recursal/Fanatic-Fandom huggingface dataset:
Priority queue

A **priority queue** is an "abstract data type to efficiently support finding the item with the highest priority across a series of operations. The basic operations are: insert, find-minimum (or maximum), and delete-minimum (or maximum). Some implementations also efficiently support join two priority queues (meld), delete an arbitrary item, and increase the priority of a item (decrease-key)".

## References

1. ↑ Paul E. Black, "priority queue", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 20 December 2004. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/priorityque.html
Polypeptide

A **polypeptide** is a "linear organic polymer consisting of a large number of amino-acid residues bonded together in a chain, forming part of (or the whole of) a protein molecule".

## References

1. ↑ "Definition of Polypeptide in English." *Oxford Dictionary (American English) (US)*. Oxford University Press, 2015. Web. 15 Sept. 2015.
Python

**Python** is an "interpreted, object-oriented programming language developed by Guido van Rossum. The name comes from one of van Rossum's favorite television shows, *Monty Python's Flying Circus*. Python is very portable since Python interpreters are available for most operating system platforms. Although Python is copyrighted, the source code is open source, and unlike GNU software, it can be commercially re-sold".

## External Links

* Python.org
* The Python Wiki

## References

1. ↑ "Python." *Webopedia*. QuinStreet Inc., 2015. Web. 07 June 2015.
Planar chirality

**Planar chirality** or **planar stereoisomerism** is a "term used by some authorities to refer to stereoisomerism resulting from the arrangement of out-of-plane groups with respect to a plane (chirality plane)".

## 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.
Protein

A **protein** is one of four essential building blocks of life (the other three being carbohydrates, lipids, and nucleic acids). Proteins are macromolecules "composed of one or more polypeptide chains, each with a characteristic sequence of amino acids linked by peptide bonds".

## References

1. ↑ Liou, Stephanie. "An Introduction to Proteins." *Huntington's Outreach Project for Education, At Stanford*. HOPES Stanford University, 26 June 2010. Web. 5 June 2015.
2. ↑ Nelson, David L., and Michael M. Cox. *Lehninger Principles of Biochemistry*. 5th ed. New York City: W. H. Freeman, 2011. Print.
Prothrombin

**Prothrombin** is a "glycoprotein present in the plasma that is converted into thrombin by extrinsic thromboplastin during the second stage of blood clotting; called also factor II".

## References

1. ↑ "prothrombin." *Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition*. 2003. Saunders, an imprint of Elsevier, Inc 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/prothrombin>
Quantum yield

**Quantum yield** (***Φ***) refers to the "number of defined events occurring per photon absorbed by the system".

## 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.
Private key

A **private key** or **secret key** may refer to "0ne of two keys used in public key cryptography and held privately by the recipient of encrypted data, typically used to sign digital signatures and to decrypt data that was encoded using the recipient's public key".

## References

1. ↑ "private key." *American Heritage Dictionary of the English Language, Fifth Edition*. 2011. Houghton Mifflin Harcourt Publishing Company 13 Dec. 2015 http://www.thefreedictionary.com/private+key
RNA polymerase III

**RNA polymerase III** is an enzyme used by the cell to transcribe ribosomal RNA genes.

## Further Reading

* Jasiak, Anna J., Karim-Jean Armache, Birgit Martens, Ralf-Peter Jansen, and Patrick Cramer. "Structural Biology of RNA Polymerase III: Subcomplex C17/25 X-Ray Structure and 11 Subunit Enzyme Model." *Molecular Cell* 23.1 (2006): 71-81. Print.
* Lorenzen, Kristina, Alessandro Vannini, Patrick Cramer, and Albert J. Heck. "Structural Biology of RNA Polymerase III: Mass Spectrometry Elucidates Subcomplex Architecture." *Structure* 15.10 (2007): 1237-245. Print.
* Nikitina, T. V., and L. I. Tishchenko. "RNA Polymerase III Transcription Machinery: Structure and Transcription Regulation." *Molecular Biology* 39.2 (2005): 161-72. Print.

## References

1. ↑ Kaushansky, K. "Glossary of Molecular Biology Terminology." *Hematology* 2002.1 (2000): 490-509. Print.
PSSM

A **Position-Specific Scoring Matrix** (**PSSM**) is a "profile that gives the log-odds score for finding a particular matching amino acid in a target sequence".

## References

1. ↑ Fassler J, Cooper P. *BLAST Glossary*. 2011 Jul 14. In: BLAST® Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2008-. Available from: http://www.ncbi.nlm.nih.gov/books/NBK62051/
Restricted Boltzmann machine

A **restricted Boltzmann machine** (**RBM**) is a "probabilistic
graphical model[] that can be interpreted as [a] stochastic neural network[]".

## Further Reading

* Martens, James, Arkadev Chattopadhya, Toni Pitassi, and Richard Zemel. "On the Representational Efficiency of Restricted Boltzmann Machines." *Advances in Neural Information Processing Systems* 26 (2013): 2877-885. Print.

## References

1. ↑ Fischer, Asja, and Christian Igel. "An Introduction to Restricted Boltzmann Machines." *Progress in Pattern Recognition, Image Analysis, Computer Vision and Applications: 17th Iberoamerican Congress on Pattern Recognition, CIARP 2012, Buenos Aires, Argentina, September 3-6, 2012: Proceedings*. Ed. Luis Alvarez, Marta Mejail, Luis Gomez, and Julio Jacobo. Vol. 7441. Berlin: SpringerLink, 2012. 14-36. Print. Lecture Notes in Computer Science.
SWISS-MODEL

**SWISS-MODEL** (also known as the **SWISS-MODEL Workspace**, not to be confused with the SWISS-MODEL Repository) is a "fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer)".

