OpenLLM-France/wikimedia huggingface dataset:
# Beginner's Guide to Adobe Flash/Color

Dealing with color in Flash is similar to dealing with color in other screen based applications. To begin, let's review some color basics. Color can be referred to as either reflective or transmissive. Reflective color is also known as subtractive color and can be described as red, yellow, and blue for the primary pigment colors, and green, orange and purple for the secondary pigment colors. These colors mix to produce black, or, more likely, a neutral gray or brown. Transmissive color is known as additive color. It is made up of red, green and blue, the three colors of transmissive light, which when mixed together create white light. The secondary additive colors are cyan, magenta and yellow, which, along with black, make up the process printing colors. An example of how transmissive light works would be to consider how we see grass as green, even though actually green is the channel of white light that gets retransmitted to our eye, and the red and blue light gets absorbed.
Flash, being a screen based application, uses transmissive light with the three additive primaries of red, green and blue. Since Flash is primarily a web creation tool, it must adhere to some standards for color usage on the web. For instance, monitors display color in RGB in an array of pixels in a grid. Each pixel has an address and can be made up of red, green and blue colored dots, or a mixture thereof. Each color channel, red, green or blue, can range in value from 0, completely off, to 255, completely on. Black is created from all channels being completely off; white is created from all channels being completely on. Each channel can have 256 different values creating almost unlimited color choices for the designer.
In this section we cover:
* Color Mixer
* Color Swatches
* Gradients
# Baseball/Shortstop

The shortstop plays a position typically between second base and third base. The shortstop is often the most athletic of the players on the field, having the greatest need for speed, agility, and a strong throwing arm. In the major leagues, persons who can play shortstop can often play other positions well -- but few players can ever make the successful transition to being a shortstop.
Shortstops field most ground balls, infield flies, and line drives hit between second base and third base. The ground balls have typically been hit far into the infield, but the shortstop typically has a more difficult throw than even a third baseman within the infield. If there is a runner on first base and a ground ball is hit toward him, he can usually choose to throw to the second baseman for a force on the runner from first or to first base to get the baserunner. The shortstop often makes a throw to second base so that the second baseman can then throw to first base to get another out at first base and thus a double play.
Less commonly a shortstop makes a throw to home plate or third base to get an out on a runner from third base or second base.
Shortstops are often in plays in which the catcher throws toward second base to catch a baserunner trying to steal second base. If the shortstop applies the tag to the baserunner before that baserunner has reached second base or has over-slid second base and is no longer in contact with it, the baserunner is out. The shortstop is the usual infielder to apply the tag on a baserunner caught stealing second base.
On outfield flies the shortstop often positions himself as the 'cutoff' man who takes the throw from the outfielder and then throws it with added speed and accuracy to the catcher or some infielder to make a play at another base or at home plate should there be a baserunner trying to advance bases or score.
# Bash Shell Scripting

Wikibooks Contributors Present: Bash Shell Scripting
Currently this book provides an introductory level knowledge of Bash. Go to External Programs, External links and Using man, info and help for further directions and inspirations.

## Table of Contents
### Introduction

    About Bash
    History
    Prerequisites
    How to read the book?
    A few notes on terminology
    Some notes on your shell

### Beginning Bash

    Intro Exercise
    Simple Commands
    Exit Status
    Variables
    Input-Output
    Positional Parameters
    Conditional Expressions
    Loops
    Shell Functions
    Environment

### More to Bash

    Pipelines and Substitution
    Shell Arithmetic
    External Programs
    Whiptail
    Index of Symbols

## See also

* Images with BASH src code

## Related Wikibooks

* A Quick Introduction to Unix often involves the Bash shell.
* Guide to Unix often involves the Bash shell.
* The Android/Terminal IDE uses Bash as its default command shell.
* Mac OS X Tiger/A Quick Look Under the Hood uses Bash as its default command shell.
* Shell Programming
* Bourne Shell Scripting - Bash is almost Bourne-Shell compatible.

