OpenLLM-France/wikimedia huggingface dataset:
# GNU Health/Using the FHIR REST server
## FHIR Overview

Fast Healthcare Interoperability Resources (FHIR) is a standard for exchanging healthcare information electronically developed by HL7. The standard defines a common interface for medical software interoperability. For more reading, look at the FHIR standard.

## URL Structure

The FHIR standard defines a REST API, a set of interactions with each resource. Each resource handles different types of information. Currently, the GNU Health FHIR server supports 12 resources:
* Conformance: Describes the server's FHIR capabilities.
* Patient: Patient information, like email, address, SSN, etc.
* DiagnosticReport: Completed lab tests, but not the data
* Observation: Lab data, like Uric Acid values
* Practitioner: Health professionals and their information
* Procedure: Surgeries/operations
* Condition: Diseases/diagnoses
* FamilyHistory: Family histories of patients
* Medication: Medications (not prescriptions!)
* MedicationStatement: Medications taken by a patient
* Immunization: Immunizations
* Organization: Institutions, departments, companies, etc.
Each resource has its own endpoint. For example, the Patient endpoint is found at /Patient, the DiagnosticReport endpoint at /DiagnosticReport, and so on. The only exception to this naming schema is the Conformance endpoint which is found at / and /metadata.
The interactions use HTTP verbs. Simple read and search interactions with GET, and so on.
For further reading into the REST design, read the documentation
Note: Currently, the GNU Health FHIR server has no write functionality.

## Authentication

All resources, except for Conformance, require authentication. The server authenticates with the user credentials of the underlying GNU Health/Tryton server. Login with your user credentials at /auth/login. Logout at /auth/logout. There is a simple welcome page for logged-in users at /auth/home.

## Searching / Listing

To search a resource, simply add arguments to the endpoint to refine the search. For example, /Patient, will return all the patients on the server. /Patient?name=ana will return all the patients with Ana in their name.
Note: Many search criteria for the GNU Health FHIR server are not supported yet. Refer to the FHIR documentation for more information.

## Test Server Examples

Some examples with the community FHIR server (may need to sign in):
* List all patients
* Show info for patient id #1
* List all surgeries
* List Lab results
← FHIR REST server · Synchronization Guide →
# GNU Health/Upgrade
## About GNU Health Upgrades

GNU Health is in constant development. Upgrades fix bugs and keep your system with the latest functionality. Therefore, you are advised to keep your production system with the latest version.
GNU Health will always provide the scripts and tools for you to keep your health center updated.

## Gathering Information

Get the latest GNU Health versions and announces: A key point to keep your GNU Health environment in good shape is to become part of the community. We publish GNU Health version updates and other relevant news in different media. Make sure you subscribe at least to the General users and to the health announce mailing lists.
Verify your current GNU Health version: You can check your current GNU Health database version from the client, via Administration → Modules.
Always upgrade all the GNU Health modules: When we release a version, we always pack all the official modules on it. This is important, because we test the integrity and cross-functionality among modules. So, you should never use modules from different versions. For example, you should not use health_genetics version 1.6.3 with health 1.6.2 . This is not supported and can create serious inconsistencies on your database!

## Prepare your Upgrade

Plan your upgrade process, resources and downtime: Upgrading a hospital information system requires careful planning. Make sure you choose the right time, and notice your colleagues about the new release.
Test the upgrade process in another computer: It is highly recommended that you count with a separate server, where you can test your upgrade process in a controlled environment, without impacting your production installation. Write down all the steps and issues that you run into.

