Genomics Updated 2025-07-16
Geographic information system file format Updated 2025-07-16
Gilberto Gil Updated 2025-07-16
Gilberto is definitely the most psychedelic/tribal one of the The Holy Trinity of popular Brazilian music, though he also has a boyish quality to his soul.
He is also perhaps the one that impresses Ciro Santilli the most, at times he can't help but feel:
OMG how the hell did he come up with that?!
OurBigBook.com Manifesto Updated 2025-07-16
Education has become an expensive bureaucratic exercise, completely dissociated from reality and usefulness.
It completely rejects what the individual wants to achieve, and instead attempts to mass homogenize and test people through endless hours of boredom.
And the only goals it achieves are testing student's resilience to stress, and facilitating the finding of sexual partners. True learning is completely absent.
Teachers only teach because they have to do it to get paid, not for passion. Their only true incentive is co-authoring papers.
Education is meant to help us, the students, achieve our goals through passionate learning.
And, we, the students, are individuals, with different goals and capabilities.
The way we protest is to publish the knowledge from University for free, on the Internet, so that anyone can access it.
And we do this is a law-abiding way, without copyright infringement, so that no one can legally take it down.
We come to our courses just for the useless roll calls. But we already know all the subject better than the "teacher" on the very first day.
And we are already more famous than the "teacher" online, and through the Internet have already taught more way way more people than they ever will.
The effect of this is to demoralize the entire school system at all levels, until only one conclusion is possible: implosion.
And from the ashes of the old system, we will build a new one, which does only what matters with absolute efficiency: help the individual students achieve their goals.
A system in which the only reason why university exist will be to allow the most knowledgeable students to access million dollar laboratory equipment, and to pay the most prolific content creators so they can continue content creating.
No more useless courses. No more useless tests. Only passion, usefulness and focus.
OurBigBook.com PageRank-like ranking Updated 2025-07-16
It would be really cool to have a PageRank-link algorithm that answers the key questions:However, Ciro has decided to leave this for phase two action plan, because it is impossible to tune such an algorithm if you have no users or test data.
- what is the best content for subject X.For example, if you are reading
cirosantilli/riemann-integraland it is crap, you would be able to click the buttonwhich leads you to the URL: ourbigbook.com/subject/mathematics. This URL then contains a list of all pages people have written about the subjectVersions by other authors
mathematics, sorted by some algorithm, containing for example: - who knows the most about subject X. This can be found by visiting: ourbigbook.com/users/mathematics "Top Mathematics users", which would contain the list of users sorted by the algorithm:
Perhaps it is also worth looking into ExpertRank, they appear to do some kind of "expert in this area", but with clustering (unlike us, where the clustering would be more explicit).
Other dump of things worth looking into:
GHDL Updated 2025-07-16
Examples under vhdl.
Run all examples, which have assertions in them:
cd vhdl
./runFiles:
- Examples
- Basic
- vhdl/hello_world_tb.vhdl: hello world
- vhdl/min_tb.vhdl: min
- vhdl/assert_tb.vhdl: assert
- Lexer
- vhdl/comments_tb.vhdl: comments
- vhdl/case_insensitive_tb.vhdl: case insensitive
- vhdl/whitespace_tb.vhdl: whitespace
- vhdl/literals_tb.vhdl: literals
- Flow control
- vhdl/procedure_tb.vhdl: procedure
- vhdl/function_tb.vhdl: function
- vhdl/operators_tb.vhdl: operators
- Types
- vhdl/integer_types_tb.vhdl: integer types
- vhdl/array_tb.vhdl: array
- vhdl/record_tb.vhdl.bak: record. TODO fails with "GHDL Bug occurred" on GHDL 1.0.0
- vhdl/generic_tb.vhdl: generic
- vhdl/package_test_tb.vhdl: Packages
- vhdl/standard_package_tb.vhdl: standard package
- textio
* vhdl/write_tb.vhdl: write
* vhdl/read_tb.vhdl: read - vhdl/std_logic_tb.vhdl: std_logic
- vhdl/stop_delta_tb.vhdl:
--stop-delta
- Basic
- Applications
- Combinatoric
- vhdl/adder.vhdl: adder
- vhdl/sqrt8_tb.vhdl: sqrt8
- Sequential
- vhdl/clock_tb.vhdl: clock
- vhdl/counter.vhdl: counter
- Combinatoric
- Helpers
* vhdl/template_tb.vhdl: template
OurBigBook.com Stack Exchange Updated 2025-07-16
Stack Exchange solves to a good extent the use cases:
points of view. It is a big open question if we can actually substantially improve it.
Major shortcoming are mentioned at idiotic Stack Overflow policies:
- Scope restrictions can lead to a lot of content deletion: closing questions as off-topicThis greatly discourages new users, who might still have added value to the project.On our website, anyone can post anything that is legal in a given country. No one can ever delete your content if it is legal, no matter their reputation.
