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A biological network is a method of representing systems as complex sets of binary interactions or relations between various biological entities. [1] In general, networks or graphs are used to capture relationships between entities or objects. [1]
A drawing of a graph with 6 vertices and 7 edges. In mathematics and computer science, graph theory is the study of graphs, which are mathematical structures used to model pairwise relations between objects. A graph in this context is made up of vertices (also called nodes or points) which are connected by edges (also called arcs, links or lines).
A chain graph is a graph which may have both directed and undirected edges, but without any directed cycles (i.e. if we start at any vertex and move along the graph respecting the directions of any arrows, we cannot return to the vertex we started from if we have passed an arrow). Both directed acyclic graphs and undirected graphs are special ...
Graph analytics, or network analysis, is the study of graphs that represent connections between different objects. Graphs can represent all kinds of networks in biology such as protein-protein interaction networks, regulatory networks, Metabolic and biochemical networks and much more. There are many ways to analyze these networks.
The Systems Biology Graphical Notation (SBGN) is a standard graphical representation intended to foster the efficient storage, exchange and reuse of information about signaling pathways, metabolic networks, and gene regulatory networks amongst communities of biochemists, biologists, and theoreticians.
This is especially helpful in metabolomics, a branch of systems biology that uses mass spectrometry to measure metabolite distribution information, then uses the measured intensity to construct an image. [35] Popular software tools used in systems biology modeling include massPy, Cytosim, and PySB.
A graph with three vertices and three edges. A graph (sometimes called an undirected graph to distinguish it from a directed graph, or a simple graph to distinguish it from a multigraph) [4] [5] is a pair G = (V, E), where V is a set whose elements are called vertices (singular: vertex), and E is a set of unordered pairs {,} of vertices, whose elements are called edges (sometimes links or lines).
In computer science, a graph is an abstract data type that is meant to implement the undirected graph and directed graph concepts from the field of graph theory within mathematics. A graph data structure consists of a finite (and possibly mutable) set of vertices (also called nodes or points ), together with a set of unordered pairs of these ...