OpenLLM-France/wikimedia huggingface dataset:
# Moving objects in retarded gravitational potentials of an expanding spherical shell
## Contents

* Preface
* Brief historical review
* Classical approach
* Retarded gravitational potentials
* Gravitational redshift
* Conclusion

## Appendix

* Table with computed results
* Java program

## Summary of the project

* Target audience: Astronomers, astrophysicists, physicists, mathematicians
* Learning objectives: Application of retarded gravitational potentials and gravitational redshift on very large scales.
* Contact person: User:Bautsch
* Are co-authors currently desired? Yes. Corrections of obvious errors directly in the text; content please after discussion.
* Guidelines for co-authors: Wikimedia-like.
# Movie Making Manual/Writing/Rewriting

Writing | Previous

# Rewriting

Over 80% of your time on any screenplay will be spent on rewrites. So much of screenwriting is about structure that you may have the story in the first few weeks while the rest of the time is spent reworking the script so the story works on the screen.
After you have plowed through and have a first draft script of 90-130 pages the best thing to do probably is to get a little distance from the screenplay so you can evaluate it objectively. This is probably best done by laying the script aside for a few weeks and doing something else then returning to it with fresh eyes.

## Top-Down Rewriting

Beginning writers assume that the rewriting process consists of going through the script line by line and fixing any typos or grammatical errors. After a couple of such passes they're bored and the screenplay is still weak.
To be efficient and really make progress requires being more organized and starting with the big picture. Make a series of passes through your screenplay, each time concentrating on one or two elements.
Start with the most important elements of any story such as: Is the hero really appealing and heroic? Is the villain really evil? Is there a powerful and credible conflict? Are the characters great, real, alive, right and consistent?
Strengthening these big elements might result in major restructuring of the screenplay. Only after they have been addressed is the time right to work down to issues such as spelling and grammar. Take a break for a few days at any point if necessary to get a fresh perspective.
A detailed rewriting strategy discussion

## 'Spitballing'

This rather strange term comes from William Goldman's books. It means getting together with another writer and discussing your script and coming up with ideas to solve problems you are having.
It's essential to discover whether or not your story, characters, dramatic conflict, is working. A screenplay is both a sales document for the film and the blueprint, a set of instructions to the director and the actors. An outside viewpoint is essential if you want to know if your script is going to be successful.

## Script Editors

A good script editor is invaluable. Professional editors and coverage experts can be located by searching the web and through ads in screenwriting magazines, however the cost can be prohibitive for independent filmmakers.
Another option is to enlist friends that are avid novel readers and particularly anal-retentive at spelling and grammar. Even the most successful professional writers value the feedback of their trusted friends. If the writing is interesting enough, friends will feel compensated by just getting to be the first to read the new work and share in the creative process.
Next | Screenplay Format
# Movie Making Manual/perf

* Previously known as "Techniscope"
* THX 1138 was shot in Techniscope.
* Natively 2.35:1 aspect ratio
* Uses half as much film as 4-perf
* Is difficult to find cameras and telecine facilities
* The cut for 4:3 TV is radical because there's no top and bottom to expand into
* The new, fine-grained stocks make 2-perf very attractive
* Be very careful about hairs in the gate and lens flare because there's almost no frame line
* Tough to optically print but it can be done (e.g. Multivision235)

# Links

* http://www.multivision235.com.au/
* http://www.widescreenmuseum.com/widescreen/wingts1.htm
* http://www.widescreenmuseum.com/widescreen/whywidefilm-oct1930.htm
* http://www.cinematography.net/Pages%20DW/2-perf_35mm.htm
# Movie Making Manual/Writing/Concept

