OpenLLM-France/wikimedia huggingface dataset:
# LMIs in Control/pages/systemzeroswithout feedthrough

Let's say we have a transfer function defined as a ratio of two polynomials: ${\begin{aligned}H(s)={\frac {N(s)}{D(s)}}\\\end{aligned}}$ Zeros are the roots of N(s) (the numerator of the transfer function) obtained by setting $N(s)=0$ and solving for s.The values of the poles and the zeros of a system determine whether the system is stable, and how well the system performs. Similarly, the system zeros are either real or appear in complex conjugate pairs. In the case of system zeros without feedthrough, we take the assumption that $D=0$.

## The System

Consider a continuous-time LTI system, $G$ , with minimal statespace representation $(A,B,C,0)$
       ${\begin{aligned}{\dot {x}}(t)=Ax(t)+Bu(t)\\y(t)=Cx(t)\end{aligned}}$

## The Data

The matrices:
    ${\begin{aligned}A\in \mathbb {R} ^{n\times n}\\M\in \mathbb {R} ^{n\times q}\\N\in \mathbb {R} ^{q\times n}\\\end{aligned}}$

## The LMI: System Zeros without feedthrough

The transmission zeros of $G(s)=C(sI-A)^{-}1B$ are the eigenvalues of $NAM$, where $N\in \mathbb {R} ^{q\times n},M\in \mathbb {R} ^{n\times q},CM=0,NB=0,NM=1.$. Therefore , $G(s)$ is a minimum phase if and only if there exists $P\in \mathbb {S} ^{q}$, where $P>0$ such that
       ${\begin{aligned}PNAM+M^{T}A^{T}N^{T}P<0\end{aligned}}$

## Conclusion:

If P exists, it ensures non-minimum phase. Eigenvalues of NAM then gives the zeros of the system.

## Implementation

https://github.com/Ricky-10/coding107/blob/master/Systemzeroswithoutfeedthrough

## External Links

A list of references documenting and validating the LMI.
* LMI Methods in Optimal and Robust Control - A course on LMIs in Control by Matthew Peet.
* LMI Properties and Applications in Systems, Stability, and Control Theory - A List of LMIs by Ryan Caverly and James Forbes.
* LMIs in Systems and Control Theory - A downloadable book on LMIs by Stephen Boyd.
* Control_Systems/Poles_and_Zeros
# Latin/Chapter 5 Verse

< Latin

## A Verse From the Gospel of St. Luke

Respondens Simon dixit: "Aestimo quia is, cui plus donavit". At ille dixit ei: "Recte iudicasti". Et conversus ad mulierem, dixit Simoni: "Vides hanc mulierem? Intravi in domum tuam: aquam pedibus meis non dedisti; haec autem lacrimis rigavit pedes meos et capillis suis tersit. Osculum mihi non dedisti haec autem, ex quo intravi non cessavit osculari pedes meos. Oleo caput meum non unxisti; haec autem unguento unxit pedes meos. Propter quod dico tibi: Remissa sunt peccata eius multa, quoniam dilexit multum: cui autem minus dimittitur, minus diligit." Dixit autem ad illam: "Remissa sunt peccata tua". Et coeperunt, qui simul accumbebant, dicere intra se: "quis est hic, qui etiam peccata dimittit?". Dixit autem ad mulierem: Fides tua te salvam fecit; vade in pace!".
# Latin/Common phrases
## Latin (Italic)

