OpenLLM-France/wikimedia huggingface dataset:
# Bioinformatics/The central dogma of molecular biology
## I. Central Dogma of Molecular Biology Overview

The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It was first stated by Francis Crick in 1956 and re-stated in a Nature paper published in 1970.
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.
The central dogma has also been described as "DNA makes RNA and RNA makes protein". However , the dogma also admits the reverse flow of information from RNA to DNA but not from proteins to DNA or RNA, as recalled by Francis Crick (1970). The dogma is a framework for understanding the transfer of sequence information between bipolymers sequential carrying information. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 3×3 = 9 conceivable direct transfers of information that can occur between these. The dogma classes these into 3 groups of 3: 3 general transfers (believed to occur normally in most cells), 3 special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and 3 unknown transfers (believed never to occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA (transcription), and proteins can be synthesized using the information in mRNA as a template (translation).
# Biological Physics

GOAL: In this book we will address the physics of living phenomena primarily through thermal and statistical methods. We intend this book to be a textbook book for undergraduates studying biophysics (Biological Physics) The book content will be developed by students of an undergraduate Thermal Physics class. We hope to seed this site with a good starting point in order to develop a good open source textbook for future students.

## Contents

* Chapter I: The Zeroth & First Laws
** How work, pressure, and volume are related
** Boyles Law
** Charles' Law
* Chapter II: Probability, Entropy, & the Second Law
** Stirling's Approximation
** Absorption
* Chapter III: The Third Law
** Heat Engines, Refrigerators, and Efficiency
* Chapter IV: Interactions & Equilibrium
* Chapter V: Statistical Mechanics
* Chapter VI: Free Energy
* Chapter VII: The Random Walk
* Chapter VIII: Blackbody Radiation
* Chapter IX: Figures
# Biological Physics/Absorption

When observing light absorption is defined as the <intensity exiting></intensity entering>.
Absorbance can also be written in the formula for Beer's Law: $A=\epsilon cl$
This formula written out is Absorbance = extinction coefficient × concentration × length of light path through the sample. The extinction coefficient is typically calculated by adding up the extinction coefficients of three amino acids that mimic all proteins(Tryptophan, Tyrosine, and Cytosine). Absorption is essentially a unit-less value due to the cancellation of units within the formula: {{Absorption = (<1></molar × cm>) × molar × cm}}. We can measure absorption using a spectrophotometer or spectrometer designed to measure absorption.
We can calculate the fraction of unfolded proteins, which is basically calculating the probability of unfolded proteins. In this case, the fraction of unfolded (denatured) protein can be written as follows: $f_{d}={\frac {A_{max}-A}{A_{max}-A_{min}}}$ This equates to the change in absorption due to unfolding divided by the total change observed when all protein is denatured.
Similarly, the protein fraction that remains folded or in its native state is $f_{n}={\frac {A}{A_{max}-A_{min}}}$, which is the absorption at a particular concentration, A, relative to the total absorption change observed. Note the sum of f$_d$ and f$_n$ is 1. The ratio of denatured to native protein fractions is the equilibrium constant. The equilibrium constant (K$_{eq}$) can be written as: $K_{eq}={\frac {f_{d}}{f_{n}}}$
Recall that entropy is written as: $S=k_{B}*ln(\Omega )$
So the difference in probability between denatured and natured proteins is written as: $S=k_{B}*ln({\frac {\Omega _{d}}{\Omega _{total}}})-k_{B}*ln({\frac {\Omega _{n}}{\Omega _{total}}})$
If we move Boltzmann's constant outside of the parentheses and realize that the multiplicity for the total change will cancel, we end up with the formula: $S=k_{B}[ln(\Omega _{d})-ln(\Omega _{n})$ Given algebraic properties for the natural logarithm, the formula can be re-arranged to appear as: $S=k_{B}*ln({\frac {\Omega _{d}}{\Omega _{n}}})$
Recall that enthalpy is written as: $\Delta S*T$ so that $\Delta H=k_{B}*T*ln({\frac {\Omega _{d}}{\Omega _{n}}})$
However, this says that it is unfavorable to denatured protein even though there is more denatured protein. To correct for this, we simply add a negative sign so that the resulting formula appears as: $\Delta H=k_{B}*T*ln({\frac {f_{d}}{f_{n}}})$
# Breton/Level 4