- Although you can answer your own question, there's no way to write an organized multi-page book with Stack Exchange due to shortcomings such as no table of contents, 30k max chars on answer, huge risk of deletion due to "too broad"
- Absolutely no algorithmic attempt to overcome the fastest gun in the West problem (early answers have huge advantage over newer ones): meta.stackoverflow.com/questions/404535/closing-an-old-upvoted-question-as-duplicate-of-new-unvoted-questions/404567#404567
- Native reputation system:
- if the living ultimate God of
C++upvotes you, you get10reputation - if the first-day newb of
Javaupvotes you, you also get10reputation
- if the living ultimate God of
- Randomly split between sites like Stack Overflow vs Super User, with separate user reputations, but huge overlaps, and many questions that appears as dupes on both and never get merged.
- Possible edit wars, just like Wikipedia, but these are much less common since content ownership is much clearer than in Wikipedia however
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Bioinformatics Updated 2025-07-16
Because Ciro's a software engineer, and he's done enough staring in computers for a lifetime already, and he believes in the power of Git, he didn't pay much attention to this part ;-)
According to the eLife paper, the code appears to have been uploaded to: github.com/d-j-k/puntseq. TODO at least mention the key algorithms used more precisely.
Ciro can however see that it does present interesting problems!
Because it was necessary to wait for 2 days to get our data, the workshop first reused sample data from previous collections done earlier in the year to illustrate the software.
First there is some signal processing/machine learning required to do the base calling, which is not trivial in the Oxford Nanopore, since neighbouring bases can affect the signal of each other. This is mostly handled by Oxford Nanopore itself, or by hardcore programmers in the field however.
After the base calling was done, the data was analyzed using computer programs that match the sequenced 16S sequences to a database of known sequenced species.
This is of course not just a simple direct string matching problem, since like any in experiment, the DNA reads have some errors, so the program has to find the best match even though it is not exact.
The PuntSeq team would later upload the data to well known open databases so that it will be preserved forever! When ready, a link to the data would be uploaded to: www.puntseq.co.uk/data
gitk Updated 2025-07-16
Git remote communcation Updated 2025-07-16
Git tips But which commit from master did we conflict with exactly? Updated 2025-07-16
git rebase does not tell you that, and that sucks.We only know which commit from the feature branch caused the problem.
Generally we can guess or it is not needed, but
imerge does look promising: stackoverflow.com/questions/18162930/how-can-i-find-out-which-git-commits-cause-conflicts Git tips
git log --graph Updated 2025-07-16For the strong.
git log --abbrev-commit --decorate --graph --pretty=oneline master HEADOutput:
* b4ec057 (master) 5
* 0b37c1b 4
| * fbfbfe8 (HEAD -> my-feature) 7
| * 7b0f59d 6
|/
* 661cfab 3
* 6d748a9 2
* c5f8a2c 1If we also add the As we can see, this removes any commit that is neither:
--simplify-by-decoration, which you very often want want on a real repository with many commits:* b4ec057 (master) 5
| * fbfbfe8 (HEAD -> my-feature) 7
|/
* c5f8a2c 1- under a branch or tag
- at the intersection of too branches or tags
Git tips git rebase moves commits one by one Updated 2025-07-16
In order to solve conflicts, you just have to understand what commit you are trying to move where.
E.g. if from:we do:what happens step by step is first 6 is moved on top of 5:and then 7 is moved on top of the new 6:
5 master
|
4 7 my-feature HEAD
| |
3 6
|/
2
|
1git rebase master6on5 HEAD
|
5 master
|
4 7 my-feature
| |
3 6
| |
2-----------------+
|
17on5 HEAD
|
6on5
|
5 master
|
4 7 my-feature
| |
3 6
| |
2-----------------+
|
17on5 my-feature HEAD
|
6on5
|
5 master
|
4
|
3
|
2
|
1 Git tips How to visualize the commit tree Updated 2025-07-16
Generate a minimal test repo. You should get in the habit of doing this to test stuff out.
#!/usr/bin/env bash
mkdir git-tips
cd git-tips
git init
for i in 1 2 3 4 5; do
echo $i > f
git add f
git commit -m $i
done
git checkout HEAD~2
git checkout -b my-feature
for i in 6 7; do
echo $i > f
git add f
git commit -m $i
done Glucose Updated 2025-07-16
The most important on in metabolism internals, everything else gets converted to it before being processed in the .
GNOME Chess Updated 2025-07-16
The user friendly Chess UI! Exactly what you would expect from a GNOME Project package. But also packs some punch via the Universal Chess Interface, e.g. Stockfish just works.
GNU Taler Updated 2025-07-16
Centralized system that still attempts some level of privacy.
In it, a central bank issue tokens that are stored offline in your cell phone, a bit like cash bank notes.
When you take those tokens, a corresponding amount gets removed from your bank account, a bit like cash bank notes.
When a transaction is made, tokens are put into a spent token list via central API, and cannot be double spent thereafter. The corresponding ammount is then added to the bank account of the receiver. This also means that offline transactions are not possible.
Godlike Updated 2025-07-16
This vocabulary likely entered Ciro Santilli's vernacular through playing Counter-Strike when he was a teenager.
There are unlisted articles, also show them or only show them.