## The Upgrade Process

This section summarizes the upgrade process steps for a standard installation, using the modules included in the official release at GNU.org FTP site. Any version specific information will sent via the health-announce@gnu.org mailing list, along the new release announcement, so make sure you are subscribed!
Step 1: Stop your Tryton server.
Step 2: Backup your database and GNU Health directories
Step 3: Rename the current kernel directory, with gnuhealth user:
Step 4: Download the new GNU Health version. The official GNU Health tar file contains all the modules.
Step 5: Extract the kernel and follow the instructions as in a new Installation.
Step 6: Update the Tryton configuration file trytond.conf to fit your needs. Make sure you have the right values for your installation. Compare the values with your current version, they should match. Some critical variables are:
* path
The best way to edit the configuration file is to use the GNU Health user alias editconf:
Step 7: Upgrade the database:
Step 8: Apply possible post-upgrade scripts at PostgreSQL level (one-time process)
You apply this step if you are upgrading from 3.0 to 3.2. Please remember to apply this script only once !
Step 9: Start the Tryton server:
You should be now in your new GNU Health version!
← Patches and Patchsets · Contributing →
# GNU Health/Users

← Modules · Countries →
# GNU Health/WebDAV

← Countries · Central Authentication →
* This section applies to version 3.4 of GNU Health.

## Introduction

GNU Health provides its own WebDAV and Caldav server. It allows to create and associate calendars to health professionals. The calendar entries for appointments, hospitalizations and other resources can be accessed via WebDAV clients.

## Installation

To install the webdav functionality, you need to install the following packages
* pywebdav3-gnuhealth : Python3 webDAV library for GNU Health (installed automatically when using the standard installation method)
* health_webdav3_server : GNU Health webdav server, for Python3 and GNUHealth support
* health_caldav : GNU Health calendar package with webdav3 and caldav support
* health_calendar : Main calendar for appointments
* health_inpatient_calendar : Hospitalization / bed calendar support
If you have installed GNU Health from openSUSE packages, everything is already installed.

### Setting up the WebDAV server

Check the settings for the host and port of the GNUHealth WebDAV server
In this sample from the default configuration file, the WebDAV server will accept connections from any network interface, on port 8080.
You can change the values editing the configuration file, using the command
editconf

## Creating and Assigning Calendars

In order to access a calendar, we first need to create it, and assign it to a user on our GNU Health Tryton instance.
To create a calendar, Follow the link:
Calendar -> Calendars
* Define a name to the calendar (use only letters, without punctuation or non-ascii characters).
* Assign the calendar to a user (in this example, we assign the "Cordara" Calendar to the "Administrator" user
* Finally, assign the calendar to the user that will login to GNU Health. In this example, the user associated to the "Cordara" calendar is "Administrator", with username "admin". The credentials (username and password) used in the calendar are the same as for login into the GNU Health HMIS. For security reasons, use a SSL enabled connection.

## Running the server

To start the webdav server, do the following
* Check that the GNU Health server is running
* Change to the webdav server directory
Execute the server
openSUSE comes with a systemd-service called gnuhealth-webdav. It expects the database name as parameter. If your database is gnuhealth34, you can start the service with

## Configuring the client
### Known clients

GNU Health Calendar system has been known to work on the following clients :
* Mozilla Thunderbird, Lightning
* Cadaver
* Evolution
Set the hostname and port of the GNU Health WebDAV server . The default port is 8080
The nomenclature for the URL is :
# General Biology/Gallery of Biologists

* Francis Crick chemist and molecular biologist, discovered structure of DNA molecule
* Charles Darwin the father of the science of evolutionary biology
* Richard Dawkins zoologist and biology populariser
* Stephen Jay Gould paleontologist and science populariser
* J.B.S. Haldane geneticist and evolutionary biologist, founded population genetics and the modern synthesis
* Bill Hamilton formulated theory of inclusive fitness and kin selection
* Thomas Huxley "Darwin's Bulldog", early evolutionary biologist and science populariser
* Lynn Margulis introduced the theory of eukaryotic cell origin through endosymbiosis
* Barbara McClintock geneticist and molecular biologist, discovered transposons
* Gregor Mendel discovered the basic rules of heredity
* Ernst Mayr evolutionary biologist and science populariser
* Mark Ridley science populariser
* Fred Sanger founder of DNA and protein sequencing techniques
* John Maynard Smith evolutionary biologist and science populariser
* Alfred Russel Wallace evolutionary biologist
* James Watson molecular biologist, discovered structure of DNA molecule
* Edward Wilson founded "sociobiology"
This book is intended as a compilation of biographies describing the lives and work of influential biologists.

