OpenLLM-France/wikimedia huggingface dataset:
# Pinyin/Bible/Genesis/Chapter 8

See also
* 8:1 And God kept Noah in mind, and all the living things and the cattle which were with him in the ark: and God sent a wind over the earth, and the waters went down.
* Shern jider Noah her chuarn 'shang de shengwuh, xiahng Dihqiur chui le yi zhehn feng, shuii jiuh tuih le.
* 8:2 And the fountains of the deep and the windows of heaven were shut, and the rain from heaven was stopped.
* shenyuan de quarnshuii her tian'shang de chuanghu dou bihseh le, yuu tirng le.
* 8:3 And the waters went slowly back from the earth, and at the end of a hundred and fifty days the waters were lower.
* 8:4 And on the seventeenth day of the seventh month the ark came to rest on the mountains of Ararat.
* 8:5 And still the waters went on falling, till on the first day of the tenth month the tops of the mountains were seen.
* 8:6 Then, after forty days, through the open window of the ark which he had made,
* 8:7 Noah sent out a raven, which went this way and that till the waters were gone from the earth.
* 8:8 And he sent out a dove, to see if the waters had gone from the face of the earth;
* 8:9 But the dove saw no resting-place for her foot, and came back to the ark, for the waters were still over all the earth; and he put out his hand, and took her into the ark.
* 8:10 And after waiting another seven days, he sent the dove out again;
* 8:11 And the dove came back at evening, and in her mouth was an olive-leaf broken off: so Noah was certain that the waters had gone down on the earth.
* 8:12 And after seven days more, he sent the dove out again, but she did not come back to him.
* 8:13 And in the six hundred and first year, on the first day of the first month, the waters were dry on the earth: and Noah took the cover off the ark and saw that the face of the earth was dry.
* 8:14 And on the twenty-seventh day of the second month the earth was dry.
* 8:15 And God said to Noah,
* 8:16 Go out of the ark, you and your wife and your sons and your sons' wives.
* 8:17 Take out with you every living thing which is with you, birds and cattle and everything which goes on the earth, so that they may have offspring and be fertile and be increased on the earth.
* 8:18 And Noah went out with his sons and his wife and his sons' wives;
* 8:19 And every beast and bird and every living thing of every sort which goes on the earth, went out of the ark.
* 8:20 And Noah made an altar to the Lord, and from every clean beast and bird he made burned offerings on the altar.
* 8:21 And when the sweet smell came up to the Lord, he said in his heart, I will not again put a curse on the earth because of man, for the thoughts of man's heart are evil from his earliest days; never again will I send destruction on all living things as I have done.
* 8:22 While the earth goes on, seed time and the getting in of the grain, cold and heat, summer and winter, day and night, will not come to an end.
# Osmo Documentation/DOCdrafts

Example questions for the FAQ section (frequently asked questions)
How do I export calendar data to the iCalender (.ics) format?
How do I keep track of calendar, tasks, contacts, and notes ?
How do I integrate SyncML to support the exchange of calendar data with other programs, as well as with devices?
How do I modify the existing tabs?
How do I set a deadline for each task ?
How do I create a blank wall calendar that I can fill by hand?
How do I print a calendar in landscape format for a selected month?
How do I send an appointment to another user?
How do I exchange calendar data with other programs, as well as with devices?
How do I show birthdays?
How do I showing day names?
How do I show previous and next month?
How do I insert a timeline in a day note?
How do I change details I want to see in the calendar information window?
How do I Find a simple view of a full-year calendar?
How do I jump to a specific date?
How do I print a calendar?
How do I Use data fields for managing private and business contacts?
How do I change font type and size?
How do I displays tasks, notes, and contacts in a list forma?
How do I format time expressions?
How do I hide one or more PIM components?
How do I view links with a web browser?
How do I print?
# Orthopaedic Surgery/Staging of Tumours

