recursal/Fanatic-Fandom huggingface dataset:
Alu

The ***Alu*** repeat family is a repeat family which "comprises short interspersed elements (SINEs) present in multiple copies in the genomes of humans and other primates. The *Alu* sequence is approximately 300 bp in length and is found commonly in introns, 3' untranslated regions of genes, and intergenic genomic regions. They are mobile elements and are present in the human genome in extremely high copy number. Almost 1 million copies of the *Alu* sequence are estimated to be present, making it the most abundant mobile element. The *Alu* sequence is so named because of the presence of a recognition site for the *Alu*I endonuclease in the middle of the *Alu* sequence. Because of the widespread occurrence of the *Alu* repeat in the genome, the *Alu* sequence is used as a universal primer for PCR in animal cell lines; it binds in both forward and reverse directions. The *Alu* universal primer sequence is as follows: 5′-GTG GAT CAC CTG AGG TCA GGA GTT TC-3′ (26-mer)".

## References

1. ↑ McEntyre J, Ostell J, editors. *The NCBI Handbook* [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2002-. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21106/
Biconnected graph

A **biconnected graph** is a "connected graph that is not broken into disconnected pieces by deleting any single vertex (and incident edges)".

## References

1. ↑ Paul E. Black, "biconnected graph", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 15 Oct. 2015) Available from: <http://www.nist.gov/dads/HTML/biconnectedGraph.html>
Accessible surface area

The **accessible surface area** (**ASA**) is the "surface area of a protein or macromolecule that can be contacted by water molecules or other solvent or solute molecules. Accessible surface area is measured in square Ångstroms (Å2) and is often used to assess the quality of protein structures and the strength of hydrophobic interactions".

## References

1. ↑ "APPENDIX 2 Glossary of Bioinformatics Terms." *Current Protocols in Bioinformatics* 35.2 (2011): A.2.1-.2.13. Print.
Adjacent

**Adjacent** describes two vertices of a graph if there is an edge between them. Two adjacent vertices may be referred to as neighbors.

## References

1. ↑ Paul E. Black, "adjacent", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 4 November 2004. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/adjacent.html
PS4 Informercial

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**PS4 Informercial** is the twenty-third episode of Season 6 of the UPC series. It aired on December 6th, 2016.

## Characters

* Waluigi
* Larry Koopa
* Daisy
* Red Pikmin
* Rosalina
* Mario
* Mr Enderman

## Trivia

* This episode marks Mario's 80th appearance.
* Black Consoles Matter is a parody of Black Lives Matter.
Alignment

An **alignment** is the "principal form of representation of the similarity between nucleotide or amino acid sequences whereby nucleotides or amino acids inferred to have been derived from the same ancestral residue are superimposed".

## References

1. ↑ Koonin EV, Galperin MY. *Sequence - Evolution - Function: Computational Approaches in Comparative Genomics*. Boston: Kluwer Academic; 2003. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK20257/
Accessory pigment

An **accessory pigment** is a "visible light-absorbing pigment ... in plants and photosynthetic bacteria that complement[s] chlorophylls in trapping energy from sunlight".

## References

1. ↑ Nelson, David L., and Michael M. Cox. *Lehninger Principles of Biochemistry*. 5th ed. New York City: W. H. Freeman, 2011. Print.
Peach's Quest! Episode 6

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**Peach's Quest! Episode 6** is the eighth episode of Season 7 of the UPC series (and the one hundred and eighteenth overall). It aired on February 22, 2017.

## Synopsis

The events leading up to the final battle...

## Characters

* Peach
* Luigi
* Daisy
* Rosalina
* Zelda
* Toadette
* Green Toad
* Toad
* Herbert
* Yvanne
* Ben Tennyson
* Horrid Henry
* Donkey Kong
* Ocelot
* Yoshi
* Kyle
* Begman
* Mario
* Bowser
* Wario
* Waluigi
* Shy Guy
* Bowser Junior
* Larry Koopa
* Morton Koopa Jr
* Wendy O' Koopa
* Iggy Koopa
* Roy Koopa
* Lemmy Koopa
* Ludwig von Koopa
Alpha–1–antitrypsin

**Alpha–1–antitrypsin** (also stylized as **alpha-1-antitrypsin** or **α-1-antitrypsin**; **A1AT**) is a "trypsin-inhibiting serum protein which inhibits the digestive action of elastase on the tissues of the lungs and whose deficiency is associated with the development of emphysema".

## References

1. ↑ "Alpha–1–antitrypsin." *Merriam-Webster Medical Dictionary*. Merriam-Webster, n.d. Web. 01 Nov. 2015.
Best case

**Best case** refers to either the "situation or input for which an algorithm or data structure takes the least time or resources" or "having to do with this situation or input".

## References

1. ↑ Paul E. Black, "best case", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 15 Oct. 2015) Available from: <http://www.nist.gov/dads/HTML/bestcase.html>
Adenine

**Adenine** (variously abbreviated as either **A** or **Ade**) is a "nitrogenous base that occurs in nucleotides of DNA and RNA and pairs through hydrogen bonding complementarity with thymine (in DNA) or uracil (in RNA)".

## References

1. ↑ "Glossary of Technical Terms." *RCSB Protein Data Bank*. RCSB PDB, n.d. Web. 27 July 2015.
Average mass

**Average mass** is the "mass of an ion calculated by averaging all common isotope variations. This quantity typically is used when the resolution of the instrumentation is not adequate to distinguish individual isotopes".

## References

1. ↑ "APPENDIX 2 Glossary of Bioinformatics Terms." *Current Protocols in Bioinformatics* 35.2 (2011): A.2.1-.2.13. Print.
Carrier

A **carrier** (sometimes referred to as a **genetic carrier**) is an "individual who has a recessive, disease-causing gene mutation at a particular locus on one chromosome of a pair and a normal allele at that locus on the other chromosome; may also refer to an individual with a balanced chromosome rearrangement".

