OpenLLM-France/wikimedia huggingface dataset:
# Mathematical biophysics

Mathematical biophysics is a subfield of both biophysics and mathematical biology focusing of physical and physico-chemical mechanisms involved in physiological functions of living organisms, as well as the molecular structures supporting such physiological functions.
The earlier stages of mathematical biology were dominated by mathematical biophysics, that was then described as the application of mathematics in biophysics, often involving specific physical/mathematical models of biosystems and their components or compartments.
Specific research areas of current interest in mathematical biophysics are, for example:
* Complex systems
* Quantum biophysics and biochemistry
* Automata theory,
** Cellular automata,
** Tessellation models
* complete self-reproduction, * chaotic subsystems of organisms,
* Relational biology and organismic theories.
A published monograph that included 390 references to peer-reviewed articles in mathematical and computational biophysics by a large number of authors is currently available for download as an updated PDF

## Syllabus

A syllabus of studies in mathematical biophysics at the university level may include a combination of courses, such as:
* Molecular biophysics,
* Photosynthesis and photosythetic mechanisms
* physico-chemical models of nerve conduction
* Muscle contraction mechanisms
* Quantum physics,Quantum mechanics, Quantum field theory
* Quantum biophysics
* Quantum biochemistry
* Quantum genetics
* Molecular spectroscopy: FT-IR, FT-NIR, NMR,EPR, VCD, FCS, FCCS
* X-ray diffraction and Electron microscopy
* Biostatistics, Graph theory, Algebraic topology
* Biocybernetics,
* Nonlinear dynamic systems,
* Nonequillibrium thermodynamics,
* Statistical mechanics
* Bioinformatics
* Radiological imaging: MRI, CT, PET
* Nuclear medicine
# Mathematical reasoning/Introduction/Section

In a mathematical argumentation, one tries to establish the truth of a claim by only using accepted principles. Typically, there is an audience which one would like to convince about the claim. Argumentation exists in many different contexts, in sciences, in politics, in personal relationships. There exist principles and patterns of argumentation which are typical for each context. In the political context, one invokes in general widely accepted principles like human rights, the constitution, the people and what they want, in order to enforce political decisions. The experience shows that the arguments used there are not good enough to convince everybody, and that also the interests of specific groups are represented.
Also in a mathematical argumentation one tries to establish the truth of a claim (that a computation procedure is correct, that a model is appropriate). The tools used, the strictness of the argumentation, do also depend here on the audience, the previous knowledge and motivation, the relation (bond, trust) between the persons involved (like teacher and student).
A mathematical argumentation on the scientific level shows certain standards of argumentation. A scientific argumentation exhibits the following items.
In a mathematical argumentation, these items are in particular patent. A strong hint for this is that there exists even a specific term for a mathematical argumentation: proof. A proven mathematical claim is called a theorem (or lemma or corollary).
* ↑ Here runs the border between science and philosophy.
* ↑ This is a big difference to esoterism, where "knowledge“ is passed on to the disciples only under specific conditions (secrecy, dignity).
* ↑ That does not mean at all that gaining knowledge and making discoveries is without feelings. To the contrary, doing science is fun.
* ↑ Though the generation of knowledge is heavily dependent on age and culture.
* ↑ However, in mathematics an important point of the natural sciences is missing, observation, experience, experiments. Therefore, mathematics if often not considered as a natural science. But to consider mathematics as belonging to the humanities is also difficult, hence it is often considered to be a structural science.
* ↑ In particular, definitions by example of the form "something like“ are not allowed.
* ↑ This is the subject of mathematical logic.
* ↑ They are also not patentable.
* ↑ This might be different for security-relevant cryptological research.
* ↑ Though the major part is still in the industrialized countries, but other countries are catching up quickly.
# Mathematical modeling of neural networks

Welcome to the Wikiversity learning project for Mathematical modeling of neural networks.
This "learn by doing" project provides information about how to work with mathematical models of neural networks and space for discussion of neural network models.

## NEURON simulation environment

Neuron has a Graphical User interface intended to create a user experience similar to that of using laboratory equipment. Features include:
* Channel Builder. allows realistic model features reflecting neurophysiological elements such as voltage- and ligand-gated ion channels.
* Cell Builder. for models of cells. Start from scratch or modify saved models without writing any code. Electrophysiological properties of the membrane can vary as functions of position.
* Network Builder. use it to prototype small networks then use models of several small networks to create larger networks.
* ModelView tool. helps model development, maintenance and sharing of models.