## External Links

* EvoWiki: List of Biologists
# General Biology/Gallery of Biologists/Charles Darwin

Charles Darwin (1809 - 1882), British naturalist, founder of the Theory of Evolution by means of natural selection.
Note: Darwin's books should be read with a historical mindset, as they do not always reflect current scientific opinion (though impressively, they often do). Scientifically speaking, the knowledge held in his books should be supplemented with other books in Biology.

## Links

Texts Online:
* Darwin on the Web Archive
* ibiblio library listed by author
(both of the above are Project Gutenberg mirrors.)
* Expression of Emotions in Man and Animals
* Life and Letters of Charles Darwin
* Descent of Man
* Formation of Vegetable Mould Through the Action of Worms
* Geological Observations of South America
* Geological Observations of Volcanic Islands
* Movement and Habits of Climbing Plants
* Structure and Distribution of Coral Reefs
* Variation of Plants and Animals Under Domestication
* Voyage of the Beagle
* Autobiography of Charles Darwin
# General Biology/Classification of Living Things/Viruses/Answers

1. No, since viruses target unique glycoproteins. The proteins act as a key and lock.
2. Lysogenic
3. Lysogenic
4. No, because the cold and flu are caused by viruses. Antibiotics are for bacteria.
# General Biology/Genetics/Gene Regulation

General Biology | Getting Started | Cells | Genetics | Classification | Evolution | Tissues & Systems | Additional Material
* Not all genes are expressed in a cell
* Gene expression can be turned on and off
* Multiple levels of regulation gene function
** Transcription initiation
* State of chromatin
* Transcription factors
** Post-transcriptional
* mRNA processing
* mRNA half-life
* Translational
* Post-translational
** Protein modification

## Transcriptional control

* State of chromatin
** Euchromatin: transcriptionally active
** Heterochromatin: transcriptionally inactive
** Chemical modification of histones
** Methylation of bases
* Transcription factors
** Bind to DNA at promoter or other regulatory sites (enhancers)
* Recognize base sequence through major and minor grooves
** Recruit RNA polymerase

## DNA grooves

Categories of transcription factors in eukaryotes
* Helix-turn-helix
** Two small "-helices
** Fit into DNA groove
* Homeodomain
** Highly conserved helical domains
** ~60 amino acids
* Zinc finger motif
** Zn atom bound
* Leucine zipper
** dimer

## Regulatory proteins

* Activity may depend upon allosteric binding of small molecules
** cAMP
** Co-repressors
** Inhibitors
* Binding to promoter region may “bend” DNA, making it accessible to other regulatory proteins

## Lac operon of E. coli

* Single promoter region for cluster of genes
* Regulated and transcribed as a single unit
* Operons typical in prokaryotes
* Repressor: turns OFF gene expression
lac repressor
* Turns off transcription by blocking access by RNA polymerase
* repressor in activated by allosteric binding of lactose
Regulation in eukaryotes
* Both proximal (promoter) and distal (enhancer) to gene
* Typically transcription unit encodes a single polypeptide
* Promoter
** TATA box
** Other elements (regulatory sequences) may be present
* Enhancers
** Work upstream, downstream, close, far from gene
** Bend DNA

## Alternative splicing

* Single transcript gives rise to 2 or more mature mRNAs
** encode different polypeptides with shared domains
** tissue and developmentally specific

## References

This text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland State University.
# General Biology/Genetics/Gene Expression

General Biology | Getting Started | Cells | Genetics | Classification | Evolution | Tissues & Systems | Additional Material
Flow of genetic information
* DNA → mRNA → polypeptide
* Transcription: DNA → mRNA
** RNA polymerase
** Nucleus in eukaryotes
** Transcription also makes rRNA and tRNA
* Translation: mRNA → polypeptide
** Ribosomes: protein and rRNA
** Genetic code and tRNA

## The Genetic Code

* Triplet codon
** 64 triplet codons (43)
** Experimentally deciphered in 1961
* Nearly universal
** Implies common ancestor to all living things
** Minor exceptions: certain ciliates, mitochondria, chloroplasts
* Still evolving