Brezhoneg Pevar :
| Brezhoneg Beg ar c'havr, Kraozhon Brezhoneg Pevar "Brezhoneg Pevar" is the fourth level in the Breton course. In this Beginner's course, students are introduced to simple texts, grammar complements and some phrases for a simple conversation. | Breizh Gorsedd in Brittany  Breton literature In the 19th century antiquarians and Celtic revivalists undertook the collection of folk texts, songs and stories. Writers such as Anatole Le Braz and Kervarker brought new readers to traditional Breton literature. The poet Yann-Ber Kalloc'h (1888-1917) was killed during the First World War. His posthumously-published collection Ar en deulin established his reputation as a war poet. In the 1920s a movement, in which the linguist and author Roparz Hemon played an important part, arose to introduce the trends of modern literature into Breton. The literary magazine Gwalarn provided an outlet for modern authors, such as Jakez Riou and Youenn Drezen (who published the first long novel in Breton in 1941). Per-Jakez Helias (1914-1995) wrote prose and poetry in both Breton and French. His contemporary Añjela Duval (1905-1981) wrote poetry reflective of her peasant origins, mysticism, and social conscience. |
| Lessons Kentel kentañ: Poems and Rhymes Eilved kentel: In Town Teirved kentel: Plurals Pederved kentel: More Tenses Pempved kentel: Jokes | Breizh Gorsedd in Brittany  Breton literature In the 19th century antiquarians and Celtic revivalists undertook the collection of folk texts, songs and stories. Writers such as Anatole Le Braz and Kervarker brought new readers to traditional Breton literature. The poet Yann-Ber Kalloc'h (1888-1917) was killed during the First World War. His posthumously-published collection Ar en deulin established his reputation as a war poet. In the 1920s a movement, in which the linguist and author Roparz Hemon played an important part, arose to introduce the trends of modern literature into Breton. The literary magazine Gwalarn provided an outlet for modern authors, such as Jakez Riou and Youenn Drezen (who published the first long novel in Breton in 1941). Per-Jakez Helias (1914-1995) wrote prose and poetry in both Breton and French. His contemporary Añjela Duval (1905-1981) wrote poetry reflective of her peasant origins, mysticism, and social conscience. |
# Breton/Level 4/Lesson 1

Barzhonegoù / Poems :
| Brezhoneg Lagad an Heol — Heol ! Perak out ken diwezhat o tiblouz ? Ha perak eo ken ruz da lagad ? Ha bet ac’h eus en noz-mañ ur gwall-hunvre, En deus graet dit leñvañ dre da hun ? — Na hun na hunvre na fall na mat. Beilhet am eus an noz-pad… Tra ma kouske ar c’hornôg dibled war ludu louet e lore me ’m eus graet tro an Douar. Ha gwelet am eus tud o vervel gant an naon. Gwelet ’m eus tud o vervel gant ar riv. Gwelet tud o vervel gant an dic’hoanag. Gwelet am eus tud o lazhañ tud, breudeur o ’n em dagañ. Gwelet ’m eus pobloù mac’het. Gwelet ur penntiern meur o kouezhañ dindan boled ur foll. Gwelet forzh tud o leñvañ : Ha chomet on bepred digas… Gwelet ’m eus, avat, tud o c’hoarzhin goap ouzh ar re zo er boan, Ouzh ar re zo en dienez Ouzh ar re zo dindan ar yev. Ha neuze am eus ranket leñvañ, Ma ’z eo ruz c’hoazh va lagad. — Heol ! Sec’h bremañ da zaeroù ! Mor-Breizh, emberr, a vo dous D’az lagad ruz hag entanet… Ur beure goañv 1964 Orin | English The sun's eye — Sun, why are you so late getting up? And why is your eye so red? Did you have a nightmare And weep in your sleep? — I've neither slept nor dreamt. During the night I've kept watch, While the West slept without a care On the grey ashes of its laurels, I took a trip around the World. — Sun! What did you see on your way? — I saw people dying of cold. I saw people dying of hunger. Saw people dying in despair. Saw people killing people, brothers striking each other. Saw people oppressed. Saw a great leader falling under a madman's bullets. Saw I don't know how many people weeping. And I still remained indifferent. I saw people jeer at their afflicted brother, At those in need, At those under the yoke. Then, however, I had to weep, So that my eye is still red. — Sun! Stop your weeping now. Very soon in the Breton Sea, You will soak your inflamed eye. May 1964. Source |
Geriadur / Vocabulary
BrezhonegEnglish
Lagad
Eye
Diblouz
Ruz
Red
Gwall-hunvre
Nightmare
Exercises
Go to the Quiz :
# Breton/Level 4/Lesson 2