## References

1. ↑ "Home Page." *SWISS-MODEL*. Swiss Institute of Bioinformatics (SIB), n.d. Web. 19 Sept. 2015.
Regular macromolecule

A **regular macromolecule** is a "macromolecule, the structure of which essentially comprises the repetition of a single constitutional unit with all units connected identically with respect to directional sense".

## References

1. ↑ Jenkins, A. D., P. Kratochvìl, R. F. T. Stepto, and U. W. Suter. "Glossary of Basic Terms in Polymer Science." *International Union of Pure and Applied Chemistry*. International Union of Pure and Applied Chemistry, 25 Oct. 1999. Web. 06 June 2015.
PhylomeDB

**PhylomeDB** is a "public database for complete catalogs of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees".

## References

1. ↑ "Welcome to PhylomeDB 4!" *PhylomeDB V4*. Comparative Genomics Group at CRG, n.d. Web. 07 June 2015.
Nucleophile

A **nucleophile** (or **nucleophilic reagent**) is a "reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons".

## 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.
Nucleotide

A **nucleotide** is "one of the structural components, or building blocks, of DNA and RNA" and "consists of a base (one of four chemicals: adenine, thymine, guanine, and cytosine) plus a molecule of sugar and one of phosphoric acid".

## References

1. ↑ "Nucleotide." *NCBI*. U.S. National Library of Medicine, 29 Sept. 1999. Web. 30 June 2015.
Path

A **path** is a "list of vertices of a graph where each vertex has an edge from it to the next vertex".

## References

1. ↑ Paul E. Black, "path", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 29 July 2004. (accessed 21 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/path.html
Pfam

The **Pfam** database is a "large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)".

## Release History

* Pfam 30.0 (June 2016)
* Pfam 29.0 (December 2015)
* Pfam 28.0 (May 2015)
* Pfam 27.0 (March 2013)
* Pfam 26.0 (November 2011)
* Pfam 25.0 (March 2011)
* Pfam 24.0 (July 2009)
* Pfam 23.0 (July 2008)
* Pfam 22.0 (June 2007)
* Pfam 21.0 (November 2006)
* Pfam 20.0 (April 2006)
* Pfam 19.0 (November 2005)
* Pfam 18.0 (July 2005)
* Pfam 17.0 (March 2005)
* Pfam 16.0 (October 2004)
* Pfam 15.0 (August 2004)
* Pfam 14.0 (May 2004)
* Pfam 13.0 (April 2004)
* Pfam 12.0 (January 2004)
* Pfam 11.0 (October 2003)
* Pfam 10.0 (July 2003)
* Pfam 9.0 (May 2003)
* Pfam 8.0 (February 2003)
* Pfam 7.8 (November 2002)
* Pfam 7.7 (October 2002)
* Pfam 7.6 (September 2002)
* Pfam 7.5 (August 2002)
* Pfam 7.4 (July 2002)
* Pfam 7.3 (May 2002)
* Pfam 7.2 (April 2002)
* Pfam 7.1 (March 2002)
* Pfam 7.0 (January 2002)
* Pfam 6.6 (August 2001)
* Pfam 6.5 (August 2001)
* Pfam 6.4 (May 2001)
* Pfam 6.3 (May 2001)
* Pfam 6.2 (April 2001)
* Pfam 6.1 (March 2001)
* Pfam 6.0 (January 2001)
* Pfam 5.5 (September 2000)
* Pfam 5.4 (June 2000)
* Pfam 5.3 (May 2000)
* Pfam 5.2 (March 2000)
* Pfam 5.1 (February 2000)
* Pfam 5.0 (January 2000)
* Pfam 4.4 (November 1999)
* Pfam 4.3 (September 1999)
* Pfam 4.2 (August 1999)
* Pfam 4.1 (July 1999)
* Pfam 4.0 (May 1999)
* Pfam 3.4 (January 1999)
* Pfam 3.3 (December 1998)
* Pfam 3.2 (October 1998)
* Pfam 3.1 (September 1998)
* Pfam 3.0 (July 1998)
* Pfam 2.1 (October 1997)
* Pfam 2.0 (March 1997)
* Pfam 1.0 (April 1996)
* Pfam 0.2 (January 1996)

## References

1. ↑ 1.0 1.1 1.2 "Home Page." *Pfam*. European Molecular Biology Laboratory, June 2016. Web. 15 Nov. 2016.
2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 2.15 2.16 2.17 2.18 2.19 2.20 2.21 2.22 2.23 2.24 2.25 2.26 2.27 2.28 2.29 2.30 2.31 2.32 2.33 2.34 2.35 2.36 2.37 2.38 2.39 2.40 2.41 2.42 2.43 2.44 2.45 2.46 2.47 2.48 2.49 2.50 2.51 2.52 2.53 2.54 2.55 The Pfam Consortium. "PFAM : Multiple Alignments and Profile HMMs of Protein Domains - RELEASE 28.0." N.p., 2015. Web. 15 Nov. 2016.
3. ↑ Finn, Robert D., Alex Bateman, Joey Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John Tate, and Marco Punta. "Pfam: The Protein Families Database." *Nucleic Acids Research* 42.D1 (2014): D222-230. Print.
4. ↑ Bateman, Alex, Ewan Birney, Lorenzo Cerruti, Richard Durbin, Laurence Etwiller, Sean R. Eddy, Sam Griffiths-Jones, Kevin L. Howe, Mhairi Marshall, and Erik L. L. Sonnhammer. "The Pfam Protein Families Database." *Nucleic Acids Research* 30.1 (2002): 276-80. Print.
5. ↑ Sonnhammer, Erik L. L., Sean R. Eddy, and Richard Durbin. "Pfam: A Comprehensive Database of Protein Domain Families Based on Seed Alignments." *Proteins: Structure, Function, and Genetics* 28.3 (1997): 405-20. Print.
P versus NP problem

The **P versus NP problem** is the "determination of whether all NP-problems are actually P-problems. If P and NP are not equivalent, then the solution of NP-problems requires (in the worst case) an exhaustive search, while if they are, then asymptotically faster algorithms may exist.