### Reading

* Neural network article at Wikipedia
* Familiarize yourself with the NEURON simulation environment.
* Neural Networks modules at Wikibooks; from a Computer Science perspective.

### Activity

The NEURON software package is available for Windows, Mac and Unix. Download the NEURON software from the Download and Install page.

#### OSX

The documentation for NEURON states that the version for use with the X11 windows interface is best for Macs. The X11 version is a 4.3 MB download. The downloaded OSX/X11 NEURON package creates a 13 MB folder for NEURON version 5.6 (The current standard version is 5.9).

### Discussion

* Did you have any problems with installing NEURON on your computer?
# EFL Interdisciplinary Projects

This is a project on EFL started by teacher Daniele Krauz with the aim of creating EFL interdisciplinary lessons based on multiple methodologies. The material provided is organized in a series of course pages by level and grammar topic as well as teacher's resources pages with a collection of free online original high quality materials for further lessons. The lessons are part of a long project started as research on using Howard Gardner's theory of Multiple Intelligences in the EFL environment for Brazilian students.

## Theories observed

Here is a collection of important theories basing the development of the projects.
What Is This Thing Called Giftedness, and How Do We Develop It? A Twenty-Five Year Perspective
Every learner has strengths or potential strengths that can be used as a foundation for effective learning and creative productivity. The Schoolwide Enrichment Model (SEM) (Reis & Renzulli, 1985) capitalizes on these strengths by offering students options to realize their own potential. Through service delivery components like Curriculum Compacting and Enrichment Clusters, students are insured of being exposed to high level and challenging learning experiences. A third component, the Total Talent Portfolio¹ (TTP) serves as the framework by which all the other elements of the model can be organized. Some questionnaires and similars are used to access the students abilities and preferences in order to offer adequate clusters and research opportinities.
* The Interest-A-Lyzer by Joseph S. Renzulli University of Connecticut - "The purpose of this questionnaire is to help you become more familiar with some of your interests and potential interests."

## Resources

* Teacher's Resources
* Reading and Writing
* Speaking
* Project Team

## See Also

* Howard Gardner
* Project Zero
* Project Good Work
* Minerva projects higher education and talent solutions
* Renzulli Center for Creativity, Gifted Education, and Talent Development
# Latin/Contribute Audio

Audio recordings need to be added to Wikimedia Commons before they can be used on Wikiversity. See commons:Latin language
Current recordings can be found at Commons:Category:Latin pronunciation

## Sentences

Most important is adding recordings of sentences.

## Missing words

You can also help with misssing words. The words that are missing can be see at Latin/Classified Vocabulary List; please note that we haven't gone through all of the tables, only as far as the Third declension masculine / feminine list.

## Recording at home

You will need to make the recordings yourself, at home, and then create separate files for each audio element.
If this seems arduous and you'd like to send a long file of all of the material, please let us know. You can upload the long file to Wikimedia Commons, and then we can do the work of separating and uploading the individual sentences or words.

## Adding files

Use your Wikipedia account, or Wikiversity account to log into Wikimedia Commons. Then use the Upload Wizard:
* Commons:Special:UploadWizard
Adding files to commons this way can be done in bulk. This makes it relatively painless.

## File format

Audio files seem to be .ogg throughout. It is probably best to stick with this format as it means the Wiki file players will work.

## Naming files

It will make our life easier if we use a consistent naming convention for audio files.
* Words: please call your files
** la-cls-wordname.ogg for classical pronunciation
** la-ecc-wordname.ogg for ecclesiastical pronunciation
* Sentences: please call your files
** la-cls-lessonname-sentence-01.ogg for classical pronunciation
** la-ecc-lessonname-sentence-01.ogg for ecclesiastical pronunciation

## Adding files to the wikiversity lessons

Once the files are uploaded, and you know the name, you can use markup in this format [[File:la-cls-puella.ogg|thumb|Puella]] which gives a player like the one in this table:
| Audio | Notes |
| Puella | This is the standard thumbnail player |
Place these into the tables in the "audio" column; add an "audio" column if needed.
# Exploratory factor analysis/Data analysis tutorial
## Software options

