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CellML Logo
CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models relevant to the field of biology. This is reflected in its name CellML, although this is simply a name, not an abbreviation. CellML is growing in popularity as a portable description format for computational models, and groups throughout the world are using CellML for modelling or developing software tools based on CellML. CellML is similar to Systems Biology Markup Language SBML but provides greater scope for model modularity and reuse, and is not specific to descriptions of biochemistry. History The CellML language grew from a need to share models of cardiac cell dynamics among researchers at a number of sites across the world. The original working group formed in 1998 consisted of David Bullivant, Warren Hedley, and Poul Nielsen; all th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CellML Logo
CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models relevant to the field of biology. This is reflected in its name CellML, although this is simply a name, not an abbreviation. CellML is growing in popularity as a portable description format for computational models, and groups throughout the world are using CellML for modelling or developing software tools based on CellML. CellML is similar to Systems Biology Markup Language SBML but provides greater scope for model modularity and reuse, and is not specific to descriptions of biochemistry. History The CellML language grew from a need to share models of cardiac cell dynamics among researchers at a number of sites across the world. The original working group formed in 1998 consisted of David Bullivant, Warren Hedley, and Poul Nielsen; all th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Markup Language
Markup language refers to a text-encoding system consisting of a set of symbols inserted in a text document to control its structure, formatting, or the relationship between its parts. Markup is often used to control the display of the document or to enrich its content to facilitating automated processing. A markup language is a set of rules governing what markup information may be included in a document and how it is combined with the content of the document in a way to facilitate use by humans and computer programs. The idea and terminology evolved from the "marking up" of paper manuscripts (i.e., the revision instructions by editors), which is traditionally written with a red pen or blue pencil on authors' manuscripts. Older markup languages, which typically focus on typography and presentation, include troff, TeX, and LaTeX. Scribe and most modern markup languages, for example XML, identify document components (for example headings, paragraphs, and tables), with the e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mathematical Model
A mathematical model is a description of a system using mathematical concepts and language. The process of developing a mathematical model is termed mathematical modeling. Mathematical models are used in the natural sciences (such as physics, biology, earth science, chemistry) and engineering disciplines (such as computer science, electrical engineering), as well as in non-physical systems such as the social sciences (such as economics, psychology, sociology, political science). The use of mathematical models to solve problems in business or military operations is a large part of the field of operations research. Mathematical models are also used in music, linguistics, and philosophy (for example, intensively in analytic philosophy). A model may help to explain a system and to study the effects of different components, and to make predictions about behavior. Elements of a mathematical model Mathematical models can take many forms, including dynamical systems, statisti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Physiome Project
The physiome of an individual's or species' physiological state is the description of its functional behavior. The physiome describes the physiological dynamics of the normal intact organism and is built upon information and structure (genome, proteome, and morphome). The term comes from "physio-" (nature) and "-ome" (as a whole). The concept of a physiome project was presented to the International Union of Physiological Sciences (IUPS) by its Commission on Bioengineering in Physiology in 1993. A workshop on designing the Physiome Project was held in 1997. At its world congress in 2001, the IUPS designated the project as a major focus for the next decade. The project is led by the Physiome Commission of the IUPS. Other research initiatives related to the physiome include: *The EuroPhysiome Initiative *The NSR Physiome Project of the National Simulation Resource (NSR) at the University of Washington, supporting the IUPS Physiome Project *The Wellcome Trust Heart Physiome Project, a ... [...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] |
MathML
Mathematical Markup Language (MathML) is a mathematical markup language, an application of XML for describing mathematical notations and capturing both its structure and content. It aims at integrating mathematical formulae into World Wide Web pages and other documents. It is part of HTML5 and is a ISO/IEC standarISO/IEC 40314since 2015. History MathML 1 was released as a W3C recommendation in April 1998 as the first XML language to be recommended by the W3C. Version 1.01 of the format was released in July 1999 and version 2.0 appeared in February 2001. In October 2003, the second edition of MathML Version 2.0 was published as the final release by the W3C Math Working Group. MathML was originally designed before the finalization of XML namespaces. However, it was assigned a namespace immediately after the Namespace Recommendation was completed, and for XML use, the elements should be in the namespace with namespace URL http://www.w3.org/1998/Math/MathML. When MathML is used i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Resource Description Framework