## External links

* Bash Reference Manual − gnu.org
* GNU Bash Reference Manual for Bash 3.2 − network-theory.co.uk
* "Section - What does {some strange unix command name} stand for?"
* Wooledge BashGuide
* Advanced Bash-Scripting Guide, by Mendel Cooper
# Bash Shell Scripting/A Few Notes On Terminology

The language of Bash commands is a Turing-complete programming language, meaning that if it is even theoretically possible for a given computation to be performed, then it is theoretically possible to perform it in Bash. Furthermore, from a practical standpoint, it is possible to do some very sophisticated things in Bash, and people often do. Nonetheless, it is usually described as a "shell-scripting language" (or similar) rather than a "programming language", and the programs written in it are usually referred to as "Bash shell scripts" (or similar) rather than "Bash programs". We will follow that convention here, preferring script for a Bash script and program only when referring to external programs that might be invoked from a Bash script.
We will also often use the term utility. This term is somewhat subjective, and usage varies, but it typically describes an external program that requires no human interaction and is intended to work well with other programs. All utilities are programs, so we will use the terms somewhat interchangeably. The extreme opposite of a "utility" is an application; that term is also subjective, with variable usage, but it typically describes an external program that has a relatively complex graphical user interface (GUI) and is not intended to work well with other programs. Since applications, by their nature, are not generally called from Bash scripts, we will have less occasion to use that term. Many programs are neither "utilities" nor "applications", and some programs have elements both of utilities and of applications.
Of the various elements of a Bash script, some are typically called commands, while others are typically called statements. We will observe this distinction here, but you need not overly concern yourself with it. Normally "command" is used in reference to invocations of external programs, of Bash built-ins such as echo that resemble external programs, of shell functions (which we will see below), and so on. Normally "statement" is used in reference to instances of Bash programming constructs such as if … then … else … fi or variable assignment (which we will see shortly). Perhaps confusingly, command is also used in reference to any Bash built-in, even if a use of that built-in would result in a "statement" rather than a "command"; for example, "an if statement" is a statement that uses "the if command". If this distinction seems too fine, do not worry; in context, it should always be sufficiently clear what is meant by one term or the other.
# Bash Shell Scripting/Exit Status

When a process completes, it returns a small non-negative integer value, called its exit status or its return status, to the operating system. By convention, it returns zero if it completed successfully, and a positive number if it failed with an error. (This approach allows multiple different errors to be distinguished by using different positive numbers.) A Bash script can obey this convention by using the built-in command exit. The following command:
terminates the shell script, returning an exit status of four, indicating some sort of error. When no exit status is specified (either because exit is run with no argument, or because the script ends without calling exit), the script returns the exit status of the last command it ran.
One way that exit statuses are used is with the Bash operators && ("and") and || ("or"). If two commands are separated by &&, then the command on the left is run first, and the command on the right is only run if the first command succeeds. Conversely, if they are separated by ||, then the command on the right is only run if the command on the left fails.
For example, suppose we want to delete the file file.txt and recreate it as a blank file. We can delete it using the common Unix utility rm ("remove"), and recreate it using the common Unix utility touch; so, we might write this:
But really, if rm fails, we don't want to run touch: we don't want to recreate the file if we failed to delete it to begin with. So, we can write this instead:
This is the same as before, except that it won't try to run touch unless rm has succeeded.
A third Boolean-like operator, ! ("not"), inverts the exit status of a command. For example, this command:
is equivalent to rm file.txt, except that it will indicate success if rm indicates failure, and vice versa. (This is not usually useful when exit statuses are used as actual exit statuses, indicating success or failure, but we will soon see some extended uses of exit statuses where a "not" operation is more useful.)
The exit status of a command is (briefly) available as $?. This can be useful when it is necessary to distinguish between multiple different failure statuses; for example, the grep command (which searches for lines in a file that match a specified pattern) returns 0 if it finds a match, 1 if it finds no matches, and 2 if a genuine error occurs.
# Bash Shell Scripting/About Bash
## What is Bash?