In order to participate in this learning project, you will need access to an appropriate statistics package.
At this stage, notes are only available for SPSS (proprietary software), but over time it is hoped to provide notes for R (free software):
* SPSS
* How to use R
# Exploratory factor analysis/Quiz

Exploratory factor analysis practice quiz

## Acknowledgments

Several of these questions are based on items from http://www.johnwiley.com.au/highered/mr2e/content017/ch15/mc_ch15_aak07.html
# Linux System programming in plain view

This course belongs to the Electrical & Computer Engineering Studies

## Introduction

* Introduction (pdf)

## File System

* File System (pdf)
* File Pointer (pdf)
* System Calls (pdf)

## Process

* Process (pdf)

### Inter Process Communication

* IPC (Inter Process Communication) (pdf)
* Socket (pdf)
* Message Queue (pdf)
* Semaphore (pdf)
* Signal (pdf)
* Shared Memory (pdf)

## Thread

* POSIX thread (pthread) (pdf)
# Linux server administration/acct

Acct package allows to activate process accounting in Linux. Installing acct package in Ubuntu activates accounting by default.
* Configuration: /etc/default/acct
* Logs file: /var/log/account/pacct

## Activities

* Install in Ubuntu acct accounting package and deactivate it changing ACCT_ENABLE="1" to ACCT_ENABLE="0" in /etc/default/acct and stopping it /etc/init.d/acct stop
* Activate accounting by executing accton on and deactivate it by executing accton off and check status service acct status
# Linux server administration/apt

Advanced Package Tool, or APT, is a free software user interface that works with core libraries to handle the installation and removal of software on Debian, Ubuntu and other Linux distributions. Main Advanced Package Tool (APT) binaries are: apt, apt-get and apt-cache

## Basic apt-get/apt commands

* Installing: apt install PACKAGE_NAME
* apt show PACKAGE_NAME or aptitude show PACKAGE_NAME
* apt policy PACKAGE_NAME Provides source repository for a given package.
* apt-get update && apt-get upgrade
* Showing pending to update packages: apt-get upgrade --dry-run or apt-get upgrade -s
** /usr/lib/update-notifier/apt-check --human-readable

## Basic apt-cache commands

* apt-cache search
* apt-cache policy List source repository configured included priorities of each source.
* apt-cache showpkg PACKAGE_NAME. See also: apt show PACKAGE_NAMEdpkg -s PACKAGE_NAME

## Relevant configuration files and directories

* /etc/apt/sources.list: Configuration files with locations to fetch packages from.
* /etc/apt/sources.list.d/: directory with additional source list fragments.

## Updates

* To collect information about what installed packages can be upgraded:
** apt update
** apt list --upgradable
** apt-get upgrade --dry-run or apt-get upgrade -s
** apt update && apt-upgrade
* To upgrade all installed packages: apt upgrade
* apt dist-upgrade (see also do-release-upgrade)
* apt Automatic updates

### Holding packages

To avoid packages from being upgrade when upgrading use apt-mark command
* apt-mark hold PACKAGE_NAME
* apt-mark unhold PACKAGE_NAME
* apt-mark showhold

### Single upgrade

* To upgrade only a package: apt-get install --only-upgrade PACKAGE_NAME

## Activities

* Read differences between apt upgrade and apt dist-upgrade: https://unix.stackexchange.com/a/304887
* Read Linux server administration/apt/Automatic updates
* Install software-properties-common package to be able to use apt-add-repository Python command available since 2004.

## See Also

* dpkg, dnf and snap
* w:Deb_(file_format) to understand .deb internal format an included files: preinst, postinst, prerm and postrm.
* RPM (Linux)
* pkgutil (MacOS)
* brew (MacOS), command of the Homebrew package management software w:Homebrew (package management software)
* pkg (FreeBSD)
* w:apt-file to view the contents of debian packages on remote repositories
* opkg
* Package manager
* docker
* ↑ https://askubuntu.com/a/347805/897490
* ↑ http://manpages.ubuntu.com/manpages/xenial/man8/apt-cache.8.html#options
* ↑ https://wiki.debian.org/SourcesList
* ↑ https://askubuntu.com/questions/640986/how-to-get-a-list-of-installed-packages-held-back-from-upgrade
* ↑ https://packages.debian.org/sid/admin/software-properties-common
# Linux server administration/Performance and Troubleshooting