E ker / In town
BrezhonegEnglish
Mond a ran e ker war velo.
I go to town biking (on a bike).
Braz eo ker Dañjerus e vez ar ruioù.
The town is large The streets are dangerous.
Kalz a otoioù a zo e ker. Taolomp evezh !
There a re a lot of cars in town. Let's be careful !
Gwelloc'h eo diskenn. Deomp war droad !
It's better to climb down. Let's walk !
News from town for my love who stayed home
Excerpt from a song by Nolwenn Korbell
BrezhonegEnglish
O vale 'n ur gêr vras pell deus ar gêr.
Walking in a big town far from home.
O kerzhout 'touez an dud trouzus 'vel yer.
Among people noisy as hens.
O c'hortoz 'lakfe 'n den e zilhad gwer.
Waiting for the man to put his green clothes.
O treuziñ straedoù ledan 'vel kant stêr
Crossing streets large as hundred rivers
Ne sonjan nemet ennoc'h, ne sonjan nemet ennoc'h.
I only think of you, I only think of you.
[Song]
Exercises
Ex 1 : Quiz
Go to the Quiz.
Ex 2 : Memory training
Write out the Breton words, section by section.
Have 2 columns, clearly separated, and write Breton and English. Then cover up one column (eg. English) with paper and write the corresponding words on the paper.
Then try it the other way round, cover up the Breton, and write out the words using the English as cues. This will be a little bit more difficult.
Repeat all this after an interval, the more you do it the easier you will remember the words. :
# Breton/Level 4/Lesson 3

Liester / Plural
UnanderLiesterEnglish
Mamm
Mammoù
Mother, mothers
Tad
Tadoù
Father
Breur
Breudeur
Brother
C'hoar
C'hoarezed
Sister
Aval
Avaloù
Apple
Lestr
Listri
Ship
Mab
Mibien
Son
Den
Tud
People
File:Liester.ogg
Internal plurals
Some names have a plural that changes the internal vowels of the name.
lestr, listri (ship)
legestr, ligistri (lobster)
mab, mibien (son)
Numerals and Plural
There is no plural after a numeral :
Daoù baotr, div blac'h,
tri mab, teir merc'h,
pevar mevel, peder matezh,
pemp bro,
ugent aval,
daoù zen warn-ugent (22 persons)
tri den ha tregont (33 persons)
Dual words
Parts of the body may have a "dual" name :
Lagad, daoulagad (eye)
skouarn, divskouarn (ear)
glin, daoulin (lap)
dorn, daouarn (hand)
gar, divhar (leg)
These dual forms may have a plural (eg. daoulagadoù).
Collective names and singulative forms
Some names have a collective meaning and may have a "singular" form.
Geot (grass), geotenn (blade of grass)
Gwez (tree), gwezenn ( a specific tree)
kouevr (copper), kouevrenn (a piece of copper)
The singulative forms are feminine and act as a singular form.
Hence, they may have a plural : geotennoù (blades of grass).
Exercises
Ex 1 : Quiz
Go to the Quiz.
Ex 2 : Memory training
Write out the Breton words, section by section.
Have 2 columns, clearly separated, and write Breton and English. Then cover up one column (eg. English) with paper and write the corresponding words on the paper.
Then try it the other way round, cover up the Breton, and write out the words using the English as cues. This will be a little bit more difficult.
Repeat all this after an interval, the more you do it the easier you will remember the words. :
# Breton/Level 4/Lesson 4