The concept is simply an idea of what the Movie will be about. Generally a writer or director will develop a concept. From there, if funding is required, a "Spec Script" may be written and presented to a board. If the funding is given, a writer may be hired to develop the concept further and complete the script for further criticism from producers. Where funding is not required, a Director may choose to just write the script and shoot the final product.
Developing a concept can be one of the hardest steps in the film making process as a good concept can either make or break a movie, however there are few simple methods to developing an idea. One of these is dreaming. Lucid Dreaming is a popular method for coming up with story concepts as it allows the mind to freely develop and remember a scene. It is advised to write down dreams soon after you wake up to avoid forgetting.
Another method to coming up with scarier concepts is to change a small aspect of something common and similar to everyone. Steven Moffat commonly uses this method in his writing for Doctor Who. Some of his examples include;
* The Weeping Angels - Statue of angels that only move when not being viewed.
* The Empty Child - Removing a face with a gas mask is a simple way to remove someone's identity.
A concept is the only thing some directors need. For example, in w:Paranormal Activity, the Director (Oren Peli) opted for retro scripting, where the actors are given an outline of the plot and improvise dialogue. This is ideal for found footage as the actor is reacting to a scene and not memorize dialogue.
# Movie Making Manual/perf (continued)

* Uses less film than 4-perf
* Is natively 1.85:1
* Easy to get the cameras and telecine

## Links

* http://www.cinematography.net/Pages%20DW/3PerfSuper35mmForScope.htm
# Movie Making Manual/You the Filmmaker/Growing as an Artist

Should you read the excellent Irving Stone books about Van Gogh ("Lust for Life") and Michelangelo ("The Agony and the Ecstacy") what you will take from them is a new appreciation of the learning process and development of the artist. Both of these men accepted that it would take them years to get to grips with their media — as not only did they want to master their mediums but both were revolutionizing them, taking both painting and sculpture into unexplored territories. The realisation both artists had was that not only would the development take time but that they also needed to live life along the way.
Peter Biskind (a close observer of filmmakers and filmmaking) said that, apart from a few exceptional cases (Welles, Tarantino), it takes at least five to ten years for a director to learn this art/craft. Sometimes it seems like we can be in a huge rush to get there: we make a couple of shorts and then want to make a feature with a big budget. Michelangelo spent years drawing, working with wax and clay before being trusted with expensive marble.
Go a bit easy on yourself if a few years into your film career you have not made something with which you are hugely pleased; this is a complex art form requiring many technical skills and a lot of knowledge and experience, and the tools are in the midst of a huge revolution. Expect things to take awhile.
# Muggles' Guide to Harry Potter/Magic/Billywig
## Overview

A Billywig is an insect native to Australia. Its speed is so great that most Muggles or wizards cannot recognize it until they are stung by it. It grows up to an inch long.

## Extended Description

The effect of a Billywig sting is giddiness followed by levitation. Some wizards have tried to make a Billywig repeatedly sting them to enjoy the side-effects of the Billywig's sting, but too many stings will make the witch or wizard float for days, and if the witch or wizard is allergic to Billywig stings, they may float forever. Dried Billywig stings are used in many potions, and are reputed to be used in making the popular Wizarding treat, Fizzing Whizzbees.

## Questions

Study questions are meant to be left for each student to answer; please don't answer them here.
# Muggles' Guide to Harry Potter/Magic/Augurey
## Overview

An Augurey, or Irish Phoenix, is a small greenish-black bird that resembles a vulture and can emit a distinctive low cry. Being shy creatures, they stay primarily within their tear-shaped nests and fly only in periods of heavy rain.

## Extended Description

Though native to Britain and Ireland, the Augurey has also been spotted throughout northern Europe. They make their nests in bramble and thorn and their diet consists mostly of large insects and fairies.
In the past, wizards associated the cry of the Augurey with death, and a few early wizards are believed to have succumbed to a heart attack upon being surprised by the wail of an unseen augurey. Later it was determined that, instead of foretelling death, the augurey's cry signalled an impending rain shower.
The Augurey has been used as a home weather forecaster, though its persistent moaning during the winter months can be unbearable for some. As Augurey feathers repel ink, they are ineffective for quills.