* Performance tools:
*** memory: vmstat, free, sar -r
** Disk tools: iostat, iotop, hdparm, sar -d, ionice, hdparm and dd
** Network: ntop, nmap, ping, fping, ncat, mtr, traceroute, tracepath
**** Kernel: perf, strace, ftrace, Dtrace
** cgroups and docker: systemd-cgtop, docker stats
* Troubleshooting tools: cfg2html, ansible-cmdb , sysreport, sosreport and acct
# Linux server administration/Zabbix

Zabbix is an open source monitoring software for networks, operating systems and applications. It is designed following a Client-server architecture to monitor and track the status of various services components: network, servers, and network hardware.
You can installing it using official Zabbix installation instructions or running it using a docker container

## Running Zabbix under docker

* docker pull zabbix/zabbix-server-mysql
* docker run --name some-zabbix-server-mysql -e DB_SERVER_HOST="some-mysql-server" -e MYSQL_USER="some-user" -e MYSQL_PASSWORD="some-password" -d zabbix/zabbix-server-mysql:tag

## Activities

* Install Zabbix using docker containers
# Linux server administration/Scheduling
## Overview

Cron is driven by a crontab (cron table) file, a configuration file that specifies shell commands to run periodically on a given schedule. The crontab files are stored where the lists of jobs and other instructions to the cron daemon are kept. Users can have their own individual crontab files and often there is a system-wide crontab file (usually in /etc or a subdirectory of /etc) that only system administrators can edit.
Each line of a crontab file represents a job, and looks like this:
The syntax of each line expects a cron expression made of five fields, followed by a shell command to execute.

## Logging

Cron execution logs can be saved to specific file using rsyslog service.
* In Ubuntu uncomment in /etc/rsyslog.d/50-default.conf the line:
    #cron.* /var/log/cron.log
    and restart rsyslog service: sudo systemctl restart rsyslog
* In Debian uncomment in /etc/rsyslog.conf the line:
    #cron.* /var/log/cron.log
# Linux server administration/Backup and Restore

* Testing Your Restore
* Incremental Backup Strategy
* Common Backup Mistakes
* Linux Recovery Skillset
* Demo - Backup & Restore

## Tools for Backup & Restore

* Amanda
* Areca Backup
* Bacula, used by Mediawiki since 2013.
* Bareos fork of Bacula
* Borg
* Clonezilla
* Drive Imaging
* mtools
* tar - For Tape Archives and cpio - Copy Input/Output
* rsync
* dd - Convert Files
* dump Command
* w:duplicity (software) python software suite that provides encrypted, digitally signed, versioned, remote backup
* Mondo Rescue

## Commercial Backup products

Different commercial products provide Backup and recovery capabilities such as Commvault, Veritas NetBackup and Veritas Backup Exec, Veeam Backup & Replication, Arcserve.

## Database backups software

* Oracle Recovery Manager (RMAN), command-line and Enterprise Manager-based tool, is the preferred method for backing up and recovering an Oracle database
# Mean value theorem for definite integrals/Riemann/Fact

Suppose that $[a,b]$ is a compact interval, and let
    $f\colon [a,b]\longrightarrow \mathbb {R}$
be a continuous function.
$c\in [a,b]$ such that
    $\int _{a}^{b}f(t)\,dt=f(c)(b-a)\,.$
# Meaning of Market
## Concept

The word 'market' has been derived from the Latin word "Mercatus" which means to trade, merchandise or a place where business is transacted.
When used in general sense, market means a place where goods and services are purchased and sold. Thus buyers and sellers meet in the market for buying and selling the goods.
When used in dynamic sense, market may also include the following:
* an area of operation;
* any organization by which the exchange of goods is effected;
* the art of buying and selling; and
* inhabitants of the country, example take the market of any country. It refers to the total population of that country and its aggregate purchasing power.

## Definitions

According to Chapman, "the term market refers not to a place but a commodity or commodities and buyers and sellers who are in different competition with one another".
According to Philip Kotler, "market is the set of actual and potential buyers of a product".
* ↑ Chapman, Economics
* ↑ Philip Kotler and Gary Armstrong, Principles of Marketing,1999,p.9.
# Mean value theorem/First out of second/Exercise

Prove the mean value theorem out of the second mean value theorem.
# Mean value theorem for definite integrals/Riemann/Section

For a Riemann-integrable function $f\colon [a,b]\rightarrow \mathbb {R}$, one may consider
    ${\frac {\int _{a}^{b}f(t)\,dt}{b-a}}$
as the mean height of the function, since this value, multiplied with the length $b-a$ of the interval, yields the area below the graph of $f$. The Mean value theorem for definite integrals claims that, for a continuous function, this mean value is in fact obtained by the function somewhere.