The Preterite Tense
For definitions, see Level 2, Lesson 3
Tables
Verb Bezañ (To be) - Preterite
Preterite Tense Personal formPreterite Tense Impersonal formContinuous Tense Personal formContinuous Tense Impersonal formSituation TenseEnglish meaning
e voen
me a voe
I was (once)
e voes
te a voe
You were once (sg.)
e voe
eñ a voe
He was once
e voe
hi a voe
She was once
e voemp
ni a voe
We were once
e voec'h
c'hwi a voe
You were once (pl.)
e voent
int a voe
They were once
e voed
Impersonal passive
Regular Verb Skrivañ (To write) - Preterite
Preterite Tense Personal formPreterite Tense Impersonal formWith auxiliary Personal formEnglish meaning
ul levr a skrivis
me a skrivas ul levr
skrivañ a ris ul levr
I wrote a book
ul levr a skrivout
te a skrivas ul levr
skrivañ a rejout ul levr
You wrote a book (sg.)
ul levr a skrivas
eñ a skrivas ul levr
skrivañ a reas ul levr
He wrote a book
ul levr a skrivas
hi a skrivas ul levr
skrivañ a reas ul levr
She wrote a book
ul levr a skrivomp
ni a skrivas ul levr
skrivañ a rejomp ul levr
We wrote a book
ul levr a skrivoc'h
c'hwi a skrivas ul levr
skrivañ a rejoc'h ul levr
You wrote a book (pl.)
ul levr a skrivont
int a skrivas ul levr
skrivañ a rejont ul levr
They wrote a book
ul levr a skrivod
skrivañ a rejod ul levr
Impersonal passive
The Future Tense
Tables
Verb Bezañ (To be) - Future
Future Tense Personal formFuture Tense Impersonal formContinuous Tense Personal formContinuous Tense Impersonal formSituation TenseEnglish meaning
e vin (vezin)
me a vo
I shall be
e vi (vezi)
te a vo
You will be (sg.)
e vo (vezo)
eñ a vo
He will be
e vo (vezo)
hi a vo
She will be
e vimp (vezimp)
ni a vo
We shall be
e viot (vezot)
c'hwi a vo
You will be (pl.)
e vint (vezint)
int a vo
They will be
e vior (vezor)
Impersonal passive
Regular Verb Skrivañ (To write) - Future
Future Tense Personal formFuture Tense Impersonal formWith auxiliary Personal formEnglish meaning
ul levr a skrivin
me a skrivo ul levr
skrivañ a rin ul levr
I shall write a book
ul levr a skrivi
te a skrivo ul levr
skrivañ a ri ul levr
You will write a book (sg.)
ul levr a skrivo
eñ a skrivo ul levr
skrivañ a raio (ray) ul levr
He will write a book
ul levr a skrivo
hi a skrivo ul levr
skrivañ a raio (ray) ul levr
She will write a book
ul levr a skrivimp
ni a skrivo ul levr
skrivañ a raimp ul levr
We shall write a book
ul levr a skrivot
c'hwi a skrivo ul levr
skrivañ a reot ul levr
You will write a book (pl.)
ul levr a skrivint
int a skrivo ul levr
skrivañ a raint ul levr
They will write a book
ul levr a skrivor
skrivañ a reor ul levr
Impersonal passive
Exercises/Ober
Self training
Now , you have seen how its done.
Take the verbs from Level 2, Lesson 1 and write them down if you haven't already.
Now change them into their preterite tense and future tense.
Now underneath , make some sentences up , for each verb. EG. Me a zo er skol o teskiñ kembraeg (I learn Welsh in school). Me a vo er skol evid teskiñ kembraeg (I will learn Welsh in school).
Quiz
Go to the quiz :
# Breton/Level 3/Lesson 4/Quiz

Multiple choices
Verb Bezañ (To be)
Choose the correct Breton form(s) :
1
I was (once).
E oan.
Ez on.
E vezen.
2
They were (usually).
Ez edod.
Emaint.
E vezent.
3
You were (pl. - once).
E vezemp.
E oar.
E oac'h.
4
I was.
E oar.
E oan.
E vezen.
Ez emañ.
E vefen.
Edon.
Choose the English translation(s) :
5
E vezemp.
We were (usually).
They are (now).
He is (situation). :
# Breton/Level 3/Lesson 4