## See Also

* Autosomal recessive
* Carrier rate
* Carrier testing
* Compound heterozygote
* Double heterozygote
* Heterozygote
* Obligate carrier
* Obligate heterozygote
* X-linked recessive

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2015. *Illustrated Glossary*. Available from: http://www.ncbi.nlm.nih.gov/books/NBK5191/
Activator

An **activator** is a "DNA-binding protein that stabilizes construction of the RNA polymerase II transcription initiation complex".

**Activator** may also refer to a "positive modulator of an allosteric enzyme".

## References

1. ↑ Brown TA. *Genomes*. 2nd edition. Oxford: Wiley-Liss; 2002. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21126/
2. ↑ Nelson, David L., and Michael M. Cox. *Lehninger Principles of Biochemistry*. 5th ed. New York City: W. H. Freeman, 2011. Print.
Aedes aegypti whole-genome sequencing project

The ***Aedes aegypti* whole-genome sequencing project** is a "joint effort between the Broad Institute and The Institute for Genomic Research (TIGR) funded by the National Institute of Allergy and Infectious Diseases" whose goals are "to produce and publicly release a whole-genome assembly and auto-annotation of the *Aedes* genome representing 8X sequence coverage".

## References

1. ↑ "Project Information." *Aedes Aegypti Database*. Broad Institute, 9 Apr. 2014. Web. 20 July 2015.
CRAN

The **Comprehensive R Archive Network** (**CRAN**) is a "network of ftp and web servers around the world that store identical, up-to-date, versions of code and documentation for R".

## References

1. ↑ "The Comprehensive R Archive Network." *The Comprehensive R Archive Network*. Institute for Statistics and Mathematics of WU, 2015. Web. 06 June 2015.
Aequorin

## Further Reading

* Kurose, K et al. “Bioluminescence of the Ca2+-Binding Photoprotein Aequorin after Cysteine Modification.” *Proceedings of the National Academy of Sciences of the United States of America* 86.1 (1989): 80–84. Print.
* Shimomura, Osamu, Frank H. Johnson, and Yo Saiga. "Extraction, Purification and Properties of Aequorin, a Bioluminescent Protein from the Luminous Hydromedusan, *Aequorea*." *Journal of Cellular and Comparative Physiology* 59.3 (1962): 223-39. Print.
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

***Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids*** is a book written by Richard Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison which "provides the first unified, up-to-date and self-contained account of such methods, and more generally of probabilistic methods of sequence analysis, presented in a Bayesian framework".

## References

1. ↑ "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids Paperback – May 13, 1998." *Amazon.com*. Amazon.com, Inc, n.d. Web. 11 June 2015.
Bowser Junior's Weak Slumber Party

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**Bowser Junior's Weak Slumber Party** is the third episode of Season 7 of the UPC series. It will air on February 7th, 2017.

## Plot

This episode starts off with Bowser Junior, Zelda, and Toad. Toad asks Bowser Junior if there are any cookies but Bowser Junior says no. Junior says that there is 7-Up. They go upstairs and Baby Mario and Diddy Kong arrive. They watch a movie, but Bowser Junior does not like the way Diddy and Toad are dressing. He makes up an excuse that he is getting potato chips and then jumps off a balcony.

## Characters

* Bowser Junior
* Toad
* Zelda
* Baby Mario
* Diddy Kong (debut)
* Mario
* Peach
* Donkey Kong (debut)

## Trivia

* This episode marks the debut of Donkey and Diddy Kong.
Artificial neural network

An **artificial neural network** (**ANN**, often simply referred to as a neural network) is a "computing system made up of a number of simple, highly interconnected processing elements, which process information by their dynamic state response to external inputs".

## References

1. ↑ Caudill, Maureen. "Neural Networks Primer, Part I." *AI Expert* 2.12 (1987): 46-52. Print.
Atomic mass unit

An **atomic mass unit** (**amu**; also referred to as a **dalton** or **unified atomic mass unit**) is a "unit of mass equal to 1/12 the mass of the most abundant isotope of carbon, carbon-12, which is assigned a mass of 12".

## Further Reading

* Murray, Kermit K., Robert K. Boyd, Marcos N. Eberlin, G. John Langley, Liang Li, and Yasuhide Naito. "Definitions of Terms Relating to Mass Spectrometry (IUPAC Recommendations 2013)." *Pure and Applied Chemistry* 85.7 (2013): 1515-609. Print.

## References

1. ↑ "atomic mass unit." *American Heritage Dictionary of the English Language, Fifth Edition*. 2011. Houghton Mifflin Harcourt Publishing Company 11 Oct. 2015 <http://www.thefreedictionary.com/atomic+mass+unit>
Agonist

In biochemistry, **agonist** refers to a "substance that initiates a physiological response when combined with a receptor".

In anatomy, **agonist** refers to a "muscle whose contraction moves a part of the body directly".

## References

1. ↑ 1.0 1.1 "Definition of Agonist in English." *Oxford Dictionary (American English) (US)*. Oxford University Press, 2015. Web. 27 Sept. 2015.
Amino sugar

An **amino sugar** is a "monosaccharide in which an alcoholic hydroxyl group is replaced by an amino group".

## References

1. ↑ National Research Council (US) Committee on Assessing the Importance and Impact of Glycomics and Glycosciences. *Transforming Glycoscience: A Roadmap for the Future*. Washington (DC): National Academies Press (US); 2012. Appendix E, Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK115030/
ASTD

The **Alternative Splicing and Transcript Diversity** (**ASTD**) database project is a project which aimed to create a "database of alternative splice events and transcripts of genes from human, mouse and rat".