The answer is not currently known, but determination of the status of this question would have dramatic consequences for the potential speed with which many difficult and important problems could be solved".

## References

1. ↑ Weisstein, Eric W. "P Versus NP Problem." From *MathWorld*--A Wolfram Web Resource. http://mathworld.wolfram.com/PVersusNPProblem.html
RxNorm

**RxNorm** is a "normalized naming system for generic and branded drugs and a tool for supporting semantic interoperation between drug terminologies and pharmacy knowledge base systems".

## References

1. ↑ "RxNorm Overview." *U.S National Library of Medicine*. U.S. National Library of Medicine, n.d. Web. 04 Sept. 2015.
Plant molecular biology

**Plant molecular biology** is the "study of the molecular basis of plant life. It is particularly concerned with the processes by which the information encoded in the genome is manifested as structures, processes and behaviours".

## References

1. ↑ "Plant Molecular Biology." *Nature.com*. Nature Publishing Group, n.d. Web. 12 June 2015.
Phenol

Generally speaking, **phenol** or **phenolic** (sometimes referred to as a **phenolic compound**) refers to "any of a class of aromatic organic compounds having at least one hydroxyl group attached directly to the benzene ring".

## External Links

* Chapter 1 - FAMILIES OF PHENOLIC COMPOUNDS AND MEANS OF CLASSIFICATION

## References

1. ↑ "phenol." *American Heritage Dictionary of the English Language, Fifth Edition*. 2011. Houghton Mifflin Harcourt Publishing Company 4 Oct. 2015 http://www.thefreedictionary.com/phenol
Pancreas

The **pancreas** is a "large gland behind the stomach that secretes digestive enzymes into the duodenum".

## External Links

* What Is The Pancreas? - The Sol Goldman Pancreatic Cancer Research Center

## References

1. ↑ "Definition of Pancreas in English." *Oxford Dictionary (American English) (US)*. Oxford University Press, n.d. Web. 11 Sept. 2015.
Optical purity

**Optical purity** refers to the "ratio of the observed optical rotation of a sample consisting of a mixture of enantiomers to the optical rotation of one pure enantiomer".

## 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.
Triosephosphate isomerase

**Triosephosphate isomerase** or **triose phosphate isomerase** (**TIM**; sometimes also referred to as **phosphotriose isomerase**) is an "isomerizing enzyme that catalyzes the reversible interconversion of D-glyceraldehyde 3-phosphate and dihydroxyacetone phosphate, a reaction of importance in glycolysis and gluconeogenesis; a deficiency of this enzyme will result in hemolytic anemia and severe neurologic deficits".

## External Links

* Triose Phosphate Isomerase Structure & Mechanism - Proteopedia, life in 3D

## References

1. ↑ "Triose phosphate isomerase." *Farlex Partner Medical Dictionary*. 2012. Farlex 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/Triose+phosphate+isomerase>
PyMOL

**PyMOL** is a "Python-enhanced molecular graphics tool" which "excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories".

## External Links

* PyMOL | www.pymol.org
* PyMOLWiki

## References

1. ↑ Bell, Blaine, Silverstein, and Thomas Holder. "PyMOL Molecular Graphics System." *SourceForge*. Slashdot Media, 04 May 2015. Web. 11 Sept. 2015.
Noncompetitive inhibition

**Noncompetitive inhibition** refers to the "inhibition of enzyme activity by substances that combine with the enzyme at a site other than that utilized by the substrate".

## References

1. ↑ "noncompetitive inhibition." *Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition*. 2003. Saunders, an imprint of Elsevier, Inc 1 Nov. 2015 http://medical-<dictionary.thefreedictionary.com/competitive+inhibition>
Synchrotron

A **synchrotron** is an "accelerator in which charged particles are accelerated around a fixed circular path by an electric field and held to the path by an increasing magnetic field".

## References

1. ↑ "synchrotron." *American Heritage Dictionary of the English Language, Fifth Edition*. 2011. Houghton Mifflin Harcourt Publishing Company 17 Dec. 2015 <http://www.thefreedictionary.com/synchrotron>
TRNA

**tRNA** (**transfer RNA**) refers to "any of a class of small, cloverleaf forms of RNA that transfer unattached amino acids in the cell cytoplasm to the ribosomes for protein synthesis".

## References

1. ↑ "tRNA." *Random House Kernerman Webster’s College Dictionary*. 2010. 2010 K Dictionaries Ltd. Copyright 2005, 1997, 1991 by Random House, Inc. 23 Oct. 2015 <http://www.thefreedictionary.com/tRNA>
Pairwise alignment

A **pairwise alignment** is an alignment which consists of two aligned sequences and is "typically produced as the output of a database search".

## 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/
Recursion

**Recursion** is an "algorithmic technique where a function, in order to accomplish a task, calls itself with some part of the task".