Pronunciations are first given in the Ecclesiastical Pronunciation (Based on Italian, and used in some ceremonies by the Catholic church, and usually heard in recordings of classical music). These pronunciations are followed by the classical pronunciation (a reconstruction of how scholars believe the Romans pronounced these expressions)
For example — “of light” lucis /'luʧis/ (LOO-cheess) /'luːkis/ (LOO-kiss), with (LOO-cheess) being the ecclesiastical pronunciation, and (LOO-kiss) how the Romans said lucis.
| Translation | Latin | IPA (Ecclesastical) | Pseudo-English | IPA (Classical) | Pseudo-English |
| Latin | lingua Latina | /'lingwa la'tina/ | (lah-TEE-nah) | /'lingwa la'tiːna/ | (lah-TEE-nah) |
| hello | ave! | /'ave/ | (Ah-vay) | /'aweː/ | (Ah-way) |
| welcome | salve! | /salve/ | (Sal-vay) | /salveː/ | (Sal-way) |
| goodbye | vale! | /'vale/ | (vah-lay) | /'waleː/ | (wah-lay) |
| please | si placet | /si 'plaʧet/ | (see PLAH-chet) | /siː 'plakɛt/ | (see PLAH-ket) |
| thank you | gratias tibi ago | /'gratsias 'tibi 'ago/ | (GRAH-tsee-as TI-bee AH-goh) | /'graːtiaːs 'tibi 'agoː/ | (GRAH-tee-as Ti-bee AH-goh) |
| that one | ille/ illa/ illud | /'ilːe, 'ilːa, 'ilːud/ | (ILL-lay, ILL-lah, ILL-lood) | /'ilːɛ, 'ilːa, 'ilːud/ | (ill-leh, ill-lah, ill-lood) |
| how much? | quot? | /kwot/ | (quote) | /kwot/ | (quote) |
| yes | certe, ita vero | /'ʧerte/ | (CHAIR-tay) | /'kɛrteː/ | (ker-tay) |
| no | non, nullo modo | /'non, 'nulːo 'modo/ | (noan, NUL-loh MO-doh) | /'noːn, 'nuːlːo 'mɔdoː/ | (known, NUL-oh MO-doh) |
| sorry | ignosce mihi | /i'ɲoʃe 'mihi/ | (een-YOH-shay MEE-hee) | /i'ŋnoːskɛ 'mihi/ | (ing-know-skeh Mi-hee) |
| I don’t understand | non comprehendo | /noŋ kompre'hendo/ | (noan com-pray-HEN-doh) | /noːŋ komprɛ'hɛndoː/ | (known com-pray-HEN-doh) |
| where's the bathroom? | ubi sunt latrinae? | /'ubi sunt la'trine/ | (OO-bee soont lah-TREE-nay) | /'ubi sunt la'triːnai/ | (OO-bee soont lah-tri-neye) (neye rhyming with eye) |
| generic toast | salutem! | /sa'lutem/ | (sah-LOO-taym) | /sa'luːtɛ̃/ | (sah-LOO-tehm) |
| Do you speak English? | loquerisne anglice? | /lokwe'risne 'aŋgliʧe/ | (loh-quay-RISS-nay AHNG-glee-chay?) | /lɔkwɛ'risnɛ 'aŋglikeː/ | (loh-queh-riss-neh ahngli-kay?) |
# Latin/Dictionary

< Latin

### External links

* Perseus Project online latin dictionary
* Online Latin word list
* Whitaker's Words Probably the most complete
* Wiktionary Contains a large number of Latin words
# Latin/Grammar

This Appendix is Divided into Two Sections:
* Grammatical Definitions A a comprehensive glossary of Latin and English Grammatical Definitions.
* Latin Noun and Verb Tables A comprehensive list of noun (substantive, adjective and pronoun) and verb tables.
# Latin/Chapter 4 Verse