## Theorem

Suppose that $[a,b]$ is a compact interval, and let
    $f\colon [a,b]\longrightarrow \mathbb {R}$
be a continuous function. Then there exists some $c\in [a,b]$ such that
    $\int _{a}^{b}f(t)\,dt=f(c)(b-a)\,.$

### Proof

On the compact interval, the function $f$ is bounded from above and from below, let $m$ and $M$ denote the minimum and the maximum of the function. Due to fact, they are both obtained. Then, in particular, $m\leq f(x)\leq M$ for all $x\in [a,b]$, and so
    $m(b-a)\leq \int _{a}^{b}f(t)\,dt\leq M(b-a)\,.$
Therefore, $\int _{a}^{b}f(t)\,dt=d(b-a)$ with some $d\in [m,M]$. Due to the Intermediate value theorem, there exists a $c\in [a,b]$ such that $f(c)=d$.
$\Box$
# Mean value theorems for integration/Product of two functions/Exercise

Let
    $f,g\colon [a,b]\longrightarrow \mathbb {R}$
be two continuous functions and let $g(t)\geq 0$ for all $t\in [a,b]$. Prove that there exists $s\in [a,b]$ such that
    $\int _{a}^{b}f(t)g(t)dt=f(s)\int _{a}^{b}g(t)dt\,.$
# Mean value theorem for definite integrals/Riemann/Fact/Proof

On the compact interval, the function $f$ is bounded from above and from below, let $m$ and $M$ denote the minimum and the maximum of the function. Due to fact, they are both obtained. Then, in particular, $m\leq f(x)\leq M$ for all $x\in [a,b]$, and so
    $m(b-a)\leq \int _{a}^{b}f(t)\,dt\leq M(b-a)\,.$
Therefore, $\int _{a}^{b}f(t)\,dt=d(b-a)$ with some $d\in [m,M]$. Due to the Intermediate value theorem, there exists a $c\in [a,b]$ such that $f(c)=d$.
# Mean value theorem of differential calculus/From mean value theorem of integral calculus/Exercise

Prove the mean value theorem for differential calculus for differentiable functions
    $g\colon \mathbb {R} \longrightarrow \mathbb {R}$
and a compact interval $[a,b]\subset \mathbb {R}$, using the mean value theorem of integral calculus (you do not have to show that the average velocity is obtained in the interior of the interval).
# Measure Theory
## Design Principles

This course is designed with a few principles in mind.

### Natural Proofs

The most core design principle for this course, which I am calling "natural proofs", is
    No step, whether it's a definition, theorem, or step in a proof, should ever "come out of nowhere".
Any abandonment of this principle, basically gives up on the job of being a teacher rather than just a reference source. Besides that, it fails to expose the actual process of discovering mathematics, which is the fundamental skill that one should learn as a mathematician.
The litmus test for whether a leap is too large, is this: Would an average student (measured however you like) feel as though they could have eventually come up with this step, given enough time and observations? If a student does not feel that the could have come up with a step, on their own, then the course instructions should break the task into smaller and more natural components. Often this can be done by making certain smaller observations or guesses, which could motivate the needed step.
But these observations and guesses should never seem inhuman: Again, after making these intermediate motivations, the author should again apply the test: "is this sufficient for the student to feel that they could have come up with it themselves, given time and observations?"

### Other Design Principles

* Exercises are embedded as part of the text, and these are as frequent and manageable as possible. As soon as something is introduced, there should be exercises on it, if at all possible. But these kinds of exercises should not discourage or impede a student -- they should just invite the student to "get their hands dirty" with these new things they've just encountered.
* Hard exercises, or results that are not essential, can be good as exercise. However, those should be kept in pages containing "Optional Exercises" in their titles.
* History and context are used "just enough" to help the reader understand what these things are and why we're doing this.
Because exercises are a part of the text, I will eventually want to make a solution guide. However, I will only try to get around to this after I've completed the main content of the text.