Ciro Santilli @cirosantilli 37

In terms of hard physics/mathematics, this book takes the approach of spending a few paragraphs in some chapters describing in high level terms some of the key ideas, which is a good compromise. It does sometime fall into the sin of to talk about something without giving the real name to not scare off the audience, but it does give a lot of names, notably it talks a lot about Lagrangian mechanics. And it goes into more details than Surely in any case.

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Genome Updated 2025-07-16

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Genomics Updated 2025-07-16

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Study of the genome, one of the omics.

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Geographic information system file format Updated 2025-07-16

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Gilberto Gil Updated 2025-07-16

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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?!

Figure 2.
Gilberto Gil in the cover of his 1977 album Refavela
. Source.

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OurBigBook.com / Manifesto Updated 2025-07-16

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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.

We reject this bullshit.

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.

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OurBigBook.com / PageRank-like ranking Updated 2025-07-16

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It would be really cool to have a PageRank-link algorithm that answers the key questions:

what is the best content for subject X.
For example, if you are reading cirosantilli/riemann-integral and it is crap, you would be able to click the button
Versions by other authors
which leads you to the URL: ourbigbook.com/subject/mathematics. This URL then contains a list of all pages people have written about the subject mathematics, sorted by some algorithm, containing for example:
- ourbigbook.com/johnsmith/riemann-integral
- ourbigbook.com/cirosantilli/riemann-integral
This URL would also contain a list of issues/comments that are related to the subject.
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:
- ourbigbook.com/johnsmith
- ourbigbook.com/cirosantilli

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.

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:

en.wikipedia.org/wiki/Hilltop_algorithm

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GHDL Updated 2025-07-16

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github.com/ghdl/ghdl

Examples under vhdl.

First install GHDL. On Ubuntu:

sudo apt install verilator

Tested on Verilator 1.0.0, Ubuntu 22.04.

Run all examples, which have assertions in them:

cd vhdl
./run

Files:

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
Applications
- Combinatoric
  - vhdl/adder.vhdl: adder
  - vhdl/sqrt8_tb.vhdl: sqrt8
- Sequential
  - vhdl/clock_tb.vhdl: clock
  - vhdl/counter.vhdl: counter
Helpers
* vhdl/template_tb.vhdl: template

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OurBigBook.com / Stack Exchange Updated 2025-07-16

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Stack Exchange solves to a good extent the use cases:

I have a very specific question, type it on Google, find top answers
I have an answer, and I put it here because it has a much greater chance of being found due to the larger PageRank than my personal web page will ever have

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-topic
This 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 get 10 reputation
- if the first-day newb of Java upvotes you, you also get 10 reputation
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

Bibliography:

dev.to/codemouse92/has-stackoverflow-become-an-antipattern-3icb (archive)

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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

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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

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gitk Updated 2025-07-16

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Figure 1.
gitk 2.34.1 running on Ubuntu 22.04 with a simple repository.

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Git remote communcation Updated 2025-07-16

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Git tips / But which commit from master did we conflict with exactly? Updated 2025-07-16

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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

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Git tips / git log --graph Updated 2025-07-16

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For the strong.

git log --abbrev-commit --decorate --graph --pretty=oneline master HEAD

Output:

* b4ec057 (master) 5
* 0b37c1b 4
| * fbfbfe8 (HEAD -> my-feature) 7
| * 7b0f59d 6
|/
* 661cfab 3
* 6d748a9 2
* c5f8a2c 1

If we also add the --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

As we can see, this removes any commit that is neither:

under a branch or tag
at the intersection of too branches or tags

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Git tips / git rebase moves commits one by one Updated 2025-07-16

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In order to solve conflicts, you just have to understand what commit you are trying to move where.

E.g. if from:

5 master
|
4 7 my-feature HEAD
| |
3 6
|/
2
|
1

we do:

git rebase master

what happens step by step is first 6 is moved on top of 5:

6on5 HEAD
|
5 master
|
4                 7 my-feature
|                 |
3                 6
|                 |
2-----------------+
|
1

and then 7 is moved on top of the new 6:

7on5 HEAD
|
6on5
|
5 master
|
4                 7 my-feature
|                 |
3                 6
|                 |
2-----------------+
|
1

All good? so OK, let's move the my-feature to the new 7:

7on5 my-feature HEAD
|
6on5
|
5 master
|
4
|
3
|
2
|
1

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Git tips / How to visualize the commit tree Updated 2025-07-16

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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

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