Haec est fabula De Faciebus Iani. Ianus, ut dicebatur, erat unus deorum, cui facies duae erant. Altera earum enim in futura et altera in praeterita prospiciebat.
Apollo ei olim sic dixit: "Nonne tibi facies est, qua tempus praesens spectes?" Et paulo post Ianus ita respondit:
"Mundus - orbis terrarum cyclus est similiter ac tempus est cyclicum. Et initium omnium et finem video. Omnia prospicio aeternusque sum, neque opus est porro videre, quae palam iaceant."
Diu cogitavit Apollo de verbis Iani hominesque acutissimā mente in omni orbe terrarum conquaesivit eo consilio, ut ipse tam sapiens ut Ianus fieret. Postea cum quibusdam illustrissimis viris collocutus est, quo sapientior esset. Eo facto tamen unus eorum, cui Minervus nomen, Apollinem monuit, ne summam quaereret sapientiam, quam novisse nullum alium quam Ianum oportebat. Revenit autem Apollo ad Ianum eumque, ut veritatem cognosceret, ea summa rogavit.
"Intellegisne omnino quid roges?" inquit Ianus, "Si dis par fueris, omnibus iuribus privari possis."
Itaque Apollo cognovit sapientissimum omnium fuisse, a quo monitus est.
Translation below:
This is the story of the faces of Janus. Janus, as it used to be said, was one of the gods who had two faces. It was that one spied into the future while the other into the past.
Apollo once had said to him, "Have you not a face with which to see the present?" After a few moments, thus spoke Ianus:
"The world is a circle. Time is a circle. I see both the beginning and end of all living things. I am foreseeing and eternal; therefore, it is not necessary for me to see that which is lying out of sight."
Apollo thought about these words for a very long time, and thus, that he might become wise like Janus, he sought the keenest minds of the land. He then was speaking with some great men that he might become wiser. However, one, whose name was Minervus, warned him not to seek the ultimate/highest truth because it may only be known by Janus. But he returned again to ask Janus that he might obtain the truth.
"Do you even know for what you're asking? If you enter onto the same level (of the Gods), all your rights might be snatched from you," said Janus.
And so Apollo knows now that the same man who had warned him was the wisest of all.
# Latin/Chapter 3 Verse

The following poem is written in Hendecasyllabic. It is an introductory, dedication poem written by the poet Gaius Valerius Catullus.
It is commonly referred to as "Catullus 1" or by its first line.
    Cui dono lepidum novum libellum
    arida modo pumice expolitum?
    Corneli, tibi: namque tu solebas
    meas esse aliquid putare nugas.
    Iam tum, cum ausus es unus Italorum
    omne aevum tribus explicare cartis...
    Doctis, Iuppiter, et laboriosis!
    Quare habe tibi quidquid hoc libelli—
    qualecumque, quod, o patrona virgo,
    plus uno maneat perenne saeclo!
# Latin/Chapter 2 Verse
## Using a Dictionary

Foremost, Latin verbs are listed using the present indicative first person singular active construct of the verb. For example, to find the meaning of the verb amāre, you must find amō listed in the dictionary. Some verbs like esse and ferre are highly irregular and use different stems to form the perfect tenses.
Nouns are usually much easier. They are always given in the nominative singular. If you see a noun such as vōcem and do not know what it is, do not fret. If you look for voc- in the dictionary, you will not find what you are looking for. The ending -em typically belongs to the third-declension accusative; thus, be aware that third-declension nouns have radically changing stems. Those that have the consonant c or g usually have the consonant x in the nominative singular. Thus the nominative singular of vōcem is vōx, and rēx becomes rēgem in the accusative singular. There are plenty of other simple rules which you will learn through experience.
Words that do not conjugate or decline (like prepositions and particles) are listed under their only form.

## Exercise 1
### Vocabulary

* affectus, -ūs, m., goodwill
* confessiō, -ōnis, f., confession
* dē, from, about, concerning
* liber, librī, m., book
* malus -a -um, evil, bad
* placeō -ēre + dative, to please (placuīsse is a perfect infinitive)
* filia, -ae f., daughter
* puella, -ae f., girl

### Other Difficulties

* quod ad mē attinet, as far as I'm concerned
* cum scriberentur, when they were written (imperfect passive subjuntive)
* quid sentiant, what they think (present subjunctive in indirect question)
* ipsī viderint, (loosely) they will see in their own way (future perfect)
* eōs placēre sciō, accusative-infinitive construction for indirect statement: "I know they [the books] please"