## References

1. ↑ Paul E. Black and Patrick Rodgers, "recursion", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 30 September 2013. (accessed 16 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/recursion.html
Optimal alignment

An **optimal alignment** of two sequences is the alignment "with the highest score under a given scoring system".

## 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/
RRNA

**rRNA** (**ribosomal RNA**) is the "type of RNA thought to be transcribed from DNA in the nucleoli of cell nuclei, subsequently forming the component of ribosomes on which the translation of messenger RNA into protein chains is accomplished".

## References

1. ↑ "ribosomal RNA." *American Heritage Dictionary of the English Language, Fifth Edition*. 2011. Houghton Mifflin Harcourt Publishing Company 23 Oct. 2015 <http://www.thefreedictionary.com/ribosomal+RNA>
Rosetta Code

**Rosetta Code** is a wiki which focuses on programming chrestomathy, i.e. presenting "solutions to the same task in as many different [programming] languages as possible ... [in order] to demonstrate how languages are similar and different, and to aid a person with a grounding in one approach to a problem in learning another".

## References

1. ↑ "Rosetta Code." *Rosetta Code*. Semantic MediaWiki, 5 Aug. 2011. Web. 13 Oct. 2015.
Open addressing

**Open addressing** or **closed hashing** refers to a "class of collision resolution schemes in which all items are stored within the hash table. In case of collision, other positions are computed, giving a probe sequence, and checked until an empty position is found. Some ways of computing possible new positions are less efficient because of clustering".

## References

1. ↑ Paul E. Black, "open addressing", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 3 July 2006. (accessed 12 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/openAddressing.html
Ternary search tree

A **ternary search tree** (**TST**; sometimes referred to as a **prefix tree**) is a "3-way tree where every node's left subtree has keys less than the node's key, every middle subtree has keys equal to the node's key, and every right subtree has keys greater than the node's key. If the key is a multikey (string, array, list, etc.), the middle subtree organizes by the next subkey (character, array or list item, etc.)".

## References

1. ↑ Paul E. Black, "ternary search tree", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 13 January 2014. (accessed 12 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/ternarySearchTree.html
Protein kinase

A **protein kinase** is an "enzyme that catalyzes the phosphorylation of serine, threonine, or tyrosine groups in enzymes or other proteins, using ATP as a phosphate donor".

## References

1. ↑ "protein kinase." *Dorland's Medical Dictionary for Health Consumers*. 2007. Saunders, an imprint of Elsevier, Inc 31 Oct. 2015 <http://medical-dictionary.thefreedictionary.com/protein+kinase>
Substitution

A **substitution** is the "presence of a non-identical amino acid at a given position in an alignment".

## References

1. ↑ Fassler J, Cooper P. *BLAST Glossary*. 2011 Jul 14. In: BLAST® Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2008-. Available from: http://www.ncbi.nlm.nih.gov/books/NBK62051/
RiceGAAS

**RiceGAAS** (**Rice Genome Automated Annotation System**) is a "rice genome automated annotation system. This system integrates programs for prediction and analysis of protein-coding gene structure".

## References

1. ↑ "RiceGAAS." *RiceGAAS: Rice Genome Automated Annotation System*. Ministry of Agriculture, Forestry and Fisheries of Japan, 16 Sept. 2008. Web. 20 July 2015.
TreeBASE

**TreeBASE** is a "repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis".

## References

1. ↑ "TreeBASE Web." *TreeBASE Web*. N.p., Apr. 2014. Web. 07 June 2015.
ORFeomics

**ORFeomics** is the study of the ORFeome which refers to the totality of DNA sequences which begin with the start codon ATG, end with a nonsense codon, and contain no stop codon.

## References

1. ↑ Lee, Jae K., ed. *Statistical Bioinformatics: A Guide for Life and Biomedical Science Researchers*. Hoboken: Wiley, 2010. Print.
PacBio Bioinformatics Training Wiki

The **PacBio Bioinformatics Training Wiki** is a GitHub page which provides "resources for learning more about PacBio data and bioinformatics analysis, and includes content suitable for both beginners and experts".

## References

1. ↑ Ripp, Frank. "PacificBiosciences/Bioinformatics-Training." *GitHub*. GitHub, Inc., 17 July 2014. Web. 10 June 2015.
PDBalert

**PDBalert** is a "web-based automatic system that alerts users as soon as a PDB structure with homology to a protein of interest becomes available. Users can upload their personal protein sequences of interest. Once a week, when new proteins are released to the PDB database, PDBalert compares these with the users' sequences. When a significant match is found, the user is alerted by an email containing a link to the search results".

## References

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

**RNA-seq** (also stylized as **RNAseq** or **RNA-Seq**; abbreviated from **RNA sequencing**) or **whole transcriptome shotgun sequencing** (**WTSS**) is an "approach to transcriptome profiling that uses deep-sequencing technologies".

## References

1. ↑ Wang, Z., M. Gerstein, and M. Snyder. "RNA-Seq: A Revolutionary Tool for Transcriptomics." *Nature Reviews. Genetics*. 10.1 (2009): 57-63. Print.
Regulome

A regulome is a "complete set of regulons, where a regulon is the complete set of genes positively and negatively regulated by a specific regulatory protein".

## Further Reading

* Werner, Thomas. "Proteomics and Regulomics: The Yin and Yang of Functional Genomics." *Mass Spectrometry Reviews* 23.1 (2003): 25-33. Print.