## References

1. ↑ "Alternative Splicing and Transcript Diversity (ASTD)." *Index of /pub/databases/astd*. EMBL-EBI, 2 Dec. 2008. Web. 20 July 2015.
Mario Saves Christmas! Part 1

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**Mario Saves Christmas! Part 1** is the 34th episode of Season 5 of the UPC series. It will air on December 22nd, 2015. It is a Christmas special.

## Plot

Bowser has kidnapped Santa, so Rudolph tries to get Mario and Luigi's attention!

## Characters

* Mario
* Luigi
* Peach
* Daisy
* Rosalina
* Baby Mario
* Link
* Yoshi
* White Yoshi (opening)
* Bowser
* Bowser Junior
* Ludwig von Koopa
* Lemmy Koopa
* Santa Claus
* Rudolph

## Trivia

* This is the fourth UPC holiday special.
* A script extract confirms that Link and Rosalina will be in this video.
* This is the second UPC video to exceed the 20 minute mark, the first being Halloween! Part 2. Interestingly, they are both parts of a two parter.
* UPC said that Baby Mario and Link were overexaggerating when they said Lucina is the rarest amiibo ever.

## Errors

* In the opening, Bowser says the parents were wrapping their present's gifts instead of children's gifts.
* The opening also shows White Yoshi, however he does not make a scene in the video. It is possible he will show up in Part 2.
7th Grade! Part 8

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**7th Grade! Part 8** is the sixth episode of Season 7 (and the one hundred and seventeenth overall) of the UPC series. It aired on February 16, 2017.

## Characters

* Toad
* Diddy Kong
* Yvanne
* Herbert
* Toadette
* Green Toad
* Red Pikmin
* Yellow Pikmin
* Baby Mario
* Link
* Shy Guy
* Horrid Henry
* Bowser Junior
* Kamek
* Amy Rose
* Zelda
* Sheep
* Mario
* Luigi
* Mr Enderman
* Mrs Enderman
* Chef
* Oiram
* Kyle (mentioned)

## Trivia

* This episode marks Kamek's 30th appearance.
* This episode reveals that Mrs Enderman survived the gunshot.
Aquaporin

An **aquaporin** (**AQP**; formerly referred to as a **water channel protein**, abbreviated as **WCP**) is a member of a family of "small membrane-spanning proteins (monomer size approximately 30 kDa) that are expressed at plasma membranes in many cells types involved in fluid transport".

## Further Reading

* Benga, Gheorghe. "Water Channel Proteins (later Called Aquaporins) and Relatives: Past, Present, and Future." *IUBMB Life* 61.2 (2009): 112-33. Print.

## References

1. ↑ Verkman, A. S., and A. K. Mitra. "Structure and Function of Aquaporin Water Channels." *American Journal of Physiology. Renal Physiology*. 278.1 (2000): F13-28. Print.
CPAN.pm

**CPAN.pm** (sometimes **cpan.pm** and often referred to simply as **CPAN** or **cpan**) is a Perl module which is "used to download and install Perl software from the CPAN archive".

## External Links

* CPAN - query, download and build perl modules from CPAN sites - metacpan.org

## References

1. ↑ "The CPAN Frequently Asked Questions." *Comprehensive Perl Archive Network*. Perl.org, n.d. Web. 22 June 2015.
BLASTN

**Nucleotide BLAST** (usually shortened as **BLASTN** or **blastn**, and sometimes also referred to as **Standard Nucleotide BLAST**) is a tool which allows a user to "search with a nucleotide sequence against nucleotide databases for locally similar sequences with tblastn".

## External Links

* Nucleotide BLAST: Search nucleotide databases using a nucleotide query

## References

1. ↑ "Search Tools." *Bioinformatics Toolkit*. Department of Protein Evolution at the Max Planck Institute for Developmental Biology, Tübingen, 2015. Web. 09 June 2015.
Active site

An **active site** is the "region of an enzyme molecule where the substrate binds and undergoes a catalyzed reaction".

## References

1. ↑ Lodish H, Berk A, Zipursky SL, et al. *Molecular Cell Biology*. 4th edition. New York: W. H. Freeman; 2000. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK21607/
CSS

**Cascading Style Sheets** (**CSS**) is a stylesheet language that "defines how HTML elements are to be displayed".

**CSS** may also refer to Central Structure Store, closed-source software, or cross-site scripting (although the latter is more often abbreviated as "XSS").

## External Links

* What is Cascading Style Sheets (CSS)? Webopedia

## References

1. ↑ "CSS Introduction." *W3schools.com*. Refsnes Data, n.d. Web. 24 June 2015.
CDNA library

A **cDNA library** is a "collection of copy (cDNA) fragments that have been made by reverse transcriptase from the mRNA of a particular cell, organ, or organism".

## References

1. ↑ "cDNA library." *Farlex Partner Medical Dictionary*. 2012. Farlex 23 Oct. 2015 <http://medical-dictionary.thefreedictionary.com/cDNA+library>
Alphabetical list of databases on the Molecular Biology Database List

## 0-9

* 16SMD
* 23SMD
* 5S rRNA Data Bank

A

* A Mutation Spectra Database
* AARSDB
* AAindex
* ACeDB
* AMmtDB
* APC Gene Database
* ARRAYdb
* ASDB
* Ares Lab Intron Site
* Asthma and Allergy Gene Database
* AtDB
* Atlas of Genetics and Cytogenetics in Oncology and Haematology
* Atlas of Primate Brain

B

C

D

E

F

G

H

I

J

K

L

M

N

O

P

Q

R

S

T

U

V

W

X

Y

Z
Autosomal dominant

**Autosomal dominant** is a term which "describes a trait or disorder in which the phenotype is expressed in those who have inherited only one copy of a particular gene mutation (heterozygotes); specifically refers to a gene on one of the 22 pairs of autosomes (non-sex chromosomes)".