### Passage

* Confessiōnum meārum librī tredecim et dē malīs et dē bonīs meīs deum laudant iūstum et bonum atque in eum excitant humānum intellectum et affectum. Interim quod ad mē attinet, hoc in mē ēgērunt cum scriberentur et agunt cum leguntur. quid dē illīs aliī sentiant, ipsī viderint; multīs tamen frātribus eōs multum placuīsse et placēre sciō.
* to be translated into English
# Latin I prose

Lesson Vocabulary :
| Latin | English |
| fulgeo, -ere | to shine |
| aperio, -ire | to open |
| dormio, -ire | to sleep |
| habeo, -ere | to have |
| semper | always |
| tempto, -are | to try |
| dico, -ere | to speak, say |
| femina | woman |
| facio, -ere | to make |
| ecce! | look! |
| velle: volo vis vult volumus vultis volunt | to wish, want: I want you want he/she wants we want you want they want |
| turba | crowd |
| attonitus | astonished |
| tantus, -a, -um | so great |
| susurro, -are | to whisper |
| patefacio, -ere | to open, disclose |
| rideo, -ere | to laugh |
The following is a nice easy short story for the Latin novice:

### Lucius ad forum it

Sol fulget. Lucius oculos aperit. Videt uxorem suam, Octaviam. Octavia dormit. Ergo, Lucius ad forum it.
Lucius multos amicos habet. Unus ex amicis Claudius est. Claudius semper in foro est. Claudius temptat dicere cum feminis, quod Claudius multas feminas amat. Multae feminae, tamen, Claudium non amant.
Lucius ad forum ambulat. Multos Romanos videt. Unus Romanorum ad cives orationem facit. Est Claudius!
"Ecce! Ecce!" dicit Lucius. Lucius vult dicere cum amico. Claudius, tamen, dicit ad turbam.
"Amicus meus, Lucius" dicit, "hominem necavit."$^A$
Lucius anxius respondet, "Quid dicis, amice?"
Claudius est attonitus. Dicit, "Te non video, mi Luci..."
Lucius respondet, "hominem non necavi! Cur tanta dicis?" Claudius susurrat, "Volo videri$^B$ fortissimus, amice. Feminae te amant. Me dolent$^C$."
Lucius omnia$^D$ turbae$^E$ patefacit.
Multae feminae ad Claudium misserimum rident. Mox, etiam Claudius ad se ridet.
* $^A$ Necavit is the perfect form of necare, meaning "he killed." For more, check out the next chapter.
* $^B$ Videri means "to appear," (or more literally, "to be seen") and is the passive infinitive of video. There is more on that in chapters 2-4.
* $^C$ Me dolet means "makes me suffer".
* $^D$ Omnia means "everything".
* $^E$ turbae is the dative case of "turba", meaning "to the crowd".
# Next Generation Sequencing (NGS)/Authors
## Contributing authors

* Vicky Schneider Started this book and co-drafted initial chapter structure and foreword.
* Magnus Manske (discuss • contribs) Does bits and pieces
* Dan Bolser (discuss • contribs) Content facilitator.
* Marco Li (discuss • contribs) Does whatever I can.
* Daniel Zerbino Drafted the initial foreword and chapter structure.
* Federico M. Giorgi Contributed to the RNASeq parts (differential expression analysis and transcriptome assembly)
* Nikolay Vyahhi added and updated information about SPAdes assembler and more.
* Björn Usadel added and updated information about pre-processing.
* Vahid Shariati contributed to introduction about NGS and Data Analysis.

## Contributors by chapter
### De novo assembly and De novo RNA assembly

    Content was imported from SEQwiki originally with major contributions from Björn Usadel, and novel content by Daniel Zerbino

### Next Generation Sequencing (NGS)/RNA

    Content was imported from SEQwiki originally with major contributions from Björn Usadel.

### Alignment

    Content was uploaded from original materials developed by Myrto Kostadima and Xi Li. Additional content was imported from SEQwiki originally with major contributions from Jing-Woei Li.