* Orthopaedic Surgery
* INTRODUCTION ·
* AUTHORS ·
* ACKNOWLEDGEMENTS ·
* NOTE TO AUTHORS
* 1.Basic Sciences ·
* 2.Upper Limb ·
* 3.Foot and Ankle ·
* 4.Spine ·
* 5.Hand and Microsurgery ·
* 6.Paediatric Orthopaedics ·
* 7.Adult Reconstruction ·
* 8.Sports Medicine ·
* 9.Musculoskeletal Tumours ·
* 10.Injury ·
* 11.Surgical Procedures ·
* 12.Rehabilitation ·
* 13.Practice
* Current Chapter: Basic Sciences
| | Staging of Tumours | |
| <<Nomenclature | Staging of Tumours | Evaluation of Tumours>> |
Benign soft tissue tumors are classified using the musculoskeletal tumor society staging system. Arabic numerals denote benign condidtions and Roman numerals malignant. Stage 1 inactive Stage 2 active Stage 3 locally aggressive. Marginal section is appropriate for the first two categories whereas wide local excision is appropriate for the third.
Superficial lesions less than 1.5 cm especially with slow growth characteristics,assymtomatic, non-fixed and soft are suitable for excisional biopsy, otherwise incisional biopsy if fine needle or core biopsy is not your preferred approach. Beware the ganglion cyst that isn't. Upon encountering instead a solid tumor which does not appear to be a giant cell tumor of tendon sheath or a schwannoma, or a hemangioma which have fairly characteristic appearances, avoid the temptation to proceed directly to marginal resection, instead, perform an incisional biopsy. If a malignant lesion is encountered then close, observing meticulous hemostasis. Layered closure, tourniquet deflated first to confirm hemostasis, compressive bulky dressing.
After the fact is the wrong time to then check for adenopathy. It is also too late to take back that esmarch exsanguination. It is also too late to take back the transverse incision and the subcutaneous flap, and the exposure of major neurovascular structure that might have been avoided. In other words, plan the approach to even benign lesions as if you are about to encounter an unexpected malignant fibrous histiocytoma, or synovial sarcoma or epithelioid sarcoma.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8727762
# Orthopaedic Surgery/Upper Limb

* Orthopaedic Surgery
* INTRODUCTION ·
* AUTHORS ·
* ACKNOWLEDGEMENTS ·
* NOTE TO AUTHORS
* 1.Basic Sciences ·
* 2.Upper Limb ·
* 3.Foot and Ankle ·
* 4.Spine ·
* 5.Hand and Microsurgery ·
* 6.Paediatric Orthopaedics ·
* 7.Adult Reconstruction ·
* 8.Sports Medicine ·
* 9.Musculoskeletal Tumours ·
* 10.Injury ·
* 11.Surgical Procedures ·
* 12.Rehabilitation ·
* 13.Practice
| | Upper Limb | |
| <<Surgical Approaches | Upper Limb | Shoulder>> |
CHAPTER 2: Upper Limb

## Shoulder

* Disorders of The Rotator Cuff
** Impingement Syndrome
** Calcification of Rotator Cuff
** Disorders of Biceps Tendon
** SLAP lesions
** Adhesive Capsulitis
* Instability of The Shoulder
** Anterior Instability
** Posterior Instability
** Multidirectional Instability
* Disorders of the Glenohumeral Joint
** Tuberculosis
** Rheumatoid Arthritis
** Osteoarthritis
** Rapidly Destructive Arthropathy
** Osteonecrosis
* Glenohumeral Arthroplasty
* Disorders of Scapula and Clavicle
** Scapular Instability
** Grating Scapula
** Septic Arthritis of Sternoclavicular joint
** Sternoclavicular Hyperosteosis
** Osteoarthritis of Acomioclavicular Joint