Bash is a "Unix shell": a command line interface for interacting with the operating system. It is widely available, being the default shell on many GNU/Linux distributions and formerly on Mac OSX, with ports existing for many other systems. It was created in the late 1980s by a programmer named Brian Fox with the request of Richard Stallman, working for the Free Software Foundation. It was intended as a free software alternative to the Bourne shell (in fact, its name is an acronym for Bourne Again SHell), and it incorporates all features of that shell, as well as new features such as integer arithmetic and job control.

## What is shell scripting?

In addition to the interactive mode, where the user types one command at a time, with immediate execution and feedback, Bash (like many other shells) also has the ability to run an entire script of commands, known as a "Bash shell script" (or "Bash script" or "shell script" or just "script"). A script might contain just a very simple list of commands — or even just a single command — or it might contain functions, loops, conditional constructs, and all the other hallmarks of imperative programming. In effect, a Bash shell script is a computer program written in the Bash programming language.
Shell scripting is the art of creating and maintaining such scripts.
Shell scripts can be called from the interactive command-line described above, or they can be called from other parts of the system. One script might be set to run when the system boots up; another might be set to run every weekday at 2:30 AM; another might run whenever a user logs into the system.
Shell scripts are commonly used for many system administration tasks, such as performing disk backups, evaluating system logs, and so on. They are also commonly used as installation scripts for complex programs. They are particularly suited to all of these because they allow complexity without requiring it: if a script just needs to run two external programs, then it can be a two-line script, and if it needs all the power and decision-making ability of a Turing-complete imperative programming language, then it can have that as well.
* ↑ "Bash - GNU Project - Free Software Foundation". Retrieved 28 November 2017.
# Bash Shell Scripting/External Programs

Bash, as a shell, is actually a 'glue' language. It helps programs to cooperate with each other, and benefits from it. Always Search The Internet for what you want -- there are lots of command line utilities available.

## Using whiptail

Whiptail is a program that allows shell scripts to display dialog boxes to the user for informational purposes, or to get input from the user in a friendly way. Whiptail is included by default on Debian and various other GNU/Linux distributions.
    From the GNU/Linux Dictionary: whiptail is a "dialog" replacement using newt instead of ncurses.
    From its README: whiptail is designed to be drop-in compatible with dialog(1), but has fewer features: some dialog boxes are not implemented, such as tailbox, timebox, calendarbox, etc.
See Bash Shell Scripting/Whiptail.

## Using AWK

See AWK and man awk (man gawk).

## Using sed

See sed and man sed.

## Using grep

See grep and man grep.

## Using man, info and help

These three programs are where you can find help or reference from. man displays roff manual pages, info displays texinfo documentations, while help displays builtin helps.
Appending --long-help, --help or --usage to a command-line program may also gives you the usage information. Possible synonyms include -H and -h.
Just try these out:
Pressing h in man and info's interfaces can also give you some direction.
# Bash Shell Scripting/History

Brian Fox began coding Bash on January 10, 1988, after Richard Stallman became dissatisfied with the lack of progress being made by a prior developer. Stallman and the Free Software Foundation (FSF) considered a free shell that could run existing shell scripts so strategic to a completely free system built from BSD and GNU code that this was one of the few projects they funded themselves, with Fox undertaking the work as an employee of FSF. Fox released Bash as a beta, version .99, on June 8, 1989, and remained the primary maintainer until sometime between mid-1992 and mid-1994, when he was laid off from FSF.
Since then, Bash has become by far the most popular shell among users of Linux, becoming the default interactive shell on that operating system's various distributions. It has also been ported to many other platforms.
# Agrodatabase/202 - Topics, Units and Valuations/Valuations