The Imperfect Tense
For definitions, see Lesson 3
Tables
Verb Bezañ (To be) - Imperfect
Imperfect Tense Personal formImperfect Tense Impersonal formContinuous Tense Personal formContinuous Tense Impersonal formSituation TenseEnglish meaning
e oan
me a oa
e vezen
me a veze
edon
I was
e oas
te a oa
e vezes
te a veze
edos
You were (sg.)
e oa
eñ a oa
e veze
eñ a veze
edo
He was
e oa
hi a oa
e veze
hi a veze
edo
She was
e oamp
ni a oa
e vezemp
ni a veze
edomp
We were
e oac'h
c'hwi a oa
e vezec'h
c'hwi a veze
edoc'h
You were (pl.)
e oant
int a oa
e vezent
int a veze
edont
They were
e oad
e vezed
edod
Impersonal passive
Regular Verb Skrivañ (To write) - Imperfect
Imperfect Tense Personal formImperfect Tense Impersonal formWith auxiliary Personal formEnglish meaning
ul levr a skriven
me a skrive ul levr
skrivañ a raen ul levr
I wrote a book
ul levr a skrives
te a skrive ul levr
skrivañ a raes ul levr
You wrote a book (sg.)
ul levr a skrive
eñ a skrive ul levr
skrivañ a rae ul levr
He wrote a book
ul levr a skrive
hi a skrive ul levr
skrivañ a rae ul levr
She wrote a book
ul levr a skrivemp
ni a skrive ul levr
skrivañ a raemp ul levr
We wrote a book
ul levr a skrivec'h
c'hwi a skrive ul levr
skrivañ a raec'h ul levr
You wrote a book (pl.)
ul levr a skrivent
int a skrive ul levr
skrivañ a raent ul levr
They wrote a book
ul levr a skrived
skrivañ a raed ul levr
Impersonal passive
The Imperative Tense
Tables
Verb Bezañ (To be) - Imperative
Imperative Tense Personal formEnglish meaning
bez
be (sg.)
bezet
let him be
bezet
let her be
bezomp
let us be
bezit
be (pl.)
bezent
let them be
Regular Verb Skrivañ (To write) - Imperative
Imperative Tense Personal formEnglish meaning
skriv
write (sg.)
skrivet
let him write
skrivet
let her write
skrivomp
let us write
skrivit
write (pl.)
skrivent
let them write
Exercises/Ober
Self training
Now , you have seen how its done.
Take the verbs from Level 2, Lesson 1 and write them down if you haven't already.
Now change them into their Imperfect tense and Imperative tense.
Now underneath , make some sentences up , for each verb. EG. Me a zo er skol o teskiñ kembraeg (I learn Welsh in school). Me a veze er skol o teskiñ kembraeg (I learned Welsh in school).
Quiz
Go to the quiz :
# Breton/Level 4/Lesson 5

* Exercises
* Go to the Quiz
# Chemical Information Sources/CIIM/PubChem

Chemical Information Instructional Materials
* PubChem Help (NLM NCBI)
* Principles of PubChem Course (NCBI)
* PubChem Listserv (Indiana University)
# Chemical Information Sources/CIIM/General Information about Chemical Publications or Databases

Chemical Information Instructional Materials
* Index to Some Library of Congress Classification Numbers Relevant to Chemistry (Wiggins, Indiana)
* From Bits to Bytes: The Chemical Information Cycle, "Chemical Information in The Computer Age" (Poster: Journal of Chemical Education Chemistry Currents; no 3, Winter 1988)
* Online Chemical Databases--Many Paths to Information, "Chemical Information in the Computer Age" (Poster: Journal of Chemical Education Chemistry Currents; no. 4, Summer 1989)
# Chemical Information Sources/CIIM/Gmelin Handbook of Inorganic and Organometallic Chemistry