## References

1. ↑ Andrade, Miguel A., and Michael A. Rudnicki. "Regulome." *Reviews in Cell Biology and Molecular Medicine* (2006): n. pag. Print.
Protein database

A **protein database** is "one or more datasets about proteins, which could include a protein's amino acid sequence, conformation, structure, and features such as active sites. Protein databases are compiled by the translation of DNA sequences from different gene databases and include structural information. They are an important resource because proteins mediate most biological functions".

## References

1. ↑ "Protein Databases." *Nature.com*. Nature Publishing Group, 2015. Web. 07 June 2015.
X-ray powder diffraction

**X-ray powder diffraction** (**XRD**) is an "analytical technique primarily used for phase identification of a crystalline material [that] can provide information on unit cell dimensions".

## References

1. ↑ Dutrow, Barbara L., and Christine M. Clark. "X-ray Powder Diffraction (XRD)." *Geochemical Instrumentation and Analysis*. Science Education Resource Center at Carleton College, 20 June 2015. Web. 14 Sept. 2015.
Phyloproteomics

**Phyloproteomics** is an "analytical tool that solves the issue of comparability between proteomic analyses, utilizes a total spectrum-parsing algorithm, and produces biologically meaningful classification of specimens".

## References

1. ↑ Abu-Asab, Mones, Mohamed Chaouchi, and Hakima Amri. "Phyloproteomics: What Phylogenetic Analysis Reveals about Serum Proteomics." *Journal of Proteome Research* 5.9 (2006): 2236-240. Print.
PSI-BLAST

**PSI-BLAST** (**Position-Specific Iterative BLAST**) is an "iterative search using the protein BLAST algorithm. A profile is built after the initial search that is then used in subsequent searches. The process may be repeated, if desired, with new sequences found in each cycle used to refine the profile".

## References

1. ↑ Fassler, Jan, and Peter Cooper. "PSI-BLAST." *BLAST Glossary*. U.S. National Library of Medicine, 14 July 2011. Web. 05 June 2015.
Random forest

A **random forest** (**RF**) is a "meta estimator that fits a number of decision tree classifiers on various sub-samples of the dataset and use averaging to improve the predictive accuracy and control over-fitting".

## References

1. ↑ "3.2.4.3.1. Sklearn.ensemble.RandomForestClassifier." *Scikit-learn 0.17.1 Documentation*. Scikit-learn Developers, n.d. Web. 20 June 2016.
Polynomial time

**Polynomial time** refers to "when the execution time of a computation, *m*(*n*), is no more than a polynomial function of the problem size, *n*. More formally *m*(*n*) = *O*(*nk*) where *k* is a constant".

## References

1. ↑ Paul E. Black, "polynomial time", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 13 August 2004. (accessed 13 December 2015) Available from: http://www.nist.gov/dads/HTML/polynomialtm.html
Perl and Unix for Bioinformatics

***Perl and Unix for Bioinformatics*** is a course offered by PerlSource Informatics that gives students "exposure to standard bioinformatics tools and techniques that can be applied to such diverse tasks as genome annotation, comparative genomics, [and] new target identification for drug discovery".

## References

1. ↑ "Perl and Unix for Bioinformatics." *ISCB*. International Society for Computational Biology, Inc., 27 Mar. 2011. Web. 08 June 2015.
SAM format

**SAM** (**Sequence Alignment/Map**) **format** is a "generic format for storing large nucleotide sequence alignments". It is a "TAB-delimited text format consisting of a header section, which is optional, and an alignment section. If present, the header must be prior to the alignments. Header lines start with ‘@’, while alignment lines do not. Each alignment line has 11 mandatory fields for essential alignment information such as mapping position, and variable number of optional fields for flexible or aligner specific information".

## References

1. ↑ "SAMtools." *SourceForge*. Slashdot Media, 12 Sept. 2012. Web. 14 Oct. 2015.
2. ↑ The SAM/BAM Format Specification Working Group. "Sequence Alignment/Map Format Specification." *GitHub*. GitHub, Inc., 28 Aug. 2015. Web. 14 Oct. 2015.
Proportional reporting ratio

A **proportional reporting ratio** (**PRR**) is the "proportion of spontaneous reports for a given drug that are linked to a specific adverse outcome, divided by the corresponding proportion for all or several other drugs".

## Further Reading

* Tatonetti, Nicholas P. et al. “Data-Driven Prediction of Drug Effects and Interactions.” *Science Translational Medicine* 4.125 (2012): 125ra31. PMC. Web. 4 Sept. 2015.

## References

1. ↑ Rothman, Kenneth J., Stephan Lanes, and Susan T. Sacks. "The Reporting Odds Ratio and Its Advantages over the Proportional Reporting Ratio." *Pharmacoepidemiology and Drug Safety* 13.8 (2004): 519-23. Print.
UniProtKB/Swiss-Prot

**UniProtKB/Swiss-Prot** (often referred to simply as **Swiss-Prot**) is the "manually annotated and reviewed section of the UniProt Knowledgebase (UniProtKB). It is a high quality annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions. Since 2002, it is maintained by the UniProt consortium and is accessible via the UniProt website".

## References

1. ↑ "UniProtKB/Swiss-Prot." *ExPASy*. SIB Swiss Institute of Bioinformatics, n.d. Web. 05 June 2015.
Protein kinase A

**Protein kinase A** (**PKA**) or **cAMP-dependent protein kinase** is a "tetrameric protein composed of two regulatory subunits that bind cAMP, and two catalytic subunits that catalyze the transfer of a phosphoryl group from ATP to a target enzyme".