| Id-SCA | - | VALUATIONS |
| 101.110 | - | QUALITY - INTENSITY -Influence |
| 101.111 | - | VERY GOOD |
| 101.112 | - | GOOD, tall, long, big, easy, INTENSE |
| 101.113 | - | REGULAR, MEDIA, MODERATE |
| 101.114 | - | MALO, LOW, short, small, HARD, SCARCE, LIGHTWEIGHT |
| 101.115 | - | VERY BAD, NULL, NO, PRICELESS |
| 101.200 | - | TOLERANCE - RESISTANCE |
| 101.210 | - | very tolerant |
| 101.220 | - | TOLERANT, ADAPTABLE, RESISTANT |
| 101.230 | - | MEDIUM, MODERATE, REGULAR, TOLERANT |
| 101.240 | - | SENSITIVE, LOW, LOW TOLERANCE |
| 101.250 | - | ZERO TOLERANCE |
| 101.400 | - | NEED - PREFERENCE |
| 101.410 | - | VERY DEMANDING |
| 101.420 | - | DEMANDING |
| 101.430 | - | PREFER |
| 101.440 | - | REGULAR ADAPTATION |
| 101.450 | - | NOT DEMANDING |
| 101.500 | - | SPEED |
| 101.510 | - | VERY FAST |
| 101.520 | - | QUICK |
| 101.530 | - | MODERATE FAST |
| 101.540 | - | REGULAR, MEDIA, MODERATE |
| 101.550 | - | MODERATE SLOW |
| 101.560 | - | SLOW |
| 101.570 | - | VERY SLOW |
# Agrodatabase/21 - Crop Prontuary - Data

VEGETABLES
Tuber vegetables
Tropical tuber vegetables
* Cassava
* Sweet potatoes
* Yams
Root vegetables
* Carrots
* Radishes
* Turnips
Bulb vegetables
* Garlic
* Onions
Fruiting vegetables
* Tomatoes
* Peppers
* Aubergines
* Cucumbers
* Courgettes
* Melons
* Pumpkins
* Watermelons
* Chayote
Brassica vegetables
* Broccoli
* Cauliflower
* Head cabbage
* Chinese cabbage
Leaf vegetables
* Lettuce
* Scarole
* Spinach
* Beet leaves
* Celery
Stem vegetables
* Asparagus
* Globe artichokes
# Agrodatabase/202 - Topics, Units and Valuations/Units

| Id-SCA | - | UNITS |
| 111000 | - | SPACE |
| 111.101 | - | mm |
| 111110 | - | cm |
| 111120 | - | m |
| 111.212 | - | m2 |
| 111221 | - | m2/ha |
| 111222 | - | plants/m2 |
| 111.223 | - | plants/ha |
| 111510 | - | m3 |
| 111.520 | - | m3/ha |
| 112000 | - | TIME |
| 112300 | - | hours |
| 112400 | - | days |
| 112500 | - | weeks |
| 112700 | - | month |
| 112800 | - | years |
| 113000 | - | MASS |
| 113100 | - | gr |
| 113.112 | - | gr/ha |
| 113.121 | - | seeds/gr |
| 113.122 | - | gr/1000 seeds |
| 113.131 | - | mg/lt |
| 113200 | - | kg |
| 113.211 | - | kg/m2 |
| 113.410 | - | ton/ha |
| 113.410 | - | TONS / HAS. |
| 113.611 | - | kg/ha |
| 114000 | - | CLIMATE |
| 114.160 | - | Cº |
| 115000 | - | PERCENTAGE |
| 115.100 | - | ppm |
| 115.200 | - | 0/00 |
| 115.300 | - | % |
| 116000 | - | UNITS TECHNICAL SPECIFIC |
| 116.554 | - | fu/ha |
| 116.555 | - | fu/tm |
| 116.574 | - | kcal |
| 116.711 | - | dS/m |
| 116.721 | - | pH |
| 117.010 | - | nº |
| 117.011 | - | nº/ha |
# Bioinformatics/Introduction

Bioinformatics is a branch of biology which implements the use of computers to help answer biological questions. Classical biology involves the use of experiments, where a hypothesis is formed and objectively tested. Bioinformaticians, too, perform experiments but they may involve building computational models or using analyses to derive useful information from raw data. The possibilities of using computers with biology are vast: any biological problem can involve the use of computers.
However when one mentions bioinformatics, some applications pop up more often than others. These might include sequence alignments, searching for sequence patterns and other work with DNA, RNA or protein sequence data. This is because of the increasing amount of genome sequencing projects being completed and the usefulness that computers have brought to the analysis of genomic sequences.
Bioinformatics is a growing discipline and as computers get more sophisticated, it will be a very important complement to experimental biology.