## Transcription

* RNA polymerase
** NTP substrates
** Synthesizes single stranded RNA complementary to template strand of DNA
** New nucleotides to 3’ end
* Begins at promoter site
** no primer necessary
* Ends at terminator site
* Much posttranscriptional modification in eukaryotes

## Transcription bubble

Promoter site
* Prokaryotes
** -10 nt, TATA box
** -35 nt, additional signal
* Eukayotes
** -25, TATAAA box
** Additional signals upstream
* Promoters may be strong or weak
* In eukaryotes, access to promoter depends upon state of chromatin coiling

## Eukaryote mRNA

* Synthesized as pre-mRNA, processed in nucleus
* 5’ end: GTP cap placed in inverted position
** Essential for ribosome recognition
* 3’ end: poly-A tail; non-templated addition of ~50-250 A nucleotides; stability
* Introns: intervening sequences removed

## Translation

* Requires:
** mRNA
** tRNA
** ribosomes
** translation factors (various proteins)
* In prokaryotes, takes place on growing mRNA
* In eukaryotes, in cytoplasm on free ribosomes and RER
* AUG start codon to stop codon

## Translation in bacteria

tRNA
* Transfer RNA
* Two important parts
** Anticodon
* Hydrogen bonds with mRNA codon
** 3’ end
* Accepts amino acid (using energy of ATP)
* Aminoacyl-tRNA synthetase

## Aminoacyl tRNA synthase

* Enzyme used to bind amino acid from the cytoplasm to tRNA, which then transfers that amino acid to the ribosome for polypeptide formation

## Translation

* Initiation complex
** Small ribosomal subunit
** mRNA
** fMet-tRNA (prokaryotes only; met-tRNA in eukaryotes)
** Initiation factors
* Elongation
** Ribosome
** mRNA
** tRNAs
** Elongation factors

## Elongation, translocation

* incoming tRNA enters the A site
* rRNA catalyzes peptide bond formation. Note that growing peptide is attached to what was incoming tRNA at P site after translocation.
* empty tRNA leaves via E site; recycled
* A site ready for next charged tRNA

## Introns/exons

* In eukaryotes, coding regions of gene may be interrupted by introns, noncoding regions of DNA (RNA)
* Introns
** 22- >10,000 nt in length
** 5’ GU … 3’ AG removal sequence
** Not essential to genes
** May constitute >90% of gene
* removed from pre-mRNA to form mRNA
* Exon: often codes for functional domain of protein
** translatable mRNA

## References

This text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland State University.
# General Biology/Evolution

General Biology | Getting Started | Cells | Genetics | Classification | Evolution | Tissues & Systems | Additional Material
* Introduction
* Evolution of Life
* Animal Evolution
* Human Evolution
General Biology | Getting Started | Cells | Genetics | Classification | Evolution | Tissues & Systems | Additional Material
# General Biology/Genetics

General Biology | Getting Started | Cells | Genetics | Classification | Evolution | Tissues & Systems | Additional Material
* Inheritance
* DNA, The Genetic Material
* Gene Expression
* Gene Regulation
* Mutation
* Recombinant DNA Technology
General Biology | Getting Started | Cells | Genetics | Classification | Evolution | Tissues & Systems | Additional Material
# Guide to Game Development/3D Modelling
## 3D Modelling Software

* Autodesk Maya
* Autodesk 3DS MAX
* Cinema 4D
* Z-Brush
* Blender
          Free
* Wings 3D
          Free
* Cheetah 3D
          Mac Only

## External Links

* Best Modeling Software for Unity
# Guide to Game Development/Audio/Sound effects
## External Links

* Creating a Synthesizer for Retro Sound Effects
# Guide to Game Development/Introduction/About the book
## Information

This book was started on 30th May 2014. It's designed to cover all aspects of game development to hopefully help people of all different skill levels in a variety of different ways.

## Requirements

This book requires you to have learned basic programming languages. I will be using C and Assembly Language, with some information on how to make things simple using OOP. Moreover, you should have some basic information on how things work in programming, such as arrays, objects, decisions, structuring programs and that kind of stuff.