### Next Generation Sequencing (NGS)/RNA

    Additional content was imported from SEQwiki originally with major contributions from Björn Usadel.
# Next Generation Sequencing (NGS)/Chromatin conformation capture

Chromatin conformation capture (3C) technologies are used to discover which regions of DNA are physically co-located in space, through ligation and sequencing the hybridised product. The original 3C experiments counted the level of interaction between two regions of interest and subsequent assays using NGS have scaled this up to measure genome-wide contacts.

## Overview
### Useful background

An understanding of the components of chromatin (DNA along with everything bound to it) and the cell cycle help understand what causes and effects the interactions measured by chromation conformation capture.

### Objective

Interaction frequencies between either two selected fragments (3C), a bait region against all other fragments (4C), an all-against-all sampling of a given region (5C) or genome-wide assesment of interaction frequencies (Hi-C).

### Biological questions

Through these techniques we can study from single enhancer-gene interactions up to the global principles of genome organisation.

## Inputs and outputs
### Inputs

* Raw hybrid or paired reads

### Outputs

* Interaction frequencies between chosen regions
* Topological domains and other physical chromatin structures

## Experimental design

The resolution at which a 3C-based experiment can be analysed is determined by two factors:
* The primary restriction enzyme used to fragment the DNA
* The sequencing depth over the target region
A 6-cutter restriction enzyme (such as HindIII) limits the resolution to fragments with mean size of around 3.5 kb, whereas a 4-cutter such as DpnI reduces fragment size by around an order of magnitude.

## Typical steps in the method

* Map reads to reference genome. In the case of paired reads (Hi-C), reads should be mapped independently and not using an alignment program with "paired-end mode" or similar. This mode will likely impose constraints on the distance between mapped paired reads, when in this assay even contacts many megabases away (and in trans across chromosomes) still give useful information.

## Next steps

Normalisation and correction for contact biases can be done using a number of published tools.

## 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.

## References

* ↑ Janos Posfai (2011) Distribution of restriction site distances (theoretical "fragment lengths") in the human genome.
# Next Generation Sequencing (NGS)/ABySS

We need to get google sparsehash first assuming you don't have root privileges and your name is USER we install in a local include directory
Now get ABySS (assuming you have the BOOST libraries installed)
For more details about the installation process see the ABySS entry or install the .deb if you have a Debian compliant system.
We now run ABySS with a kmer size of 25 and require at least n=10 links to join contigs.
# Next Generation Sequencing (NGS)/Big Data
## Big Data
### Data Deluge

The first problem you face is probably the large size of the NGS FASTQ files - the "data deluge" problem. You no longer only have to deal with microplate readings, or digitalized gel photos; the size of NGS data can be huge. For example, compressed FASTQ files from a 60x human whole genome sequencing can still require 200Gb. A small project with 10–20 whole genome sequencing (WGS) samples can generate ~4TB of raw data. Even these estimates do not include the disk space required for downstream analysis.

### Storing data

Referenced from a post from BioStars:
* Very high end: enterprise cluster and SAN.
* High end: Two mirrored servers in separate buildings or Cloud.
* Typical: External hard drives and/or NAS with raid-5/6

### Moving data

Moving data between collaborators is also non-trivial. For RNA-Seq samples, FTP may suffice, but for WGS data, shipping hard drives may be the only solution.

### Externalizing compute requirements from the research group

It is difficult for a single lab to maintain sufficient computing facilities. A single lab will probably own some basic computing hardware; however, many tasks will have huge computational demands (e.g. memory for de novo genome assembly) that require them to be performed elsewhere. An institution / core facility may host a centralized cluster. Alternatively, one might consider doing the task on the cloud.
* NIH maintains a centralized computing cluster called Biowulf.
* Bioinformatics cloud computing is suggested. EBI has adopted a cloud-based platform called Helix Nebula.