## Further reading

* Raul Isea The Present-Day Meaning Of The Word Bioinformatics, Global Journal of Advanced Research, 2015
* Ilzins, O., Isea, R. and Hoebeke, J. Can Bioinformatics Be Considered as an Experimental Biological Science 2015
# Bioinformatics/Other Data/Medical

Medical Informatics is the application of informatics to medicine.
# Bioinformatics/Biological Diversity

This Part is heavy on broad concept and relatively light on useful technical details. I should probably move this to the end (after I decide what to do with the topics presently found in Part IV) even though that rather bruises the narrative.
I don't actually know much (well, relatively speaking) about computer models for entire populations - but that is certainly computational biology and should absolutely be included here.
The first chapter will explain the differences in sequence that allow organisms to thrive in different environments or on different chemical substrates.
The second chapter will discuss the relationship between the observed complexity of an organism and the complexity of that organisms genome.
The third chapter discusses how whole-genome analysis leads to the conclusion that there existed a single, common ancestor to all known life forms. There will be some discussion of how we come to that conclusion, what we think we known about this ancestral organism. If there's room, I may include a chapter on the Origins of Life on Earth.
Chapter four is self-explanatory.
Chapter five will discuss how whole genome analysis leads us to conclude that Chloroplasts and Mitochondria are descended from eubacterial endosymbionts.
Chapter six is essentially devoted to computational studies of genes related to development - particularly in comparison to their homologs found in single celled organisms such as Yeast.
Chapter seven discusses means of measuring effective population sizes - and what the effective population size means in terms of the real diversity of an organismal genome. If the population genetics textbook is ever finished I hope to life most of this from there.
Chapter eight extends the discussion in chapter seven to the special case when a population splits into multiple groups in limited genetic contact.
# Bioinformatics/Bayesian Algorithms

Bayesian algorithms are useful if there exists a limited amount of experimental data and one wants to evaluate a hypothesis which is based on that data. For example, if we pose the question whether i is true given j, we want to know the posterior probability P(i|j) (probability of i if j is already given). But this posterior probability is not directly inferable from the data, so we reverse the statement: If our hypothetical i were true (=given), what is the probability of j? What we can say, is that the probability of a true i with given j times the probability of j is equal to the probability of true j with i given times the probability of i. We can put this into a mathematical form: $P(i|j)*P(j)=P(j|i)*P(i)$ . Then a little rearrangement leads to what we want to know: what is the probability of a true i given the data j? $P(i|j)=[P(j|i)*P(i)]/P(j)$
# Bioinformatics
## Contents

* Foreword
* Introduction
* Part One: Molecular Biology
** The central dogma of molecular biology
** DNA structure
** RNA structure
** Protein & Nucleic acid
** Human Genome
* Part Two: Sequence Searches and Alignment
** Sequence Databases
** Nucleic Acid Search Algorithms
** Nucleic Acid Alignment Algorithms
** Protein Alignment Algorithms
* Part Three: Phylogenetics
** Understanding Phylogenetic Trees
** Distance Algorithms
** Parsimony Algorithms
** Likelihood Algorithms
** Bayesian Algorithms
* Part Four: Genomics
** Whole Genome Assembly
* Part Five: Gene Expression
* Part Six: Protein Structure
*** Protein Folding
*** Protein structure prediction
**** Secondary structure prediction
**** Homology modelling
**** De novo structure prediction
**** Contact Prediction
*** CASP
* Part Seven: Proteomics
* Part Eight: Metabolomics
* Part Nine: Metagenomics
* Part Ten: Biological sequences and biological diversity
** Chemical diversity, arising from sequence diversity, allows biological diversity
** How biological complexity is expressed in genomic differences
** Biological sequence data indicate a common ancestor for all living things
** Unique features of biological sequences derived from extremophiles
** The genetic origins of oxygen adapted life, mitochondria and chloroplasts
** The genetic origins of multi-cellularity
** A living species is defined as much by genetic diversity as by the genome of any particular individual
** How genetic variability within a species allows for speciation
* Part Eleven: Other types of biological data
** Medical informatics
** Environmental or population data
** Morphological data
** Relational databases and biological data
* Glossary