## See Also

* De novo mutation
* Germline mosaicism
* Heterozygote
* Mode of inheritance
* Penetrance
* Variable expressivity

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2015. *Illustrated Glossary*. Available from: http://www.ncbi.nlm.nih.gov/books/NBK5191/
Ocelot

Hair
 Gender
 Eyes
 Age
 Family
 Health Status
 D.O.B
 Religion

**Ocelot** is a main character in the UPC series. He originated from Minecraft. He was killed by Bowser in Super Mario: The Movie Part 7 and was revived off-screen and killed again in Super Mario: The Movie 2 Part 1. He is a few grades higher than Toad. He debuts in the UPC update Will Make Videos Soon.

## Video Appearances

* Will Make Videos Soon
* Sheep's Birthday
* Why There Has Been A Lack Of Videos
* Toad Reads A Book
* Super Mario: The Movie Part 1
* Super Mario: The Movie Part 2
* Super Mario: The Movie Part 3
* Super Mario: The Movie Part 4
* Super Mario: The Movie Part 5
* Super Mario: The Movie Part 6
* Super Mario: The Movie Part 7
* Toad Reads A Book Part 2
* Super Mario: The Movie 2 Part 1
* Toad Plays Out!
* My Minecraft Plush Collection
* Mario's Family Go To Torquay!
* Father's Day!
* Marioade Informercial
* Mario's Amnesia!
* Bowser's Prophecy
* The Magic Animal Club
* Toad Goes To School! Part 4
* Mama Luigi's Pizza Place Informercial
* Mario's Day Out!
* Luigi's Marriage Problem!
* Mario's Family Go Camping!

**Overall: 26 appearances**
B-tree

A **B-tree** is a tree structure (a type of data structure) that is "optimized for situations when all or part of the tree must be maintained on a secondary storage device such as an optical disk or tape".

## External Links

* 5.4.1 Definition of B-Trees
* B-Tree Visualization
* B-Trees

## References

1. ↑ "B-tree." *Webopedia*. QuinStreet Inc., 2015. Web. 22 Sept. 2015.
BMCD

The **Biological Macromolecule Crystallization Database** (**BMCD**) is a database which "contains molecule, crystal and crystallization data for macromolecules for which diffraction quality crystals have been obtained".

## References

1. ↑ Gilliland, Gary, Michael Tung, Jane Ladner, Travis Gallagher, and The Structural Biology Group, Biochemical Science Division of CSTL at NIST. "Introduction." *Biological Macromolecule Crystallization Database (version 4.03)*. U.S. Department of Commerce, 2009. Web. 06 June 2015.
Biopolymer

A **biopolymer** is a "macromolecule[] (including proteins, nucleic acids and polysaccharides) formed by [a] living organism[]".

## External Links

* Green Chemistry: The Nexus Blog: The Many Faces of Biopolymers|ACS Network

## References

1. ↑ IUPAC. Compendium of Chemical Terminology, 2nd ed. (the "Gold Book"). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997). XML on-line corrected version: http://goldbook.iupac.org (2006-) created by M. Nic, J. Jirat, B. Kosata; updates compiled by A. Jenkins. ISBN 0-9678550-9-8. doi:10.1351/goldbook.
BioRobot 9600

The **BioRobot 9600** is a "robotic workstation with integrated modules and QIAGEN certified protocols for sample preparation and high-precision liquid handling".

## References

1. ↑ "Specifications of the QIAGEN BioRobot 9600." *Izasa Scientific, Instrumentación Científica*. Izasa Scientific, n.d. Web. 22 Sept. 2015.
Catalytic triad

## External Links

* Mechanism of Chymotrypsin and Catalytic Triad - YouTube

## Further Reading

* Ekici, Özlem Doğan, Mark Paetzel, and Ross E. Dalbey. “Unconventional Serine Proteases: Variations on the Catalytic Ser/His/Asp Triad Configuration.” *Protein Science : A Publication of the Protein Society* 17.12 (2008): 2023–2037. *PMC*. Web. 2 Nov. 2015.
* Polgár, L. "The Catalytic Triad of Serine Peptidases." *Cellular and Molecular Life Sciences* 62.19-20 (2005): 2161-172. Print.
Bioinformatics Wikia

<hero description="Welcome to the Bioinformatics Wiki! Here we are determined to provide as much information about bioinformatics as possible, with tutorials and examples of code as well as helpful programs and databases." imagename="" cropposition="" />

## Welcome to the Bioinformatics Wikia

Welcome to the Bioinformatics Wiki! Here we are determined to provide as much information about bioinformatics as possible, with tutorials and examples of code as well as helpful programs and databases. So what is bioinformatics exactly? Luscombe, Greenbaum, and Gerstein proposed a definition in a 2001 paper saying that bioinformatics is "conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale". The Wiki was started in June of 2015 and now contains 1,501 articles.

File:Placeholder
Cancer

**Cancer** refers to "any one of a large number of diseases characterized by the development of abnormal cells that divide uncontrollably and have the ability to infiltrate and destroy normal body tissue".

## External Links

* What Is Cancer? - National Cancer Institute

## References

1. ↑ Mayo Clinic Staff. "Cancer." *Mayo Clinic*. Mayo Foundation for Medical Education and Research, 23 May 2015. Web. 27 July 2015.
Aneuploidy

**Aneuploidy** is the "occurrence of one or more extra or missing chromosomes leading to an unbalanced chromosome complement, or, any chromosome number that is not an exact multiple of the haploid number".

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2015. *Illustrated Glossary*. Available from: http://www.ncbi.nlm.nih.gov/books/NBK5191/
Bayesian network

A **Bayesian network** is a "method in machine learning used to predict a feature in a dataset given some known but incomplete information" which is "based on Bayes' rule for conditional probability".