## Elbow

* Acquired Deformities
** Cubitus Varus
** Cubitus Valgus
** Pulled Elbow
* Osteochondritis Dissecans
* Loose Bodies
* Tuberculosis
* Rheumatoid Arthritis
* Gout and Pseudogout
* Osteoarthritis
* Neuropathic Arthritis
* Stiffness of Elbow
* Recurrent Elbow Instability
* Repetitive Strain Sydromes
** Lateral Epicondylitis
** Medial Epicondylitis
** Baseball Pitcher's Elbow
* Bursitis

## Wrist

* Wrist Pain
* Acquired Deformities
* Chronic Instability of The Wrist
** Instability of Distal Radio-Ulnar Joint
** Longitudinal Instability of Radio-Ulnar Joint
** Disorders of Triangular Fibrocartilage Complex
** Carpal Instability
* Kienbock's Disease
* Tuberculosis
* Rheumatoid Arthritis
* Osteoarthritis
** Radio-Carpal Osteoarthritis
** Distal Radio-Ulnar Arthritis
** Carpometacarpal Osteoarthritis
** Scapho-Lunate Advanced Collapse
* Tenosynovitis
** De Quervain's Disease
** Intersection Syndrome
** Flexor Tendinitis
** Repetitive Syndromes
* Ganglions
** Simple Ganglion Cysts
** Compound Palmar Ganglion
* Carpal Tunnel Syndrome
* Distal Radius Fractures

## Hand

See Hand and Microsurgery
# Maxima/Installation
## Dependencies

* gnuplot,
* tex
** texinfo
** texi2html
** texlive-latex-recommended
* GNU autotools
** automake 1.9
** autoconf2.13
* tk 8.4.
* lisp
** sbcl ( sudo apt-get install sbcl)
* libgmp3-dev
* libreadline5-dev
* libncurses5-dev
* sharutils
* libxmu-dev
* libxaw7-dev
* wxWidgets library for wxMaxima
** libwxgtk3.0-dev
** libwxbase3.0-dev
* compiler is GNU g++ for wxWidgets library
* build-essential
* imagemagick
* ibus-gtk
* ibus-gtk3

## Steps

* Download and install ready made Maxima deb packages
** from Ubuntu repositories ( old versions )
** from other sites
* Compile your own maxima package
* compile maxima from sources ( without creating deb packages )
Now the best is a git method

## From Ubuntu repositories

You can make use of :
* Synaptic ( Graphical package manager)
* apt-get.
In second case write in command line:
This method can get old version which gets some trouble, like
Uninstall such Maxima version

## From PPA
### wxmaxima

From repositiories by Istvan Balhota

## From sources

Before compilation, you should have all dependent packages

### CVS

This procedure does not create a deb package.

### Using git
#### maxima/xmaxima

If you have git and SBCL then :
Now one can run it from inside the source directory.
The result :
Xmaxima can also be run :
or bash file :
wxMaxima is not present now.
Where is Maxima after standard ( as above) installation ?
example result :
Note that it is a different directory then after apt-get installation. One can have 2 ( or more ) versions of Maxima on the disk )

#### wxmaxima
## Problems

* Open a terminal
* type : sudo apt-get install gdb
* after gdb is installed type : gdb wxmaxima
* run and wait until it crashes
* and type : backtrace

## References

* ↑ compiled deb packages for Maxima 5.20.1-1 by Istvan Blahota
* ↑ help from ubuntu community about Maxima
* ↑ How to build your own Maxima package by Andras Somogyi
* ↑ Install from Ubuntu repositories by Mario Rodriguez Riotorto
* ↑ launchpad : blahota wxmaxima
* ↑ How to build Maxima by Rupert Swarbrick
# Maxima/Operators

"=" means syntactic equality. Check : is(equal(a,b))
# Maxima/Plots
## Complex Functions

* Visualizing Complex Functions with Conformal Mapping ( themaximalist )

### Topologist's sine curve

Topologist's comb :
* ↑ themaximalist visualizing-complex-functions-by-their-images-over-concentric-circles
# Maxima/Help
### bash

