Heat mapA heat map (or heatmap) is a 2-dimensional data visualization technique that represents the magnitude of individual values within a dataset as a color. The variation in color may be by hue or intensity. "Heat map" is a relatively new term, but the practice of shading matrices has existed for over a century. Heat maps originated in 2D displays of the values in a data matrix. Larger values were represented by small dark gray or black squares (pixels) and smaller values by lighter squares.
K-nearest neighbors algorithmIn statistics, the k-nearest neighbors algorithm (k-NN) is a non-parametric supervised learning method first developed by Evelyn Fix and Joseph Hodges in 1951, and later expanded by Thomas Cover. It is used for classification and regression. In both cases, the input consists of the k closest training examples in a data set. The output depends on whether k-NN is used for classification or regression: In k-NN classification, the output is a class membership.
Sequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
Biomolecular structureBiomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary.
ShapeA shape or figure is a graphical representation of an object or its external boundary, outline, or external surface, as opposed to other properties such as color, texture, or material type. A plane shape or plane figure is constrained to lie on a plane, in contrast to solid 3D shapes. A two-dimensional shape or two-dimensional figure (also: 2D shape or 2D figure) may lie on a more general curved surface (a non-Euclidean two-dimensional space). Lists of shapes Some simple shapes can be put into broad categories.
Ribbon diagramRibbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organisation of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure, such as the balls for the oxygen atoms attached to myoglobin's active site in the adjacent figure. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Principal component analysisPrincipal component analysis (PCA) is a popular technique for analyzing large datasets containing a high number of dimensions/features per observation, increasing the interpretability of data while preserving the maximum amount of information, and enabling the visualization of multidimensional data. Formally, PCA is a statistical technique for reducing the dimensionality of a dataset. This is accomplished by linearly transforming the data into a new coordinate system where (most of) the variation in the data can be described with fewer dimensions than the initial data.
Map layoutMap layout, also called map composition or (cartographic) page layout, is the part of cartographic design that involves assembling various map elements on a page. This may include the map image itself, along with titles, legends, scale indicators, inset maps, and other elements. It follows principles similar to page layout in graphic design, such as balance, gestalt, and visual hierarchy. The term map composition is also used for the assembling of features and symbols within the map image itself, which can cause some confusion; these two processes share a few common design principles but are distinct procedures in practice.
Independent component analysisIn signal processing, independent component analysis (ICA) is a computational method for separating a multivariate signal into additive subcomponents. This is done by assuming that at most one subcomponent is Gaussian and that the subcomponents are statistically independent from each other. ICA is a special case of blind source separation. A common example application is the "cocktail party problem" of listening in on one person's speech in a noisy room.