## References

1. ↑ "APPENDIX 2 Glossary of Bioinformatics Terms." *Current Protocols in Bioinformatics* 35.2 (2011): A.2.1-.2.13. Print.
Acid-base reaction

An **acid-base reaction** is a "type of chemical process typified by the exchange of one or more hydrogen ions, H+, between species that may be neutral (molecules, such as water, H2O; or acetic acid, CH3CO2H) or electrically charged (ions, such as ammonium, NH4+; hydroxide, OH−; or carbonate, CO32-)".

## References

1. ↑ "acid-base reaction". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*. Encyclopædia Britannica Inc., 2015. Web. 09 Sep. 2015 <http://www.britannica.com/science/acid-base-reaction>.
Absorbance

**Absorbance** (sometimes referred to as **optical density**, abbreviated as **OD**) is the "logarithm of the ratio of incident to transmitted radiant power through a sample (excluding the effects on cell walls)".

## References

1. ↑ IUPAC. Compendium of Chemical Terminology, 2nd ed. (the "Gold Book"). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997). XML on-line corrected version: http://goldbook.iupac.org (2006-) created by M. Nic, J. Jirat, B. Kosata; updates compiled by A. Jenkins. ISBN 0-9678550-9-8. doi:10.1351/goldbook.
Diddy Kong

Hair
 Gender
 Eyes
 Age
 Family
 Health Status
 D.O.B
 Religion

**Diddy Kong** is a minor character in the UPC series. His first appearance was in Bowser Junior's Weak Slumber Party.

## Video Appearances

### Main Series

* Bowser Junior's Weak Slumber Party
* 7th Grade! Part 7
* 7th Grade! Part 8
* 7th Grade! Part 11
* 7th Grade! Part 13
* Pesach!

### UPC Updates

* What I Got For Hanukkah 2016

**Overall: 7 appearances**
Acetylation

**Acetylation** (sometimes referred to as **ethanoylation**) refers to any "chemical reaction that adds an acetyl chemical group (CH3C=O, sometimes abbreviated in chemical structures as Ac) and is a type of acylation reaction".

## References

1. ↑ "Acetylation." *Nature.com*. Nature Publishing Group, n.d. Web. 11 Oct. 2015.
Allelic variant of unknown significance

An **allelic variant of unknown significance** (also referred to as an **unclassified variant** or a **variant of uncertain significance**, which is often abbreviated as **VUS**) is an "alteration in the normal sequence of a gene, the significance of which is unclear until further study of the genotype and corresponding phenotype in a sufficiently large population; complete gene sequencing often identifies numerous (sometimes hundreds) allelic variants for a given gene".

## See Also

* Allele
* Benign variant
* Disease-causing mutation
* Mutation
* Polymorphism
* Sequence alteration

## External Links

* Allelic variant of unknown significance - Glossary Entry - Genetics Home Reference

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2015. *Illustrated Glossary*. Available from: http://www.ncbi.nlm.nih.gov/books/NBK5191/
Bioinformatics Algorithms (Part 1)

***Bioinformatics Algorithms (Part 1)*** was a Coursera course offered by UC San Diego that was the "first in a two-part series covering some of the algorithms underlying bioinformatics. It has now been split into three smaller courses".

## References

1. ↑ "Bioinformatics Algorithms (Part 1)." *Coursera*. Coursera Inc., 2015. Web. 7 June 2015.
BioWiki

**BioWiki** is the wiki of the bioinfo-core, a "worldwide body of people that manage or staff bioinformatics cores within organizations of all types including academia, academic medical centers, medical schools, biotechs and pharmas", but may also refer to this wiki, the Bioinformatics Wikia.

## References

1. ↑ "Main Page." *BioWiki*. MediaWiki, 18 Mar. 2015. Web. 10 June 2015.
Asymptotically tight bound

**Asymptotically tight bound** describes "when the asymptotic complexity of an algorithm exactly matches the theoretically proved asymptotic complexity of the corresponding problem. Informally, when an algorithm solves a problem at the theoretical minimum".

## References

1. ↑ Sandeep Kumar Shukla, "asymptotically tight bound", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 06 September 2015) Available from: http://www.nist.gov/dads/HTML/asymptoticallyTightBound.html
ABC transporter

An **ABC transporter** (**ATP-binding cassette transporter**) is a "member of a large family of membrane transporters with sequences that make up ATP-binding cassettes".

## References

1. ↑ Nelson, David L., and Michael M. Cox. *Lehninger Principles of Biochemistry*. 5th ed. New York City: W. H. Freeman, 2011. Print.
Ludwig's Twitter Account!

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**Ludwig's Twitter Account!** is the fourteenth episode of Season 6 of the UPC series. It aired on November 9th, 2016.

## Synopsis

Ludwig creates a Twitter account and shows Larry. However, Larry creates a Twitter account of his own...

## Characters

* Ludwig von Koopa
* Larry Koopa

## Trivia

* This is the first Ludwig social media video where Bowser Junior is absent.
Asymptotic bound

An **asymptotic bound** is a "curve representing the limit of a function. That is, the distance between a function and the curve tends to zero. The function may or may not intersect the bounding curve".

## References

1. ↑ Paul E. Black, "asymptotic bound", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 15 Oct. 2015) Available from: <http://www.nist.gov/dads/HTML/asymptoticBound.html>
Autosomal

**Autosomal** refers to "any of the chromosomes other than the sex-determining chromosomes (i.e., the X and Y) or the genes on these chromosomes".

## References

1. ↑ Pagon RA, Adam MP, Ardinger HH, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2015. *Illustrated Glossary*. Available from: http://www.ncbi.nlm.nih.gov/books/NBK5191/
Annotation

**Annotation** is the "process of attaching additional information about a data entry, for example a gene sequence or protein sequence. Annotations can be structural (for example, identifying a protein coding region) or functional (for example adding biological information about the function of a protein). Annotation can also refer to the whole entry (an entire protein) or a particular feature (a protein domain). Annotation can be performed automatically or manually by curators".