* info maxima

### Maxima commands

* dependencies
* infolists
* describe
# Maxima/Methods of use

Maxima is flexible software, and can be used with a number of different methods:
* online , without installation
* offline = after installation
** Graphical User Interface (GUI)
** from console ( without GUI)
*** interactive ( also one can load program files using load or bash function)
*** bash mode
Run maxima, use program c.mac and save output to c.txt file:

## References

* ↑ Maxima CAS online by CESGA
# Maxima/Outputs and warnings

* ratprint : false; /* remove "rat :replaced " */
* using $ instead of ; at the end of the line ( not inside function where , ends the line )
* return from the function
* "warning: encountered undefined variable ... in translation." This is warning from compile when function uses global variable without using in in tha arguments list. You have to include the variables in the function's list
# Maxima/Objects

* atom
** number
** name
** string
* list of atoms
# Maxima/Names
## References

* ↑ Maxima by Example: Ch. 1, Introduction to Maxima by Edwin L. Woollett
# Maxima/Numbers
## Number types
### Binary numbers
### Complex numbers
#### Argument

Principial value of argument of complex number in turns carg produces results in the range (-pi, pi] . It can be mapped to [0, 2*pi) by adding 2*pi to the negative values
On can order list of complex points according to it's argument :

### rational numbers

* rat
* ratp
Rationalize with limit denominator:

## Predicate functions

Compare :
List of predicate functions ( see p at the end ) :
* abasep
* alphacharp
* alphanumericp
* atom
* bfloatp
* blockmatrixp
* cequal
* cequalignore
* cgreaterp
* cgreaterpignore
* charp
* clessp
* clesspignore
* complex_number_p from to_poly package
* constantp
* constituent
* diagmatrixp
* digitcharp
* disjointp
* elementp
* emptyp
* evenp
* featurep
* floatnump ( compare : isreal_p)
* if
* integerp
* intervalp
* is
* isreal_p from to_poly package
* lcharp
* listp
* listp
* lowercasep
* mapatom
* matrixp
* matrixp
* maybe
* member
* nonnegintegerp
* nonscalarp
* numberp
* oddp
* operatorp
* ordergreatp
* orderlessp
* picture_equalp
* picturep
* poly_depends_p
* poly_grobner_subsetp
* polynomialp
* prederror
* primep
* ratnump
* ratp
* scalarp
* sequal
* sequalignore
* setequalp
* setp
* stringp
* subsetp
* subvarp
* symbolp
* symmetricp
* taylorp
* unknown
* uppercasep
* zeroequiv
* zeromatrixp
* zn_primroot_p
See also :
* declare
** property:
*** rational, irrational, real, imaginary, complex,
*** even, odd,
*** decreasing, increasing
*** evenfun, oddfun

## Number Theory

There are functions and operators useful with integer numbers

### Elementary number theory

In Maxima there are some elementary functions like the factorial n! and the double factorial n!! defined as ${\frac {n!}{k!}}$ where $k$ is the greatest integer less than or equal to $n/2$

#### Divisibility

Some of the most important functions for integer numbers have to do with divisibility:
all of them well documented in help. you can view it with the '?' command.
Function ifactors takes positive integer and returns a list of pairs : prime factor and its exponent. For example :
It means that : $8=2^{3}\,$

#### Other Functions

Continuus fractions :
* ↑ stackoverflow question : rationalize-number-with-limit-denominator
* ↑ maxima manual : Category Declarations-and-inferences
# Maxima/Numerical methods
## Newton method

Functions
* newton for equation with function of one variable
* mnewton is an implementation of Newton's method for solving nonlinear equations in one or more variables.

### newton

load :
Code :

### mnewton

One can use Newton method for solving systems of multiple nonlinear functions. It is implemented in mnewton function. See directory :
which uses linsolve_by_lu defined in :
See this image for more code.
# Next Generation Sequencing (NGS)/Method template

Each method section should have the following general format:
Here is a version you can copy paste:
Here is how it will look:

## Overview

A brief description of the method here, broadly covering what we are doing and why.