## Questions

Study questions are meant to be left for each student to answer; please don't answer them here.
# Muggles' Guide to Harry Potter/Magic/Avis
## Overview

The Avis spell causes a flock of birds to appear out of the end of the caster's wand.

## Extended Description

This spell is used by Mr. Ollivander as part of the process of testing Krum's wand in the Wand Weighing ceremony. Krum's wand is a very sturdy wand, made of hornbeam and dragon heartstring, thicker than most; the Avis spell causes it to give a report like a gun as it creates a flock of small, twittering birds that fly off through the open window.
In Harry's sixth year, Hermione performs this spell twice: once in Transfiguration class, where she is the only person to be able to do it, unsurprisingly; and once a week later when she is suffering jealousy from Lavender and Ron's budding romance.

## Analysis

This is a sixth-year spell; creation of living creatures, unlike Transfiguration from non-living objects, is not taught to Hogwarts students until quite late in their education. As such, it is a decent test of the capabilities of a wand.
Avis in Latin translates directly to "bird".

## Questions

Study questions are meant to be left for each student to answer; please don't answer them here.
# Muggles' Guide to Harry Potter/Magic/Banishing Charm
## Overview

Banishing Charms are the opposite of Summoning Charms, and are used to send an object away from the caster.

## Extended Description

Banishing charms are more difficult than summoning charms as you are not only impelling an object to move, but ideally you are also telling it where to move to. In Professor Flitwick's class, we see that while nearly everyone has managed to send objects away from themselves (though in the case of Neville's efforts, sometimes it is the wrong object), only the best of the students is able to send their pillows unerringly into the box where they are intended to go.
We never hear the actual invocation of the banishing charm.

## Questions

Study questions are meant to be left for each student to answer; please don't answer them here.
# Muggles' Guide to Harry Potter/Magic/Bat Bogey Hex
## Overview

The Bat-Bogey Hex apparently causes the victim to be attacked by large, bat-winged bogies.

## Extended Description

While the effect of this spell is never completely defined, we do see or hear of its being used a few times. This is one of Ginny Weasley's specialties, almost a signature spell; she uses it on Draco Malfoy to escape from the Inquisitorial Squad when she is being held captive in Dolores Umbridge's office in Harry Potter and the Order of the Phoenix, and it is her use of this spell on another student in the Hogwarts Express in Harry Potter and the Half-Blood Prince that brings her to the attention of Professor Slughorn.

## Questions

Study questions are meant to be left for each student to answer; please don't answer them here.
# Muggles' Guide to Harry Potter/Magic/Bezoar
## Overview

A bezoar is a stone (actually a ball of compacted hair) that is removed from the stomach of a goat, and the ingestion of such a stone is said to cure most poisons.

## Extended Description

We are first introduced to this artifact when Professor Snape asks Harry, in his first-ever Potions lesson, where he would go to find a bezoar.
The bezoar appears a second time in Harry Potter and the Goblet of Fire when it is the "key ingredient" that Harry forgets to add to his antidote in Potions class because of his anxiety over preparing to ask Cho Chang to the Yule Ball.
Bezoars are not mentioned again until Harry Potter and the Half-Blood Prince. In Professor Slughorn's Potions class, Harry is called upon to produce an antidote. Rather than creating a complex potion that would counter the mix of poisons in question, he simply retrieves a bezoar from the supplies cabinet. Professor Slughorn absently tucks it into his bag.
The bezoar then becomes vital to the story as Ron is given some poisoned mead while visiting Professor Slughorn; while Slughorn panics, Harry recalls the bezoar, retrieves it from Slughorn's bag, and feeds it to Ron, thus saving Ron's life.