## References

1. ↑ "protein kinase A." *Saunders Comprehensive Veterinary Dictionary*, 3 ed.. 2007. Elsevier, Inc. 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/Protein+kinase+A>
Open Annotation Data Model

The **Open Annotation Data Model** (also referred to as the **Open Annotation Core Data Model** or **oa Data Model**) is a specification for an interoperable framework for creating associations between related resources and annotations which utilizes a methodology that conforms to the architecture of the World Wide Web.

## References

1. ↑ Bradshaw, Shannon, Dan Brickley, Leyla Jael García Castro, Timothy Clark, Phil Desenne, Timothy Cole, Anna Gerber, Antoine Isaac, Jacob Jett, Thomas Habing, Bernhard Haslhofer, Sebastian Hellmann, Jane Hunter, Randall Leeds, Andrew Magliozzi, Bob Morris, Paul Morris, Jacco Van Ossenbruggen, Stian Soiland-Reyes, James Smith, and Dan Whaley. "Open Annotation Data Model." *Open Annotation Collaboration*. Ed. Robert Sanderson, Paolo Ciccarese, and Herbert Van De Sompel. The Open Annotation Collaboration and the Board of Trustees of the University of Illinois, 08 Feb. 2013. Web. 01 Oct. 2015.
ORF

An **ORF** (**open reading frame**) is a "stretch of a chromosome that could encode a polypeptide sequence, i.e., the region between a methionine codon (ATG) that could serve to initiate protein translation, and the inframe stop codon downstream of it".

## References

1. ↑ Kaushansky, K. "Glossary of Molecular Biology Terminology." *Hematology* 2002.1 (2000): 490-509. Print.
Phylogeny

**Phylogeny** may refer to either the "evolutionary development and history of a species or trait of a species or of a higher taxonomic grouping of organisms" or "model or diagram delineating such an evolutionary history".

## References

1. ↑ "phylogeny." *American Heritage Dictionary of the English Language, Fifth Edition*. 2011. Houghton Mifflin Harcourt Publishing Company 22 Oct. 2015 <http://www.thefreedictionary.com/phylogeny>
Ornithine

**Ornithine** is an "amino acid obtained from arginine by splitting of urea; it is an intermediate in urea biosynthesis".

## References

1. ↑ "ornithine." *Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition*. 2003. Saunders, an imprint of Elsevier, Inc 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/ornithine>
Pharmacovigilance

**Pharmacovigilance** (**PV**) or **pharmacosurveillance** refers to the "science and activities relating to the detection, assessment, understanding and prevention of adverse effects or any other drug-related problem".

## References

1. ↑ "Pharmacovigilance." *WHO*. WHO, 2015. Web. 03 Sept. 2015.
2. ↑ "Introduction to Drug Utilization Research: Chapter 1: What Is Drug Utilization Research and Why Is It Needed?: 1.1. Definition and Domains." *Essential Medicines and Health Products Information Portal*. WHO, 30 July 2015. Web. 02 Oct. 2015.
Thermocycler

A **thermocycler** (variously referred to as a **thermal cycler**, **DNA amplifier**, or **PCR machine**) is an "instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time".

## References

1. ↑ "Thermocycler at UCSF?" *UCSF Cores Search*. The Regents of the University of California, 2012. Web. 22 Sept. 2015.
Query sequence

The **query sequence** (often referred to simply as the **query**) is the "input sequence ... to which all of the entries in a database are to be compared".

## References

1. ↑ Fassler J, Cooper P. *BLAST Glossary*. 2011 Jul 14. In: BLAST® Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2008-. Available from: http://www.ncbi.nlm.nih.gov/books/NBK62051/
SHELX

**SHELX** is a "set of programs for the determination of small (SM) and macromolecular (MM) crystal structures by single crystal X-ray and neutron diffraction".

## See Also

* SHELXT
* SHELXS
* SHELXL
* CIFTAB
* ShredCIF
* SHELXC
* SHELXD
* SHELXE
* AnoDe

## References

1. ↑ Sheldrick, George. "The SHELX Homepage." *The SHELX Homepage*. George Sheldrick, 19 July 2015. Web. 17 Dec. 2015.
R

**R** (also referred to sometimes as the **R Project**) is a "free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS". It is also a " GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues".

## References

1. ↑ "R: The R Project for Statistical Computing" *R*. The R Foundation, n.d. Web. 06 June 2015.
2. ↑ "What Is R?" *R*. The R Foundation, n.d. Web. 06 June 2015.
Putrescine

**Putrescine** (**1,4-Diaminobutane**; also referred to as **tetramethylenediamine**) is a "poisonous polyamine formed from the amino acid arginine during putrefaction; found in urine and feces; in certain cells, putrescine is a precursor to γ-aminobutyrate".

## References

1. ↑ "putrescine." *Farlex Partner Medical Dictionary*. 2012. Farlex 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/putrescine>
Shotgun sequencing

**Shotgun sequencing** or **shotgun cloning** is a "sequencing method that involves randomly sequenced cloned pieces of the genome, with no foreknowledge of where the piece originally came from".

## References

1. ↑ "Shotgun Sequencing - Glossary Entry." *Genetics Home Reference*. National Institutes of Health, 01 Sept. 2015. Web. 03 Sept. 2015.
Runtime

**Runtime**, **run-time**, or **run time** (also referred to as **execution time**) refers to a process which is occurring while a program is executing or to the length of time it takes to execute a software program.