The Resource Description Framework (RDF) is a World Wide Web Consortium (W3C) standard originally designed as a data model for metadata. It has come to be used as a general method for description and exchange of graph data. RDF provides a variety of syntax notations and data serialization formats with Turtle (Terse RDF Triple Language) currently being the most widely used notation. RDF is a directed graph composed of triple statements. An RDF graph statement is represented by: 1) a node for the subject, 2) an arc that goes from a subject to an object for the predicate, and 3) a node for the object. Each of the three parts of the statement can be identified by a URI. An object can also be a literal value. This simple, flexible data model has a lot of expressive power to represent complex situations, relationships, and other things of interest, while also being appropriately abstract. RDF was adopted as a W3C recommendation in 1999. The RDF 1.0 specification was published in 2004, th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
XLink
XML Linking Language, or XLink, is an XML markup language and W3C specification that provides methods for creating internal and external links within XML documents, and associating metadata with those links. The XLink specification XLink 1.1 is a W3C recommendation and the successor of XLink 1.0, which was also a W3C recommendation. Linking with XLink XLink defines a set of attributes that may be added to elements of other XML namespaces. XLink provides two kinds of hyperlinking for use in XML documents. Simple links connect only two resources, similar to HTML links. Extended links can link an arbitrary number of resources. Simple links A simple link creates a unidirectional hyperlink from one element to another via a URI. Example: Some Document Here is a link to the header. It is an anchor that points to the element with the id "someHeading" on the current page. Extended links Extended links allow multiple resources, either remote or local, to be connected by multiple ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virtual Cell
Virtual Cell (VCell) is an open-source software platform for modeling and simulation of living organisms, primarily cells. It has been designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. Concept Virtual Cell is an advanced software platform for modeling and simulating reaction kinetics, membrane transport and diffusion in the complex geometries of cells and multicellular tissues. VCell models have a hierarchical tree structure. The trunk level is the "Physiology" consisting of compartments, species and chemical reactions, and reaction rates that are functions of concentrations. Given initial concentrations of species, VCell can calculate how these concentrations change over time. How these numerical simulations are performed, is determined through a number of "Applications", which specify whether simulations will be deterministic or stochastic, and spatial or compartmental; multiple "Applications" can also speci ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metadata
Metadata is "data that provides information about other data", but not the content of the data, such as the text of a message or the image itself. There are many distinct types of metadata, including: * Descriptive metadata – the descriptive information about a resource. It is used for discovery and identification. It includes elements such as title, abstract, author, and keywords. * Structural metadata – metadata about containers of data and indicates how compound objects are put together, for example, how pages are ordered to form chapters. It describes the types, versions, relationships, and other characteristics of digital materials. * Administrative metadata – the information to help manage a resource, like resource type, permissions, and when and how it was created. * Reference metadata – the information about the contents and quality of statistical data. * Statistical metadata – also called process data, may describe processes that collect, process, or produce st ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Procedural Programming
Procedural programming is a programming paradigm, derived from imperative programming, based on the concept of the ''procedure call''. Procedures (a type of routine or subroutine) simply contain a series of computational steps to be carried out. Any given procedure might be called at any point during a program's execution, including by other procedures or itself. The first major procedural programming languages appeared circa 1957–1964, including Fortran, ALGOL, COBOL, PL/I and BASIC. Pascal and C were published circa 1970–1972. Computer processors provide hardware support for procedural programming through a stack register and instructions for calling procedures and returning from them. Hardware support for other types of programming is possible, but no attempt was commercially successful (for example Lisp machines or Java processors). Procedures and modularity Modularity is generally desirable, especially in large, complicated programs. Inputs are usua ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Programming Language
A programming language is a system of notation for writing computer programs. Most programming languages are text-based formal languages, but they may also be graphical. They are a kind of computer language. The description of a programming language is usually split into the two components of syntax (form) and semantics (meaning), which are usually defined by a formal language. Some languages are defined by a specification document (for example, the C programming language is specified by an ISO Standard) while other languages (such as Perl) have a dominant implementation that is treated as a reference. Some languages have both, with the basic language defined by a standard and extensions taken from the dominant implementation being common. Programming language theory is the subfield of computer science that studies the design, implementation, analysis, characterization, and classification of programming languages. Definitions There are many considerations when defini ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