## Analysis

Like Boomslangs and Dittany, bezoars exist in the world outside the series. In our world, bezoars are balls of compacted hair that collect in the stomach of a person or animal, and were once believed to have magical curative powers, very similar to what they are given in this series.
With bezoars being so very useful in the case of poisoning, it is rather surprising just how uncommon they are. It seems that there are only a few, even in the supply cabinet in the Potions classroom; and it seems that Professor Slughorn, aware as he is of the effects of potions, does not routinely carry one in his bag. We must assume that they form very rarely in the wild.
Because it is mentioned that it is an ingredient in the antidote Harry is making just before Christmas in the fourth book, and because it is used directly, bezoars are listed both as magical devices and potion ingredients on the Magic overview page of this work.

## Questions

Study questions are meant to be left for each student to answer; please don't answer them here.
* When was the bezoar first mentioned?
# Muggles' Guide to Harry Potter/Magic/Blibbering Humdinger
## Overview

No description of the Blibbering Humdinger is ever given to us. From the fact that only Luna Lovegood seems to believe in its existence, we can safely assume that it springs from the fertile imagination of Xeno Lovegood, her father.

## Extended Description

The Blibbering Humdinger is first mentioned in Harry Potter and the Order of the Phoenix when Luna Lovegood says that people used to think that they didn't exist. Hermione replies that they were right, because they didn't exist, causing Luna to slouch off, annoyed.
In Harry Potter and the Deathly Hallows, after the Battle of Hogwarts, Luna, seeing how tired Harry is, distracts the people around herself and Harry Great Hall by saying, "Ooh, look, a Blibbering Humdinger!" This allows Harry to don his Invisibility Cloak, and collect Ron and Hermione without anyone noticing.

## Questions

Study questions are meant to be left for each student to answer; please don't answer them here.
# Next Generation Sequencing (NGS)/Integrative platforms
## Introduction

* Open-source integrative platforms allow bioinformatics novice to carry out computationally intensive analyses online (either in public server or in private cloud).
* Numerous modules encompassing reads mapping, variant discovery, differential expression analysis and visualization are available. These tools also ensure transparency and reproducibility by recording every analysis metadata, including the tools, versions and parameters setting used during analysis.
* These platforms do not automate the entire analysis procedure and can be useful only if one is aware of what assumptions (e.g. the rationales behind the parameter choice) are being made. Note that these platforms may not necessarily be the best choice for many of the questions one is addressing. Users should also resort to the original release sites if the latest version of respective tools is needed.

## Examples of integrative platforms
### InsilicoDB

https://insilicodb.org/
The smart way to manage genomics data. Export genomics datasets to your favorite analysis tools.

### Gene Pattern

http://www.broadinstitute.org/cancer/software/genepattern/
GenePattern is a powerful genomic analysis platform that provides access to more than 240 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

### Galaxy

http://usegalaxy.org/ Galaxy is an open, web-based platform for data intensive biomedical research. Whether on this free public server or your own instance, you can perform, reproduce, and share complete analyses.

### Gene Talk

https://www.gene-talk.de GeneTalk is a web-based expert platform for analysis and interpretation of NGS data. Scientists and clinicians can filter variant call files (*.vcf) and reduce the amount of data. For diagnosis and interpretation of the data users can communicate, share data, and provide expertise to others via the platform.

### GeneProf

http://www.geneprof.org GeneProf is a web-based, bioinformatics software suite for the analysis of functional genomics experiments, e.g. RNA-seq or ChIP-seq. GeneProf supports integrated analyses of RNA-seq, ChIP-seq and other data generated using next-generation sequencing (NGS) platforms and provides a wealth of public data that can be easily compared with own results.

### Basepair

www.basepairtech.com
Basepair is a SaaS platform for genomic data analysis that lets researchers quickly analyze raw data and choose among several high quality workflows from RNA-Seq, ChIP-Seq, DNA-Seq, etc.. Their cloud-based software significantly reduces turnaround time for scientists from weeks to hours without sacrificing quality.
# Next Generation Sequencing (NGS)/Expression quantification

RNA-seq expression quantification

## Overview

* Objective: to estimate the relative abundance of transcripts from an rna-seq sample.
* Biological questions?
* Inputs:
   * Reference:
      * Annotated Genome (fasta/gff)
      * Transcriptome (fasta)
      * RNA-seq raw reads (fastq, Ilumina).
* Outputs:
   * Relative abundance per transcript.