## Difficulty

Basically, I and other contributors will try to teach you the easiest way, and we will also show some real life examples and which techniques are better where. So it purely depends on your game and skill.

## Software

This is the most common question almost every beginner programmer asks to everyone, and ends up in the person being stuck between thousands of software recommendations and advice. Believe me, I have found that NO SOFTWARE is perfect for a sound start. Most people think Visual Studio is better than every software, I agree with them. But people starting from the base of mountains know better than people who get on the summit using helicopters. So my basic advice is: Don't use anything. However, I will show you how software works and which thing works better than others.

## Thanks

Thanks for reading this book, we appreciate it!
# Guide to Game Development/Data file types/.xml

.xml is shorthand for eXtensible Markup Language, and is a widely popular format for storing data in video games. XML is essentially meta-data: that is, data about data. The programmer can extend the capabilities of XML and create their own tags, hence the term "extensible". It is a markup language in that it is made up of tags, which look something like this:

## External links

* Wikipedia page on XML
* XML in Game Development - Gamasutra
* XML in Game Development - GameDev
* XML Tutorial - W3Schools
# Guide to Game Development/Introduction

An introduction about me, the book and how it can help you (Note: reading this section won't help you with game development).

## Categories

* About the book
          Information about the book itself
* Where do I begin?
          How to use the book to help you get better/start game development.
* Discussion
          A place to ask questions and give recommendations

## Contributors to the book

* CallumPoole (discuss • contribs) 16:43, 5 June 2014 (UTC)
** Involvement: creator, currently main contributor.
* benjamin.doe talkcontribs 15:36, 16 June 2014 (UTC)
** Minor contributions to Physical motion and Mathematics
# Guide to Game Development/Audio

The music, sound effects and voice acting that will accompany the game.

## Categories

* Game music
       Music that would be played in the background of the game
* Sound effects
       A small piece of audio track that activates when a small event in a game happens (collecting a coin).
* Voice acting
       The audio used to create a voice for characters.
* Audio formats
       The file format of your audio for your game
# Guide to Game Development/Data file types
## Data file types/formats
### Text based file types

* .xml
          Easy for humans to read, levels of indentation, can take up a lot of space. Standard used for storing general data.
* .json
          Compact data file, better for humans not to see, levels of indentation.
* .txt
          Text file used for miscellaneous things.
* .ini
          Easy to read, usually used to store game options.

### Binary based file types

* .dll
* .xnb
          Used with XNA programming

## Geometry

* Wavefront .obj
          Used for storing 3D models
** Wavefront .mtl
                Material template library, used to store one or more materials within one file. Used with Wavefront .obj.
* .fbx
          File type owned by Autodesk

## Image types
### Bitmapped

* .png
          Loss-less compression, good compress
* .jpg or .jpeg
          Uses lossy compression
* .bmp
          Loss-less compression, not so amazing compression, but easier to read with code
* .gif
* .tga and TGA 2.0
* .pnm.bz2

#### Texture formats

* .mat
* .dds
          Used for DXTC (Desktop platforms: OS X, Linux, Windows & Tegra) and ATC (Andreno GPUs) textures.
* .pvr
          Used for PVRT textures (PowerVR GPUs).
* .pkm
          Used for ETC1 textures(All OGLES 2.0 devices compatibles).

### Vector

* .svg
          Scaled vector graphic

## Audio

* .mp3
* .wma
* .wav
* .ogg
* .midi
* .cda
* .rm
* .asf
* .bik

## Animation

* .anim

## Fonts

* .ttf

## Other

* .prefab

## External links
### Audio files

* Recommendations about audio files and APIs used with them
* Descriptions of audio files

### Other files
## References

* 1 2 3 http://gamedev.stackexchange.com/questions/15334/best-most-popular-image-format-for-texturing
# Guide to Game Development/Data file types/Wavefront .obj

Note that there is a difference between wavefront .obj and a programming .obj. Wavefront .obj is used for geometry, a programming .obj is used with a linker in a programming language code compilation.

## External links

* Wikipedia page on wavefront .obj
* Obj specification
* Examples of .objs