## References

1. ↑ "EMBLog Bioinformatics Glossary." *EMBLog*. EMBLog, 2013. Web. 21 July 2015.
CPAN

The **Comprehensive Perl Archive Network** (**CPAN**, often stylized as **cpan**) is a "large collection of Perl software and documentation". CPAN is also the name of a Perl module, CPAN.pm.

## References

1. ↑ "The CPAN Frequently Asked Questions." *Comprehensive Perl Archive Network*. Perl.org, n.d. Web. 22 June 2015.
Carbohydrate

A **carbohydrate** (sometimes referred to as a **saccharide**) is a "compound[] made from just three elements: carbon, hydrogen and oxygen".

## External Links

* biochemistry - The real definition of carbohydrates - Biology Stack Exchange

## References

1. ↑ "Carbohydrates." *Chemistry for Biologists*. Royal Society of Chemistry (RSC), n.d. Web. 08 Sept. 2015.
Bioinformatics in BioMed

**Bioinformatics in BioMed** is a bioinformatics wiki site in the Division of Biology and Medicine at Brown University which includes "tutorials on how to use some popular bioinformatics software, mainly related to Illumina sequence data analysis, and information about ongoing sequencing projects at Brown University".

## References

1. ↑ "Bioinformatics in BioMed." *Bioinformatics in BioMed*. Google Sites, n.d. Web. 10 June 2015.
Adaptive Huffman coding

**Adaptive Huffman coding** refers to an algorithm in which a "near-minimal variable-length character coding that changes based on the frequency of characters processed. As characters are processed, frequencies are updated and codes are changed (or, the coding tree is modified)".

## References

1. ↑ Paul E. Black, "adaptive Huffman coding", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 14 July 2008. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/adaptiveHuffman.html
A Brief Guide to Starting Your IT Career as a Linux Sysadmin

***A Brief Guide to Starting Your IT Career as a Linux Sysadmin*** is a short ebook published by the Linux Foundation which details questions like "How do I quickly go from Linux newbie to Linux professional?", "What does a Linux system administrator do?", and "How do I get my first Linux sysadmin job?".

## External Links

* DOWNLOAD: A Brief Guide to Starting Your IT Career as a Linux Sysadmin
Bubble sort

**Bubble sort** (also known as **sinking sort** or **exchange sort**) is a sorting algorithm which works by comparing each adjacent pair of items in a list in turn, swapping the items if necessary, and repeating the pass through the list until no swaps are done.

## References

1. ↑ Paul E. Black, "bubble sort", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 24 August 2009. (accessed 16 Oct. 2015) Available from: <http://www.nist.gov/dads/HTML/bubblesort.html>
Apt-get

The **apt-get** command is "a powerful command-line tool, which works with Ubuntu's Advanced Packaging Tool (APT) performing such functions as installation of new software packages, upgrade of existing software packages, updating of the package list index, and even upgrading the entire Ubuntu system".

## References

1. ↑ "Apt-Get." *Ubuntu Documentation*. Canonical Ltd., n.d. Web. 10 June 2015.
Association constant

The **association constant** or "**affinity constant**" (***Ka***; sometimes referred to as the **binding constant**) is a "mathematical constant describing the bonding affinity of two molecules at equilibrium, especially the bonding affinity of an antibody and an antigen".

## References

1. ↑ "association-constant." *The American Heritage Stedman's Medical Dictionary*. Houghton Mifflin Company. 12 Oct. 2015. <Dictionary.com http://dictionary.reference.com/browse/association-constant>.
Armed antibody

## Further Reading

* Hess, Christian, Dario Venetz, and Dario Neri. "Emerging Classes of Armed Antibody Therapeutics against Cancer." *MedChemComm* 5.4 (2014): 408-31. Print.
* Venetz, Dario, Christian Hess, Chia-Wei Lin, Markus Aebi, and Dario Neri. "Glycosylation Profiles Determine Extravasation and Disease-targeting Properties of Armed Antibodies." *Proceedings of the National Academy of Sciences* 112.7 (2015): 2000-005. Print.
Assay

An **assay** is a "biochemical or other measurement developed to quantify a biomarker".

## References

1. ↑ Committee on the Review of Omics-Based Tests for Predicting Patient Outcomes in Clinical Trials; Board on Health Care Services; Board on Health Sciences Policy; Institute of Medicine; Micheel CM, Nass SJ, Omenn GS, editors. *Evolution of Translational Omics: Lessons Learned and the Path Forward*. Washington (DC): National Academies Press (US); 2012 Mar 23. Glossary. Available from: http://www.ncbi.nlm.nih.gov/books/NBK202162/
Amphipathicity

**Amphipathicity** refers to the fact that the molecules of a substance "contain[] both a hydrophilic and a hydrophobic (lipophilic) group".

## References

1. ↑ IUPAC. Compendium of Chemical Terminology, 2nd ed. (the "Gold Book"). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997). XML on-line corrected version: http://goldbook.iupac.org (2006-) created by M. Nic, J. Jirat, B. Kosata; updates compiled by A. Jenkins. ISBN 0-9678550-9-8. doi:10.1351/goldbook.
Affinity chromatography

**Affinity chromatography** is "chromatography in which a macromolecule (as a protein) is isolated and purified by passing it in solution through a column treated with a substance having a ligand for which the macromolecule has an affinity that causes it to be retained on the column".

## References

1. ↑ "Affinity Chromatography." *Merriam-Webster*. Merriam-Webster, Incorporated, 2015. Web. 27 Sept. 2015.
CONSTRUCT query

A **CONSTRUCT query** is a "query form that builds a new graph based on matches in a data graph, along with a graph template".

