|
Metabolic Network Modelling
Metabolic network modelling, also known as metabolic network reconstruction or metabolic pathway analysis, allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways (such as glycolysis and the citric acid cycle) into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. This knowledge can then be applied to create novel biotechnology. In general, the process to build a reconstruction is as follows: # Draft a reconstruction # Refine the model # Convert mod ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
A Thaliana Metabolic Network
A, or a, is the first Letter (alphabet), letter and the first vowel of the Latin alphabet, Latin alphabet, used in the English alphabet, modern English alphabet, the alphabets of other western European languages and others worldwide. Its name in English is English alphabet#Letter names, ''a'' (pronounced ), plural English alphabet#Letter names, ''aes''. It is similar in shape to the Greek alphabet#History, Ancient Greek letter alpha, from which it derives. The Letter case, uppercase version consists of the two slanting sides of a triangle, crossed in the middle by a horizontal bar. The lowercase version can be written in two forms: the double-storey a and single-storey ɑ. The latter is commonly used in handwriting and fonts based on it, especially fonts intended to be read by children, and is also found in italic type. In English grammar, "English articles, a", and its variant "English articles#Indefinite article, an", are Article (grammar)#Indefinite article, indefinite arti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Flux Balance Analysis
Flux balance analysis (FBA) is a mathematical method for simulating metabolism in genome-scale reconstructions of metabolic networks. In comparison to traditional methods of modeling, FBA is less intensive in terms of the input data required for constructing the model. Simulations performed using FBA are computationally inexpensive and can calculate steady-state metabolic fluxes for large models (over 2000 reactions) in a few seconds on modern personal computers. The related method of metabolic pathway analysis seeks to find and list all possible pathways between metabolites. FBA finds applications in bioprocess engineering to systematically identify modifications to the metabolic networks of microbes used in fermentation processes that improve product yields of industrially important chemicals such as ethanol and succinic acid. It has also been used for the identification of putative drug targets in cancer and pathogens, rational design of culture media, and host–pathogen i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metabolic Network Reconstruction Process
Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transportation of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary (or intermediate) metabolism. Metabolic reactions may be categorized as ''catabolic'' – the ''breaking down'' of compounds (for example, of glucose to pyruvate by cel ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
National Center For Biotechnology Information
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper. The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine. NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics. GenBank NCBI had responsibility for making available the GenBank DNA seque ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LaTeX
Latex is an emulsion (stable dispersion) of polymer microparticles in water. Latexes are found in nature, but synthetic latexes are common as well. In nature, latex is found as a milky fluid found in 10% of all flowering plants (angiosperms). It is a complex emulsion that coagulates on exposure to air, consisting of proteins, alkaloids, starches, sugars, oils, tannins, resins, and gums. It is usually exuded after tissue injury. In most plants, latex is white, but some have yellow, orange, or scarlet latex. Since the 17th century, latex has been used as a term for the fluid substance in plants, deriving from the Latin word for "liquid". It serves mainly as defense against herbivorous insects. Latex is not to be confused with plant sap; it is a distinct substance, separately produced, and with different functions. The word latex is also used to refer to natural latex rubber, particularly non-vulcanized rubber. Such is the case in products like latex gloves, latex condoms ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GraphML
GraphML is an XML-based file format for graphs. The GraphML file format results from the joint effort of the graph drawing community to define a common format for exchanging graph structure data. It uses an XML-based syntax and supports the entire range of possible graph structure constellations including directed, undirected, mixed graphs, hypergraphs, and application-specific attributes.. Overview A GraphML file consists of an XML file containing a graph element, within which is an unordered sequence of node and edge elements. Each node element should have a distinct id attribute, and each edge element has source and target attributes that identify the endpoints of an edge by having the same value as the id attributes of those endpoints. Here is what a simple undirected graph with two nodes and one edge between them looks like: Additional features of the GraphML language allow its users to specify whether edges are directed or undirected, and to associ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Generative Modelling Language
Generative Modelling Language (GML) in computer graphics and generative computer programming is a very simple programming language for the concise description of complex 3D shapes. It follows the "Generative Modelling" paradigm, where complex datasets are represented by "lists of operations" rather than by lists of objects, which is for instance the case in a relational database. Overview Usual 3D file formats describe a virtual world in terms of geometric primitives. These may be cubes and spheres in a CSG tree, NURBS patches, a set of implicit functions, a triangle mesh, or just a cloud of points. The term "generative 3D modelling" describes a different paradigm for describing shape. The main idea is to replace 3D objects by object-generating operations: A shape is described by a sequence of processing steps, rather than the triangles which are the end result of applying these operations. Shape design becomes rule design. The approach can be generally applied to any shape r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SBGN
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. The system was created over several years by a community of biochemists, modelers and computer scientists. SBGN is made up of three orthogonal languages for representing different views of biological systems: ''Process Descriptions'', ''Entity Relationships'' and ''Activity Flows''. Each language defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules regarding the construction and interpretation of maps. Using these three notations, a life scientist can represent in an unambiguous way networks of interactions (for example biochemical interactions). These notations make use of an idea and symbols similar to that used by electrical and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Simple Interaction Format
Simple or SIMPLE may refer to: *Simplicity, the state or quality of being simple Arts and entertainment * ''Simple'' (album), by Andy Yorke, 2008, and its title track * "Simple" (Florida Georgia Line song), 2018 * "Simple", a song by Johnny Mathis from the 1984 album '' A Special Part of Me'' * "Simple", a song by Collective Soul from the 1995 album ''Collective Soul'' * "Simple", a song by Katy Perry from the 2005 soundtrack to ''The Sisterhood of the Traveling Pants'' * "Simple", a song by Khalil from the 2017 album ''Prove It All'' * "Simple", a song by Kreesha Turner from the 2008 album '' Passion'' * "Simple", a song by Ty Dolla Sign from the 2017 album ''Beach House 3'' deluxe version * ''Simple'' (video game series), budget-priced console games Businesses and organisations * Simple (bank), an American direct bank * SIMPLE Group, a consulting conglomeration based in Gibraltar * Simple Shoes, an American footwear brand * Simple Skincare, a British brand of soap ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioPAX
BioPAX (Biological Pathway Exchange) is a RDF/OWL-based standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data. Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are availab ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SBML
The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others. It has been proposed as a standard for representing computational models in systems biology today. History Late in the year 1999 through early 2000, with funding from the Japan Science and Technology Corporation (JST), Hiroaki Kitano and John C. Doyle assembled a small team of researchers to work on developing better software infrastructure for computational modeling in systems biology. Hamid Bolouri was the leader of the development team, which consisted of Andrew Finney, Herbert Sauro, and Michael Hucka. Bolouri identified the need for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
.jpg "Click for more on -> Generative Modelling Language")
