from:
Alchemy Mindworks Inc.
This comment block will not appear in files created with a registered version of GIF Construction SetCryptograffiti.info messages now cheaper.
Cool data embedded in the Bitcoin blockchain The largest transactions in the Bitcoin Blockchain by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16- bb41a757f405890fb0f5856228e23b715702d714d59bf2b1feb70d8b2b4e3e08 999,657 bytes. Joins a bunch of tiny inputs into a single output
- 623463a2a8a949e0590ffe6b2fd3e4e1028b2b99c747e82e899da4485eb0b6be and 5143cf232576ae53e8991ca389334563f14ea7a7c507a3e081fbef2538c84f6e both have 3,075 outputs of 1 satoshi each and a single input. We were not able to identify any meaningful data in it,
filejust saysdata, and there aren't long ASCII strings. However, the outputs were unspent as of 2021, which suggests that they might actually be data.
Analysis of some of them follows.
- dd9f6bbf80ab36b722ca95d93268667a3ea6938288e0d4cf0e7d2e28a7a91ab3 has 13107 with payload 256KB in size, but some of them at least have been spent: www.blockchain.com/btc/tx/dd9f6bbf80ab36b722ca95d93268667a3ea6938288e0d4cf0e7d2e28a7a91ab3 therefore it's not data.
filesays their payload is a DOS executable, but it must be a coincidence
Bibliography:
- www.reddit.com/r/BitcoinBeginners/comments/9dlo3w/how_to_write_arbitrary_data_on_the_bitcoin/
- bitcoin.stackexchange.com/questions/73165/how-to-store-arbitrary-data-in-the-bitcoin-blockchain-and-how-can-i-differentiat
- bitcoin.stackexchange.com/questions/32575/what-methods-are-currently-used-to-embed-additional-data-into-the-bitcoin-blockc
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