### Useful background

Links to other relevant sections of the wikibook, like this /RNA.

### Objective

What does the method achieve?

### Biological questions

Why are we doing this?

## Inputs and outputs
### Inputs

* A list of the pre-requirements for the method
** like
** this

### Outputs

* A list of the outputs
** like
** this

## Typical steps in the method

Each step has it's own template, described below.

## Next steps

Discussion of where the method leads.

## Workflows
### Example galaxy workflow

Link to an example galaxy workflow for for the method (including example datasets) on a given galaxy instance or to the XML document describing the workflow.

### Example command line workflow
## Discussion

POV discussion about the method.
Links to related discussion on BioStar:
* your search keyword on Biostars
* your search keyword on Biostars
# Next Generation Sequencing (NGS)/cover
### The back cover

A beginners book for Next Generation Sequencing (NGS), describing common bioinformatics pipelines and how to run them. This book is for anyone who has the pleasure and pain to work with NGS data day-to-day.
* "Amazing!" - Some Git.
Next Generation Sequencing (NGS), also known as High Throughput Sequencing (HTS), is a very important thing. Links to information. This book is for you to master it.

### Table of contents

* How to read this book Information on how to navigate the information in the book.
* Background knowledge
** The Biology of NGS
** Informatics
* Principles of the field
* Common workflow steps
* Common NGS applications
** De novo Genome Assembly (Method) e.g. I have 60x coverage of my genome with some various paired end data...
** Transcriptomics e.g. I have RNA-Seq data from three tissues...
** Genotyping by sequencing
** Exome-capture e.g. Something here...
** Chromatin conformation capture

## About this book

This book is a collaborative effort created by many Authors. For more details...
# Next Generation Sequencing (NGS)/Ray
## Contents

A basic knowledge of the UNIX command line is assumed.
In this tutorial, Ray will be installed in $HOME/software using its source code downloaded to $HOME/sources. A dataset will be downloaded to $HOME/datasets and it will be assembled de novo with Ray in $HOME/projects

## Installing Ray

The first thing to do is to download the Ray tarball that contains its source code.
A MPI library is required to install Ray. On Ubuntu or Debian, the package names are: openmpi-bin, libopenmpi-dev, make, g++.
Optionally, native support for compressed files can be included in Ray. This requires zlib and/or libbz2. On Ubuntu or Debian, the package names are: zlib1g-dev libbz2-dev.
With MPI installed, Ray can now be installed:

## Obtaining data

The commands below fetch E. coli data.

## Running Ray

It is a good habit to create a directory for each project. A directory will therefore be created for this tutorial.
Next, we create symbolic links to the data files so that long paths are not required.
An arbitrary number of Ray processes can be launched. In this example, 4 Ray processes are launched. These processes can be on several computers or on a single computer.
The -k parameter sets the length of k-mers.

## Assessing the assembly

Ray writes files to a single directory. Ray does several automated quality control tests.
You can list the produced files with:
The important files are these:
# Next Generation Sequencing (NGS)/SOAPdenovo

We get some E coli data from SRR001665 you could type
unpack the two files
You will need to get SOAPdenovo and the data prepare module
Also we have to make a config file. We name this cont.config
And then we scaffold using a Kmer size of 31 (the read length is 36). We use the whole SOAP pipeline by specifying the "all" parameter By setting asm_flags to 3 the same library would be used for scaffolding as well. In this case SOAP will terminate in the scaffolding step with a floating point exception as there is nothing to scaffold with. Contigs will be found nevertheless in EC.contigs.
# The Biology of NGS