## References

* ↑ Wo, H. (24 March 2011). "Question: Huge Ngs Data Storage And Transferring". Biostars. Biostar Genomics, LLC. Retrieved 28 April 2016.
* ↑ Akhlaghpour, H. (3 July 2012). "Genomic Analysis in the Cloud". YouTube. Google. Retrieved 28 April 2016.
* ↑ Schadt, E.E.; Linderman, M.D.; Sorenson, J.; Lee, L.; Nolan, G.P. (2010). "Computational solutions to large-scale data management and analysis". Nature Reviews Genetics. 11 (9): 647–57. doi:10.1038/nrg2857. PMC 3124937. PMID 20717155.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: multiple names: authors list (link)
* ↑ Lueck, R. (16 January 2013). "Big data and HPC on-demand: Large-scale genome analysis on Helix Nebula – the Science Cloud" (PDF). Trust-IT Services. Retrieved 28 April 2016.
# Manga Study Guide: Barefoot Gen/Pace

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## Pace

Pace is an important factor in Manga conventions. The pacing of the story is essentially how fast the story is progressing and how important the scene is depending on situation.
Slow pace: It makes the reader focus on the scene and gives us an impression of close up, that way emphasizes the scene. It shows that the scene is an important aspect that is worth slowing down the pace and that it plays a vital role in both story progression and character building.
Fast pace: Fast pace is used for showing quick action. The fast change of scenes give the reader the impression of fast movement as quick change enables the reader to understand and move quickly from panel to panel and imply the feeling of action on the reader.
# Manga Study Guide: Barefoot Gen/The comic and the history

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## Background of an atomic bomb that was dropped in Hiroshima (Little Boy)

At first, America was planning to perform “Operation Downfall”, to assault Japan. However, after witnessing the horror of Iojima and Okinawa battles, America changed the plan and decided to drop atomic bombs on Japanese soil. There were some opinions that they need to strike further with napalm or other type of weapons to maximize the damage, but the government decided against it. Before they dropped atomic bombs, nobody knew about the secondary damage caused by atomic bombs - radiation.
Little Boy, codename of an atomic bomb, was built with Uranium-235. Simply, Little boy detonates when 2 uranium masses collide, creating a massive heat and energy.
August 6th, 1945, 3 American planes flew above Hiroshima in order to recon the area. The citizens evacuated hastily, but nothing happened. After a few hours later, B-29 appeared on Hiroshima’s sky. The citizens thought it would be another recon plane, and continued their normal life.
But, the B-29 dropped an atomic bomb; It was 240 meter far away from Aioi bridge. Hiroshima citizens saw a very brightening light when it was detonated; some of the people were even blinded. Everything instantly burnt near the hypocenter at 3000~4000C. Soon, thermal effect and shockwave followed at 340 meter per second speed, wiping out everything on the ground (1.5 km radius). Hiroshima suffered from high radiation, heat and gray atmosphere preventing the sunlight sifting on Hiroshima’s soil.
# Manga Study Guide: Barefoot Gen/Use of cartoon violence

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## Why did the comic "Barefoot Gen" use cartoon violence?

An abbreviated strong language and violent expression. The Weekly Jump could not show a realistic violence.

### Style of manga comic’s info

In a case, Japanese comics has excessive violence and expression. But they aren’t meant to injure person. They just entertain the reader. Realistic expressions have the blood sprat, scars, and destruction and realistic faces. They look like real photographs. However comical expressions have have unrealistic motions (e.g jumping to the sky).

### Pieces of work that use realistic violence

* History- “Explain the past times with details”
* War log- “Describe events that happened in the great War”
* Mystery- ”A story to elucidate the truth of a crime.”
* Gekiga(劇画)-”Comic style of a realistic narrative”

### Pieces of work that use comical violence

* Gag manga- “Funny moment and such jokes”
* Satire- “Draw contents in derision of specific object interestingly”
* Comedy

### Pieces of work that use both expressions

* Adventure
* Action
* Fantasy
In Barefoot Gen that has very heavy and serious theme from the war. Barefoot Gen has both expressions. Because, When the scene where Gen was hit by father. Then moment, Gen cut in his mouth. (You can see a little bit of blood). So, This is a realistic expression but, he flew up by a hit shock (In some cases, people can fly up). In most cases, these expressions are comical.