Chemical Information Instructional Materials
* Using Reaxys' Inorganic and Organometallic Data for Organic Chemistry
* Beilstein and Gmelin Databases (Wixson, Rowe, Wisconsin)
* Gmelin Handbook of Inorganic Chemistry: A User's Guide (Wagner, SUNY, Buffalo)
* GMELIN Handbook of Inorganic and Organometallic Chemistry Complete Catalog, 1997/98 (Wagner, SUNY, Buffalo)
* CrossFire Gmelin Database Reference Guide (MDL, 2003)
* CrossFire Gmelin - A Tutorial (Beilstein Information, v. 2.3, 1997)
* Gmelin Handbook of Inorganic and Organometallic Chemistry (Wiggins, Indiana)
* Guidelines for the Searching of Compounds in the Gmelin Database with CrossFire - Registration of Compounds
# Chemical Information Sources/CIIM/Current Awareness, Background Reading, and Document Delivery

Chemical Information Instructional Materials
* Current Awareness Options in Chemistry (Wiggins, Indiana)
* Finding Review Articles in Chemistry (Beckman, Indiana)
* Chemistry Book Lists and Guides to Serials (Wiggins, Indiana)
# Chemical Information Sources/CIIM/Landolt-Boernstein Numerical Data and Functional Relationships in Science and Technology

Chemical Information Instructional Materials
# Chemical Information Sources/CIIM/Physical Property Searching

Chemical Information Instructional Materials
* Finding Physical Properties of Chemicals: A Practical Guidefor Scientists, Engineers, and Librarians (A. Ben Wagner, Buffalo), published as: Science and Technology Libraries 2001, 21(3/4), 27-45. (actually published Fall 2003; web version updated 2009)
* Physical and Chemical Property Data Sources (Wiggins, Indiana; Roth, CalTech)
* Chemical and Physical Data (Harkanyi, San Diego)
* Chapman and Hall Chemical Database (Dialog Bluesheet)
# Chemical Information Sources/CIIM/Examinations for Chemical Information Courses

Chemical Information Instructional Materials

##### C471 Chemical Information Sources and Services (Indiana University)

* Quiz 1. Communication in Chemistry (Fall 2000)
* Quiz 1. Communication in Chemistry(Fall 2001)
* Quiz 2. Communication in Chemistry; How and Where to Start (Fall 2000)
* Quiz 2. How and Where to Start (Fall 2001)
* Quiz 3. How and Where to Search: General (Fall 2000)
* Quiz 3. How and Where to Search: General (Fall 2001)
* Quiz 4. How and Where to Search: Specialized (Fall 2001)
# Chemical Information Sources/CIIM/History, Biography, Directories, Chemical Industry Sources

Chemical Information Instructional Materials
* Biographical Works (Dunker, Indiana)
* Directories of Chemicals, Equipment, and Software (Dunker, Indiana)
* Directories of People, Places, and Academic Programs in Chemistry (Dunker, Indiana)
# Chemical Information Sources/CIIM/Chemistry Guides

Chemical Information Instructional Materials
* Chemical Information Sources/SIRCh/Guides (Wiggins)
* Science Literature Guides (Wiggins, Indiana)
* Journals & Databases Related to Chemistry (DeGolyer, Rochester Institute of Technology)
* Recommended Databases: Chemistry (DeGolyer, Rochester Institute of Technology)
* How to Research a Chemistry Term Paper (Shackle, Arizona State)
* Chemical Literature Guides and Aids: Bibliography and Index (Heideman, Razgunas, Wiggins, Indiana)
** For an update of the above resource, see:
** Carr, Carol. "Teaching and Using Chemical Information: An Updated Bibliography." Journal of Chemical Education September 1993 70(9), 719–726.
* Organic Chemistry Part A (Harkanyi, San Diego State)
* Organic Chemistry Part B (Harkanyi, San Diego State)
* Library Resources for Identifying Unknowns (Baysinger, Stanford)
* Chemistry (Newsom, Florida)
* Chemical Engineering (Newsom, Florida)
* Guide to Selected Biotechnology Resources (Baysinger, Stanford)
* STN Database Summary Sheets (HTML)
* DIALOG Bluesheets
* Thomson Knowledge Link Product Descriptions for Library Web Sites
* Technical Documents and Tutorials (Thomson Dialog and DataStar)