# what will be in this section

## Essential concepts

# based on Lawrence Hunter's Molecular Biology for Computer Scientists (#1)
# Must be modified and shortened!
1. What is Life? 2. Living Parts: Tissues, Cells, Compartments and Organelles 3. Life as a Biochemical Process 4. The Molecular Building Blocks of Life 5. From Genes to Proteins 6. Sources of Biological Knowledge 7. Experimental Methods in Biology (link to more detailed information on NGS in #3 of the parent directory - Principles of the field)

## Survival Glossary

# DNA, RNA, gene, protein, genetic code, central dogma of [molecular] biology, transcription, translation, expression, splicing, sequencing, genetics vs genomics, transcriptomics, expressomics, ...
# linked to the sections explaining these in detail

## Useful Resources

1. Molecular Biology for Computer Scientists An introduction written by the founder of the International Society for Computational Biology (ISCB) Lawrence Hunter. The text is from 1993 but it contains all essential concepts. 46 pages.
# Next Generation Sequencing (NGS)/cover/Informatics

There is a certain degree of prior knowledge which is required and/or assumed of the user for the remaining pages of this WikiBook. This section highlights the areas of informatics knowledge that are prerequisites before embarking on an NGS bioinformatics project.

### Introduction to Linux - why use the Command Line Interface (CLI)?

Link to existing resource, tutorial

### Programming

* Python?
* R?
# Permaculture Design/Crop rotation

Crop rotation is a method of farming whereby different crops are grown systematically arranged in series on the same piece of land time after time in such a way to restore nutrients removed from the soil. • Crop rotation has principles,
Principles of crop rotation
* Avoid planting crops of the same family,
* After deep rooted crop plant a shallow rooted,
* Always include a legume,
* Allow a fallow period in which land grow natural plants,
* Plant green manure in between to protect soil from sun or add manure,
* Alternate between heavy feeders and light feeders.
Importance of crop rotation
* Crops such as legumes add nutrients to the soil as they contain nitrogen fixing bacteria in their nodules,
* Rotation prevent nutrients from become exhausted in the soil,
* Roots of different crops grow to different depth, thus taking food from different areas of the soil,
* Pests are eradicated e.g., pests that feed on cabbage will feed only on brassica family and not on solanaceous plants.
A four-year crop rotation
* The main crops to be grown first are heavy feeders e.g., tomatoes
* They should be followed by an optional crop,
* Optional crop followed by a legume,
* Finally root crop.
# PermaBlitz/Planning Manual

Before you get into planning a Blitz, maybe take a look at reports of past blitzes to get ideas:

## Summary of the stages

* Download the full book (PDF)
* Download the full book (editable)
* Order a printed book ($--)

## Are you ready?

Stuff about how to find, join, or form a PermaBlitz posse. DO you have ideas for your project? How are you designing? Budgeting.. documenting..
       Read more

## 6 weeks out, needs analysis

* Pick a date for your Permablitz
* At this stage you should arrange a consultation with a Permaculture designer to work out needs, wants and capabilities. This is best done by organising a site analysis by Permaculture designer. It is also important at this stage to give the designer a budget range so that they design your garden accordingly
       Read more

## 4 weeks out, design

* At this stage you should get back to the Permaculture designer in order to view and discuss their design for your garden. You will need to finalise this design and make sure it integrates all of your needs and wants
       Read more

## 2 weeks out, preparation and organisation

* Create a list of all the materials and resources that you will need.
* Stuff for kids?
* Animals..
* Access
* Begin the promotion of your Permablitz
* Start to grow seedlings to plant on the day
* Ask your designer to draw you up a design that is easy to read and understand so that you will be able to successfully create your permagarden
       Read more

## Permablitz

* Weed and Clear
* Create Garden beds
* Plant
* Mulch and compost
* Have a good time!
       Read more

## After

* Make sure to thank everyone who helped with your Permablitz
* Possibly arrange a follow up consultation with your Permaculture designer 1‐6 months after your Permablitz to make sure your garden is functioning to its full extent
       Read more