## Experimental Design

See (link) RNA sequencing
Typical Steps in the Method: (table or workflow or paragraph?)
* Data generation | Get some data. | Seq (link) Sequencing RNA technologies,
* Get a reference | You need a reference with all the involved transcripts for which you want relative abundance |
* RNA-seq read QC | Check the quality of the sequencing itself. |
* Adaptor trimming / quality filtering / contamination filtering | Reads will contain sequence that is not from the transcript but from the technology. |
* Mapping | Align your reads to the reference |
- Quantification | Get transcript abundance |

## Some tools and resources

* Get a reference: MetaDB (link)genome assembly and annotation (link) transcriptome denovo assembly ....
* QC: SeqWiki: FastQC, KAT
* Trimming: SeqWiki; Trimmomatic, Sickle, Cutadapt....
* Mapping: Seqwiki: tools...... ... ... ... ... ... ... .. ....
* Quant: Seqwiki: tools
# Next Generation Sequencing (NGS)/Genome Wide Association Studies
## Genome-Wide Association Studies

Genome-wide association studies (GWAS) are frequently used to identify genetic variations between two populations of organisms--one with a specific phenotype (case) and one without (control). For example, if researchers were interested with genomic variation associated with a medical disease (e.g., cancers, Alzheimer’s, or autism), researchers can search for variants that are nonrandomly present in either a control (e.g., individuals who do not have a disease) or disease-specific population (e.g. individuals who have a disease). This allows researchers to map genes that affect specific outcomes or traits. Genotypes that are disproportionately common in disease-specific populations are then candidate “genes” for the increased risk or “cause” of disease-specific phenotypes. Essentially, GWAS studies use large populations to evaluate, quantitatively, the likelihood of association between variants and phenotypic outcomes. GWAS studies can also provide information on epigenetic factors in disease processes. For example, Zhang et al. (2013) observed DNA methylation differences in genes related to alcohol metabolism in individuals with alcohol dependence compared with healthy controls.
Though GWAS studies can serve as a powerful tool for elucidating associations between genes and traits, there are some specific limitations. For example, genetic variants that are low in frequency and have small effects on traits are difficult to detect using GWAS, and genetic variants that are of high frequency with strong effects are very unusual for common diseases. Additionally, population stratification, linkage disequilibrium, and DNA pooling can bias the results.
The National Human Genome Research Institute maintains an up-to-date catalogue of GWAS studies that have published significant associations (with a p-value of less than 0.5 X 10-5 for 17 traits)

## References

* ↑ Carlson, C. S., Eberle, M. A., Kruglyak, L., & Nickerson, D. A. (2004). Mapping complex disease loci in whole-genome association studies. Nature, 429(6990), 446-452.
* ↑ Balding, D. J. (2006). A tutorial on statistical methods for population association studies. Nature Reviews Genetics, 7(10), 781-791.
* ↑ Zhang, R., Miao, Q., Wang, C., Zhao, R., Li, W., Haile, C. N., Hao, W., & Zhang, X. Y. (2013).Genome-wide DNA methylation analysis in alcohol dependence. Addiction Biology, 18, 392-403. doi: 10.1111/adb.12037
* ↑ McCarthy, M. I., Abecasis, G. R., Cardon, L. R., Goldstein, D. B., Little, J., Ioannidis, J. P., & Hirschhorn, J. N. (2008). Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nature Reviews Genetics, 9(5), 356-369.
* ↑ Hindorff LA, MacArthur J (European Bioinformatics Institute), Morales J (European Bioinformatics Institute), Junkins HA, Hall PN, Klemm AK, and Manolio TA. A Catalog of Published Genome-Wide Association Studies. Available at: www.genome.gov/gwastudies.