## References

1. ↑ Allemang, Dean, and James A. Hendler. *Semantic Web for the Working Ontologist: Effective Modeling in RDFS and OWL*. 2nd ed. Waltham: Morgan Kaufmann/Elsevier, 2011. Print.
Autofluorescence

**Autofluorescence** or **self-induced fluorescence** refers to the fluorescence of cells, molecules, or tissues when exposed to ultraviolet or visible electromagnetic radiation.

## References

1. ↑ "autofluorescence." *Medical Dictionary*. 2009. Farlex and Partners 4 Oct. 2015 http://medical-dictionary.thefreedictionary.com/autofluorescence
Big-O notation

**Big-O notation** or **big O notation** (sometimes also referred to as **Landau's symbol**) is a "theoretical measure of the execution of an algorithm, usually the time or memory needed, given the problem size *n*, which is usually the number of items".

## References

1. ↑ Paul E. Black, "big-O notation", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 31 August 2012. (accessed 06 September 2015) Available from: http://www.nist.gov/dads/HTML/bigOnotation.html
Caffe

**Caffe** is a "deep learning framework made with expression, speed and modularity in mind. It is developed by the Berkeley Vision and Learning Center ... and by community contributors".

## References

1. ↑ Jia, Yangqing, and Evan Shelhamer. "Caffe." *Caffe*. UC Berkeley Computer Vision Group, n.d. Web. 09 June 2016.
B+ tree

A **B+ tree** (variously stylized as **B+-tree** or **B+-tree**, but also referred to as a **bplustree** or **b plus tree**) is a B-tree where the leaves are also linked sequentially, thus allowing both fast random access and sequential access to data.

## External Links

* B+ Tree Basics 1 - YouTube
* B+ Tree Visualization
* B+-tree insert and delete Example
* CSci 340: B+-trees
* Data Structures: B+ Trees - YouTube

## Further Reading

* Paul E. Black, "B+-tree", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 6 November 2007. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/bplustree.html

## References

1. ↑ "b-tree." *The Free On-line Dictionary of Computing*. Denis Howe. 12 Oct. 2015. <Dictionary.com http://dictionary.reference.com/browse/b-tree>.
Bad character heuristic

The **bad character heuristics** method (also called the **missed character heuristic**, **bad character heuristic**, **bad character rule**, or **bad character shift rule**) is a rule of the Boyer-Moore Algorithm which states that, "if the first mismatch is found at position i (when scanning the pattern right to left) and *T*(*k*) is the text character that mismatches *P*(*i*), then shift the pattern right by max(1, *i* - *R*(*T*(*k*))".

## External Links

* Boyer-Moore algorithm
* String Matching - Cedar

## References

1. ↑ Blumer, Anselm. "Boyer-Moore." *COMP 150-GEN Genomic Sequence Algorithms*. Tufts University, School of Engineering, n.d. Web. 11 Oct. 2015.
Aptitude

**aptitude** is a "text-based interface to the Debian GNU/Linux package system" which "allows the user to view the list of packages and to perform package management tasks such as installing, upgrading, and removing packages".

## References

1. ↑ Burrows, Daniel. "Aptitude." *Aptitude User's Manual*. FusionForge, 2008. Web. 10 June 2015.
Celera

**Celera** is a company which was founded in 1998 with the "mission to sequence the human genome and provide clients with early access to the resulting data". Today, Celera acts as a "healthcare company focused on personalizing disease management through diagnostic products and services".

## References

1. ↑ "Our History." *Celera: Personalizing Disease Management*. Celera, 2015. Web. 03 Sept. 2015.
Adjacency-list representation

An **adjacency-list representation** (sometimes referred to simply as an **adjacency list**) is a "representation of a directed graph with *n* vertices using an array of *n* lists of vertices. List *i* contains vertex *j* if there is an edge from vertex *i* to vertex *j*. A weighted graph may be represented with a list of vertex/weight pairs. An undirected graph may be represented by having vertex *j* in the list for vertex *i* and vertex *i* in the list for vertex *j*".

## References

1. ↑ Bob Bockholt and Paul E. Black, "adjacency-list representation", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 14 August 2008. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/adjacencyListRep.html
Bioinformatics Core Wiki

**Bioinformatics Core Wiki** is a wiki which "provides expertise and infrastructure to carry out acquisition, curation, distribution of complex data sets as well as to develop and perform computations, analyses and simulations addressing a wide variety of biological questions from genomics and systems biology".

## References

1. ↑ "Main Page." *Bioinformatics Core Wiki*. MediaWiki, 6 May 2009. Web. 10 June 2015.
Biological pathway

A **biological pathway** (sometimes simply referred to as a **pathway**) is a "series of actions among molecules in a cell that leads to a certain product or a change in the cell".

## References

1. ↑ "Biological Pathways Fact Sheet." *National Human Genome Research Institute*. National Institutes of Health, 5 Apr. 2015. Web. 23 June 2015.
Boyer-Moore string search algorithm

The **Boyer-Moore** (**BM** or **BM 77**) **string search algorithm** (also referred to as the **Boyer-Moore algorithm**, the **Boyer-Moore fast string searching algorithm**, or **Boyer-Moore matching**) is a search algorithm which "compares the pattern with the text from right to left. If the text symbol that is compared with the rightmost pattern symbol does not occur in the pattern at all, then the pattern can be shifted by m positions behind this text symbol".

## External Links

* Biosequence Algorithms, Spring 2005; Lecture 3: Boyer-Moore Matching

## References

1. ↑ Lang, H. W. "Boyer-Moore Algorithm." *Algorithmen in Java*. Fachhochschule Flensburg, 17 Mar. 2001. Web. 11 Oct. 2015.
Aromatic compound

**Aromatic compound** refers to "any of a large class of unsaturated chemical compounds characterized by one or more planar rings of atoms joined by covalent bonds of two different kinds".