## External Links

* What is runtime? A Webopedia Definition

## References

1. ↑ "run-time." *WordNet 3.0, Farlex clipart collection*. 2003-2008. Princeton University, Clipart.com, Farlex Inc. 14 Oct. 2015 <http://www.thefreedictionary.com/run-time>
Pathguide

**Pathguide** is a pathway resource list which contains information about "547 biological pathway related resources and molecular interaction related resources".

## Genetic Interaction Networks

* AraNet
* BIND
* BioGRID
* BiologicalNetworks
* CADgene
* CID
* DroID
* DRYGIN
* FLIGHT
* FlyBase
* FlyMine
* FunCoup
* GeneMANIA
* GeneNet
* GeneOrienteer
* GenePath
* GermOnline
* IMP
* Interactome
* KNIFE
* MetaCore
* MIPS CYGD
* Pigment Cell Gene Resource
* Predictive Networks
* PSICQUIC
* Snap
* TetraFGD
* WormBase

## Protein Sequence Focused

* ABCdb
* ASC
* HDR
* IMG
* InBase
* MEROPS
* MitoProteome
* ModBase
* MotifMap
* NCBI BioSystems
* NRR
* ORDB
* PANTHER
* PATRIC
* PhosphoBase
* PMP
* PROFESS
* PSP
* REBASE
* SCOPEC
* Sentra
* SIMAP
* T1DBase
* TGDB
* XPD

## Other

* AANT
* AARSDB
* HCNet
* IHOP
* MedGene
* MeRNA
* NPIDB
* NPInter
* PRD
* Precise
* PRID
* PRIDB
* ProNIT
* Rhea
* SELEX\_DB
* TCDB
* TransportDB

## References

1. ↑ Bader, Gary, and Sylva Donaldson. "Pathguide: The Pathway Resource List." *Pathguide*. Sander Group at Memorial Sloan-Kettering Cancer Center and the Bader Lab, Aug. 2013. Web. 17 July 2015.
Species

A **species** (or **biological species**) is considered by many biologists to be synonymous with the phrase **Biological Species Concept** (**BSC**), that is, a species is a group "of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups".

**Species** might also refer to a chemical species.

## References

1. ↑ "What Is a Species? - Encyclopedia of Life." *Encyclopedia of Life*. Encyclopedia of Life, n.d. Web. 22 June 2015.
Squeezate

"**Squeezate**" refers to the solution that resulted from the squeezing of the excised bioluminescent tissues of the jellyfish (*Aequorea victoria*) through a cotton bag, in the experiments performed by Osamu Shimomura of Princeton University.

## Further Reading

* 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.
Systems biology

**Systems biology** is the "study of the behavior of complex biological organization and processes in terms of the molecular constituents".

## External Links

* Systems Biology as Defined by NIH|NIH Intramural Research Program
* Definition of Systems Biology - Center for Biological Systems Analysis
* What is systems biology?

## Further Reading

* Nelson, David L., and Michael M. Cox. *Lehninger Principles of Biochemistry*. 5th ed. New York City: W. H. Freeman, 2011. Print.

## References

1. ↑ Kirschner, Marc W. "The Meaning of Systems Biology." *Cell* 121.4 (2005): 503-04. Print.
~

"**~**" can refer to proportionality.

"**~**" can also refer to asymptotic equivalence.

"**~**" may also refer to the tilde approximation.

## References

1. ↑ 1.0 1.1 1.2 Paul E. Black, "~", 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/sim.html>
Peptide isoelectric point

A **peptide isoelectric point** or **protein isoelectric point** is a pH in which the net charge of a given protein is zero".

## Calculation

The isoelectric point can be calculated by plugging in zero for *Z* (i.e. making the net charge of the peptide zero) and then solving for the pH by approximation (accuracy ± 0.01).

## External Links

* Peptide Calculator Details v2
* Calculating approximate isoelectric points for amino acids and peptides

## References

1. ↑ Kozlowski, Lukasz P. "Theoretical Basis of Isoelectric Point Calculation, i.e. How to Calculate Isoelectric Point of Protein." *Calculation of Protein Isoelectric Point*. Lukasz P. Kozlowski, 2013. Web. 08 Sept. 2015.
2. ↑ "BACHEM'S PEPTIDE CALCULATOR." *Bachem*. Avenit AG, Internetagentur, n.d. Web. 8 Sept. 2015.
Transcriptomics

**Transcriptomics** is the "study of the transcriptome—the complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell—using high-throughput methods, such as microarray analysis. Comparison of transcriptomes allows the identification of genes that are differentially expressed in distinct cell populations, or in response to different treatments".

## References

1. ↑ "Transcriptomics." Nature.com. Nature Publishing Group, 2015. Web. 08 June 2015.
Van der Waals forces

**Van der Waals forces** (sometimes referred to as **van der Waals interaction**) are "attractive or repulsive forces between molecular entities (or between groups within the same molecular entity) other than those due to bond formation or to the electrostatic interaction of ions or of ionic groups with one another or with neutral molecules".

## 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.
Undecidable problem

An **undecidable problem** is a "problem that cannot be solved for all cases by any algorithm whatsoever---equivalently, whose associated language cannot be recognized by a Turing machine that halts for all inputs".

## References

1. ↑ Algorithms and Theory of Computation Handbook, CRC Press LLC, 1999, "undecidable problem", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 9 August 2004. (accessed 13 December 2015) Available from: http://www.nist.gov/dads/HTML/undecidableProblem.html
Thrombin

**Thrombin** is the "activated form of coagulation factor II (prothrombin), which catalyzes the conversion of fibrinogen to fibrin".

