Quadratic form by Ciro Santilli 40 Updated 2025-07-16
Multivariate polynomial where each term has degree 2, e.g.:
is a quadratic form because each term has degree 2:
but e.g.:
is not because the term has degree 3.
More generally for any number of variables it can be written as:
There is a 1-to-1 relationship between quadratic forms and symmetric bilinear forms. In matrix representation, this can be written as:
where contains each of the variabes of the form, e.g. for 2 variables:
Strictly speaking, the associated bilinear form would not need to be a symmetric bilinear form, at least for the real numbers or complex numbers which are commutative. E.g.:
But that same matrix could also be written in symmetric form as:
so why not I guess, its simpler/more restricted.
Wave equation solver by Ciro Santilli 40 Updated 2025-07-16
This section talks about solvers/simulators dedicated solving the wave equation. Of course, any serious solver will likely be able to solve a wider range of PDE, so this section contains mostly fun toys. For more serious stuff see: Section "PDE solver".
JavaScript toy solvers:
One parameter subgroup by Ciro Santilli 40 Updated 2025-07-16
The one parameter subgroup of a Lie group for a given element of its Lie algebra is a subgroup of given by:
Intuitively, is a direction, and is how far we move along a given direction. This intuition is especially vivid in for example in the case of the Lie algebra of , the rotation group.
One parameter subgroups can be seen as the continuous analogue to the cycle of an element of a group.
Whole cell simulation by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli started taking some notes at: github.com/cirosantilli/awesome-whole-cell-simulation. but they are going to be all migrated here.
It is interesting to note how one talks about single cell analysis, in contrast to whole cell simulation: experimentally it is hard to analyse a single cell. But theoretically, it is hard to simulate a single cell. This mismatch is perhaps the ultimate frontier of molecular biology.
Video 1.
A Computational Whole-Cell Model Predicts Genotype From Phenotype by Markus Covert (2013)
Source.
Oxford Nanopore MinION by Ciro Santilli 40 Updated 2025-07-16
One of the sequencers made by Oxford Nanopore Technologies.
The device has had several updates since however, notably of the pore proteins which are present in the critical flow cell consumable.
Official documentation: nanoporetech.com/products/minion (archive)
Figure 5.
Oxford nanopore MinION flow cell package.
Source.
Figure 6.
Oxford nanopore MinION flow cell front.
Source.
Figure 7.
Oxford nanopore MinION flow cell back.
Source.
Figure 8.
Oxford nanopore MinION flow cell pipette loading.
Source.
Figure 9.
Oxford Nanopore MinION connected to a Mac via USB.
Source.
Video 1.
Oxford Nanopore MinION software channels pannel on Mac.
Source.

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!
We have two killer features:
  1. 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-calculus
    Articles 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/derivative
  2. 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.
    Figure 2.
    You can publish local OurBigBook lightweight markup files to either https://OurBigBook.com or as a static website
    .
    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.
  3. https://raw.githubusercontent.com/ourbigbook/ourbigbook-media/master/feature/x/hilbert-space-arrow.png
  4. Infinitely deep tables of contents:
    Figure 6.
    Dynamic article tree with infinitely deep table of contents
    .
    Descendant pages can also show up as toplevel e.g.: ourbigbook.com/cirosantilli/chordate-subclade
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