## References

1. ↑ "aromatic compound". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*. Encyclopædia Britannica Inc., 2015. Web. 08 Sep. 2015 <http://www.britannica.com/science/aromatic-compound>.
Binary search

**Binary search** (also referred to as **dichotomizing search**) is a search algorithm which works by searching a sorted array by repeatedly dividing the search interval in half. The algorithm begins with an interval covering the whole array. Then, if the value of the search key is less than the item in the middle of the interval, it narrows the interval to the lower half. Otherwise the algorithm narrows it to the upper half. It then repeatedly check until the value is found or the interval is empty.

## References

1. ↑ Paul E. Black, "binary search", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 2 March 2015. (accessed TODAY) Available from: http://www.nist.gov/dads/HTML/binarySearch.html
BioITeam

The **BioITeam** (**Bioinformatics Team**) at the University of Texas at Austin is a "consortium of bio-computing scientists at the University of Texas comprised of scientists from TACC, CCBB, CSSB, GSAF, TI-3D, and SSC".

## References

1. ↑ "Home." *Bioinformatics Team (BioITeam) at the University of Texas - UT Austin Wikis*. Atlassian Confluence 5.5.7, 21 May 2015. Web. 10 June 2015.
Capacity

In graph theory, the **capacity** usually refers to the "maximum flow that may be sent through an edge or a vertex".

In graph theory, the **capacity of a cut** (sometimes simply referred to as the **capacity**) is the sum of the capacity of the edges in the cut that are oriented from a vertex *x* to a vertex *y*.

## References

1. ↑ Algorithms and Theory of Computation Handbook, CRC Press LLC, 1999, "capacity", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 17 December 2004. (accessed 15 November 2015) Available from: http://www.nist.gov/dads/HTML/capacity.html
BITS Wiki

**BITS Wiki** ("BITS" standing for "**basic bioinformatics concepts, databases and tools**") is a wiki which includes "information about the covered [bioinformatics] topics, software (installation instructions) and databases, additional useful links and recommended literature".

## References

1. ↑ "Basic Bioinformatics Concepts, Databases and Tools." *BITS Wiki*. MediaWiki, 9 Dec. 2014. Web. 10 June 2015.
Bragg's law

**Bragg's law** (also referred to as the **Bragg law** or **Bragg condition**) is the "relation between the spacing of atomic planes in crystals and the angles of incidence at which these planes produce the most intense reflections of electromagnetic radiations, such as X rays and gamma rays, and particle waves, such as those associated with electrons and neutrons. For maximum intensity of reflected wave trains, they must stay in phase to produce constructive interference, in which corresponding points of a wave (e.g., its crests or troughs) arrive at a point simultaneously. The Bragg law was first formulated by Lawrence Bragg, an English physicist".

## External Links

* Bragg's law - Online Dictionary of Crystallography

## References

1. ↑ "Bragg law". *Encyclopædia Britannica*. *Encyclopædia Britannica Online*. Encyclopædia Britannica Inc., 2015. Web. 17 Dec. 2015
<http://www.britannica.com/science/Bragg-law>.
Bioinformatics for transcriptomics

***Bioinformatics for transcriptomics*** is a bioinformatics course taught at the University of Manchester and "is delivered using a virtual learning environment called Moodle". It covers "microarray data analysis in depth, and also introduces the areas where new work is needed for next generation sequence (RNA-seq) analysis".

## References

1. ↑ "Bioinformatics for Transcriptomics." *ISCB*. International Society for Computational Biology, Inc., 15 Nov. 2011. Web. 08 June 2015.
Array

An **array** (or **array data structure**) is an "assemblage of items that are randomly accessible by integers, the index".

## References

1. ↑ Paul E. Black, "array", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 23 May 2011. (accessed 16 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/array.html
.pdb

The file extension **.pdb** indicates a file which is either a ProBID+ data file, a Program Database file (which can be opened usually by Pegasus, Quicken, MS Visual Studio, or Palm Pilot software), a Protein Data Bank file, a Tanida Demo Builder file, a PowerDesigner Database Backup file, or a Palm Desktop Database File.

## External Links

* File Extension .PDB Information
* PDB File Extension
Activity

**Activity** refers to the "true thermodynamic activity or potential of a substance, as distinct from its molar concentration".

In enzymology, **activity** (often referred to as **enzyme activity**, **enzymatic activity**, **enzyme catalytic activity**, or **catalytic activity of an enzyme**) is the "property measured by the increase in the rate of reaction of a specified chemical reaction that the enzyme produces in a specific assay system".

In reference to a radioactive material, **activity** (often referred **absolute activity**, but also as **disintegration rate** or **decay rate** and abbreviated as ***A***) refers to the "number of nuclear decays occurring in a given quantity of material in a small time interval, divided by that time interval".

## External Links

* Chapter 5: Enzymes - Introduction
* Enzyme units, activity and specific activity explained
* Enzymes Activities

## References

1. ↑ Nelson, David L., and Michael M. Cox. *Lehninger Principles of Biochemistry*. 5th ed. New York City: W. H. Freeman, 2011. Print.
2. ↑ "Units of Enzyme Activity. Recommendations 1978." *European Journal of Biochemistry* 97.2 (1979): 319-20. Print.
3. ↑ IUPAC. Compendium of Chemical Terminology, 2nd ed. (the "Gold Book"). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997). XML on-line corrected version: http://goldbook.iupac.org (2006-) created by M. Nic, J. Jirat, B. Kosata; updates compiled by A. Jenkins. ISBN 0-9678550-9-8. doi:10.1351/goldbook.
Op MediaRip *Staff Only*

== Schedule

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you work on your own time as long as you have \*at least\* one video along with one screenshot every day. if i don't approve of the video or a General dost i will simply take it down. You guys are almost to the top ranks on this Wiki keep working hard and you will be promoted. Keep in mind you guys have one of the easiest jobs so don't screw up.