## References

1. ↑ "thrombin." *Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition*. 2003. Saunders, an imprint of Elsevier, Inc 1 Nov. 2015 <http://medical-dictionary.thefreedictionary.com/thrombin>
Specific activity

In enzymology, **specific activity** (**SA**) refers to the "number of enzyme units per ml divided by the concentration of protein in mg/ml".

In biochemistry, **specific activity** refers to the "number of micromoles (μmol) of a substrate transformed by an enzyme preparation per minute per milligram of protein at 25°C; a measure of enzyme purity".

In radiochemistry, **specific activity** refers to the activity of a material divided by the mass of the material for a specified isotope, or mixture of isotopes.

## References

1. ↑ *Enzyme Units, Activity and Specific Activity Explained*. Rep. N.p.: Innova Biosciences, n.d. Print.
2. ↑ Nelson, David L., and Michael M. Cox. *Lehninger Principles of Biochemistry*. 5th ed. New York City: W. H. Freeman, 2011. 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.
Southern blot

A **Southern blot** is a "DNA hybridization procedure in which one or more specific DNA fragments are detected in a larger population by hybridization to a complementary, labeled nucleic acid probe".

## References

1. ↑ Nelson, David L., and Michael M. Cox. *Lehninger Principles of Biochemistry*. 5th ed. New York City: W. H. Freeman, 2011. Print.
Rice Annotation Database

The **Rice Annotation Database** (**RAD**) is a "contig-oriented database for high-quality manual annotation of RGP, which can present non-redundant contig analyses by merging the accumulated PAC/BAC clones".

## References

1. ↑ "Annotation Database." *Rice Annotation Database*. Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Oct. 2004. Web. 20 July 2015.
Permutation

A **permutation** (also referred to as an **arrangement number** or **order**) is a "rearrangement of the elements of an ordered list *S* into a one-to-one correspondence with *S* itself".

## References

1. ↑ Weisstein, Eric W. "Permutation." From *MathWorld*--A Wolfram Web Resource. <http://mathworld.wolfram.com/Permutation.html>
Sorted array

A **sorted array** is an "array whose items are kept sorted, often so searching is faster".

## References

1. ↑ Paul E. Black, "sorted array", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 16 November 2009. (accessed 16 Oct. 2015) Available from: http://www.nist.gov/dads/HTML/sortedarray.html
Worst case

**Worst case** may refer to the "situation or input that forces an algorithm or data structure to take the most time or resources" or "having to do with this situation or input".

## References

1. ↑ Paul E. Black, "worst case", in *Dictionary of Algorithms and Data Structures* [online], Vreda Pieterse and Paul E. Black, eds. 12 August 2014. (accessed 15 Oct. 2015) Available from: <http://www.nist.gov/dads/HTML/worstcase.html>
Unnatural base pair

An **unnatural base pair** (**UBP**) is a designed subunit (or nucleobase) of DNA which is created in a laboratory and does not occur in nature. DNA sequences have been described which use newly created nucleobases to form a third base pair, in addition to the two base pairs found in nature, A-T (adenine-thymine) and G-C (guanine-cytosine).

## References

1. ↑ Leconte, Aaron M., Gil Tae Hwang, Shigeo Matsuda, Petr Capek, Yoshiyuki Hari, and Floyd E. Romesberg. "Discovery, Characterization, and Optimization of an Unnatural Base Pair for Expansion of the Genetic Alphabet." *Journal of the American Chemical Society* 130.7 (2008): 2336-343. Print.
Deep learning

**Deep learning** (variously referred to as **deep structured learning**, **hierarchical learning**, **deep machine learning**) is a "collection of algorithms used in machine learning, used to model high-level abstractions in data through the use of model architectures, which are composed of multiple nonlinear transformations".

## References

1. ↑ "Deep Learning." *Techopedia*. Techopedia Inc., n.d. Web. 9 June 2016.
Structural alignment

A **structural alignment** is a "sequence alignment produced by superposition of the three-dimensional structures of the respective proteins".

## 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/
URI

**URI** (**Uniform Resource Identifier**) is the "generic term for all types of names and addresses that refer to objects on the World Wide Web".

## References

1. ↑ Webopedia staff. "URI - Uniform Resource Locator." Webopedia. QuinStreet Inc., 2015. Web. 07 June 2015.
2. ↑ 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.
Β-sheet

A **β-sheet** (**beta-sheet** or **beta pleated sheet**) is a description of a "structural motif of secondary structure found in proteins. Beta-sheets are made of multiple beta-strands – polypeptide chains which have an almost fully extended shape. Multiple beta-strands are formed into a beta-sheets by hydrogen bonds between strands. In particular, this intermolecular hydrogen bonding occurs between the NH-group of individual amino acids in one strand and the CO-group of individual amino acids in the adjacent strand. The beta-sheet is the second most common structural motif in proteins after the alpha-helix".

## References

1. ↑ "EMBLog Bioinformatics Glossary." *EMBLog*. EMBLog, 2013. Web. 21 July 2015.
Spike and slab restricted Boltzmann machine

A **spike and slab restricted Boltzmann machine** (**ssRBM**, variously referred to as a **spike-and-slab RBM** or **spike and slab RBM**) is a restricted Boltzmann machine that is "characterized by having both a real-valued vector, the slab, and a binary variable, the spike, associated with each unit in the hidden layer".

## References

1. ↑ Courville, Aaron, James Bergstra, and Yoshua Bengio. "A Spike and Slab Restricted Boltzmann Machine." *Journal of Machine Learning Research* 15 (2010): 233-41. Print.