Type systemIn computer programming, a type system is a logical system comprising a set of rules that assigns a property called a type (for example, integer, floating point, string) to every "term" (a word, phrase, or other set of symbols). Usually the terms are various constructs of a computer program, such as variables, expressions, functions, or modules. A type system dictates the operations that can be performed on a term. For variables, the type system determines the allowed values of that term.
DNA sequencingDNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, DNA Genographic Projects and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics.
SequencingIn genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succinctly summarizes much of the atomic-level structure of the sequenced molecule. DNA sequencing DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. So far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger.
Shotgun sequencingIn genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs. Due to this size limit, longer sequences are subdivided into smaller fragments that can be sequenced separately, and these sequences are assembled to give the overall sequence.
Sanger sequencingSanger sequencing is a method of DNA sequencing that involves electrophoresis and is based on the random incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. After first being developed by Frederick Sanger and colleagues in 1977, it became the most widely used sequencing method for approximately 40 years. It was first commercialized by Applied Biosystems in 1986. More recently, higher volume Sanger sequencing has been replaced by next generation sequencing methods, especially for large-scale, automated genome analyses.
Massive parallel sequencingMassive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged between 1993 and 1998 and have been commercially available since 2005. These technologies use miniaturized and parallelized platforms for sequencing of 1 million to 43 billion short reads (50 to 400 bases each) per instrument run.
Exome sequencingExome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome). It consists of two steps: the first step is to select only the subset of DNA that encodes proteins. These regions are known as exons—humans have about 180,000 exons, constituting about 1% of the human genome, or approximately 30 million base pairs. The second step is to sequence the exonic DNA using any high-throughput DNA sequencing technology.
Whole genome sequencingWhole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. Whole genome sequencing has largely been used as a research tool, but was being introduced to clinics in 2014.
Type theoryIn mathematics, logic, and computer science, a type theory is the formal presentation of a specific type system, and in general, type theory is the academic study of type systems. Some type theories serve as alternatives to set theory as a foundation of mathematics. Two influential type theories that were proposed as foundations are Alonzo Church's typed λ-calculus and Per Martin-Löf's intuitionistic type theory. Most computerized proof-writing systems use a type theory for their foundation, a common one is Thierry Coquand's Calculus of Inductive Constructions.
PaperPaper is a thin sheet material produced by mechanically or chemically processing cellulose fibres derived from wood, rags, grasses, or other vegetable sources in water, draining the water through a fine mesh leaving the fibre evenly distributed on the surface, followed by pressing and drying. Although paper was originally made in single sheets by hand, almost all is now made on large machines—some making reels 10 metres wide, running at 2,000 metres per minute and up to 600,000 tonnes a year.
Coated paperCoated paper (also known as enamel paper, gloss paper, and thin paper) is paper that has been coated by a mixture of materials or a polymer to impart certain qualities to the paper, including weight, surface gloss, smoothness, or reduced ink absorbency. Various materials, including kaolinite, calcium carbonate, bentonite, and talc, can be used to coat paper for high-quality printing used in the packaging industry and in magazines. The chalk or china clay is bound to the paper with synthetic s, such as styrene-butadiene latexes and natural organic binders such as starch.
Strong and weak typingIn computer programming, one of the many ways that programming languages are colloquially classified is whether the language's type system makes it strongly typed or weakly typed (loosely typed). However, there is no precise technical definition of what the terms mean and different authors disagree about the implied meaning of the terms and the relative rankings of the "strength" of the type systems of mainstream programming languages.
Substructural type systemSubstructural type systems are a family of type systems analogous to substructural logics where one or more of the structural rules are absent or only allowed under controlled circumstances. Such systems are useful for constraining access to system resources such as , locks, and memory by keeping track of changes of state that occur and preventing invalid states. Several type systems have emerged by discarding some of the structural rules of exchange, weakening, and contraction: Ordered type systems (discard exchange, weakening and contraction): Every variable is used exactly once in the order it was introduced.
Permutation groupIn mathematics, a permutation group is a group G whose elements are permutations of a given set M and whose group operation is the composition of permutations in G (which are thought of as bijective functions from the set M to itself). The group of all permutations of a set M is the symmetric group of M, often written as Sym(M). The term permutation group thus means a subgroup of the symmetric group. If M = {1, 2, ..., n} then Sym(M) is usually denoted by Sn, and may be called the symmetric group on n letters.
TupleIn mathematics, a tuple is a finite sequence or ordered list of numbers or, more generally, mathematical objects, which are called the elements of the tuple. An n-tuple is a tuple of n elements, where n is a non-negative integer. There is only one 0-tuple, called the empty tuple. A 1-tuple and a 2-tuple are commonly called respectively a singleton and an ordered pair. Tuple may be formally defined from ordered pairs by recurrence by starting from ordered pairs; indeed, a n-tuple can be identified with the ordered pair of its (n − 1) first elements and its nth element.
PermutationIn mathematics, a permutation of a set is, loosely speaking, an arrangement of its members into a sequence or linear order, or if the set is already ordered, a rearrangement of its elements. The word "permutation" also refers to the act or process of changing the linear order of an ordered set. Permutations differ from combinations, which are selections of some members of a set regardless of order. For example, written as tuples, there are six permutations of the set {1, 2, 3}, namely (1, 2, 3), (1, 3, 2), (2, 1, 3), (2, 3, 1), (3, 1, 2), and (3, 2, 1).
Cyclic permutationIn mathematics, and in particular in group theory, a cyclic permutation is a permutation consisting of a single cycle. In some cases, cyclic permutations are referred to as cycles; if a cyclic permutation has k elements, it may be called a k-cycle. Some authors widen this definition to include permutations with fixed points in addition to at most one non-trivial cycle. In cycle notation, cyclic permutations are denoted by the list of their elements enclosed with parentheses, in the order to which they are permuted.
Parity of a permutationIn mathematics, when X is a finite set with at least two elements, the permutations of X (i.e. the bijective functions from X to X) fall into two classes of equal size: the even permutations and the odd permutations. If any total ordering of X is fixed, the parity (oddness or evenness) of a permutation of X can be defined as the parity of the number of inversions for σ, i.e., of pairs of elements x, y of X such that x < y and σ(x) > σ(y). The sign, signature, or signum of a permutation σ is denoted sgn(σ) and defined as +1 if σ is even and −1 if σ is odd.
Nominal type systemIn computer science, a type system is nominal, nominative, or name-based if compatibility and equivalence of data types is determined by explicit declarations and/or the name of the types. Nominal systems are used to determine if types are equivalent, as well as if a type is a subtype of another. Nominal type systems contrast with structural systems, where comparisons are based on the structure of the types in question and do not require explicit declarations.
Product typeIn programming languages and type theory, a product of types is another, compounded, type in a structure. The "operands" of the product are types, and the structure of a product type is determined by the fixed order of the operands in the product. An instance of a product type retains the fixed order, but otherwise may contain all possible instances of its primitive data types. The expression of an instance of a product type will be a tuple, and is called a "tuple type" of expression.
