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Systems Biology Markup Language
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, Gene regulatory networks, 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 computer model, computational modeling in systems biology. Hamid Bolouri was the leader of the development team, which consisted of Andrew Finney, Herbert Sauro, and Michael ... [...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] |
Lingua Franca
A lingua franca (; ; for plurals see ), also known as a bridge language, common language, trade language, auxiliary language, vehicular language, or link language, is a language systematically used to make communication possible between groups of people who do not share a native language or dialect, particularly when it is a third language that is distinct from both of the speakers' native languages. Lingua francas have developed around the world throughout human history, sometimes for commercial reasons (so-called "trade languages" facilitated trade), but also for cultural, religious, diplomatic and administrative convenience, and as a means of exchanging information between scientists and other scholars of different nationalities. The term is taken from the medieval Mediterranean Lingua Franca, a Romance-based pidgin language used especially by traders in the Mediterranean Basin from the 11th to the 19th centuries. A world language – a language spoken internationally and by ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CellML
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] |
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] |
MIME
Multipurpose Internet Mail Extensions (MIME) is an Internet standard that extends the format of email messages to support text in character sets other than ASCII, as well as attachments of audio, video, images, and application programs. Message bodies may consist of multiple parts, and header information may be specified in non-ASCII character sets. Email messages with MIME formatting are typically transmitted with standard protocols, such as the Simple Mail Transfer Protocol (SMTP), the Post Office Protocol (POP), and the Internet Message Access Protocol (IMAP). The MIME standard is specified in a series of requests for comments: , , , , and . The integration with SMTP email is specified in and . Although the MIME formalism was designed mainly for SMTP, its content types are also important in other communication protocols. In the HyperText Transfer Protocol (HTTP) for the World Wide Web, servers insert a MIME header field at the beginning of any Web transmission. Clients ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
IETF
The Internet Engineering Task Force (IETF) is a standards organization for the Internet and is responsible for the technical standards that make up the Internet protocol suite (TCP/IP). It has no formal membership roster or requirements and all its participants are volunteers. Their work is usually funded by employers or other sponsors. The IETF was initially supported by the federal government of the United States but since 1993 has operated under the auspices of the Internet Society, an international non-profit organization. Organization The IETF is organized into a large number of working groups and birds of a feather informal discussion groups, each dealing with a specific topic. The IETF operates in a bottom-up task creation mode, largely driven by these working groups. Each working group has an appointed chairperson (or sometimes several co-chairs); a charter that describes its focus; and what it is expected to produce, and when. It is open to all who want to particip ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MATLAB
MATLAB (an abbreviation of "MATrix LABoratory") is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages. Although MATLAB is intended primarily for numeric computing, an optional toolbox uses the MuPAD symbolic engine allowing access to symbolic computing abilities. An additional package, Simulink, adds graphical multi-domain simulation and model-based design for dynamic and embedded systems. As of 2020, MATLAB has more than 4 million users worldwide. They come from various backgrounds of engineering, science, and economics. History Origins MATLAB was invented by mathematician and computer programmer Cleve Moler. The idea for MATLAB was based on his 1960s PhD thesis. Moler became a math professor at the University of New Mexico and starte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mathematica
Wolfram Mathematica is a software system with built-in libraries for several areas of technical computing that allow machine learning, statistics, symbolic computation, data manipulation, network analysis, time series analysis, NLP, optimization, plotting functions and various types of data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other programming languages. It was conceived by Stephen Wolfram, and is developed by Wolfram Research of Champaign, Illinois. The Wolfram Language is the programming language used in ''Mathematica''. Mathematica 1.0 was released on June 23, 1988 in Champaign, Illinois and Santa Clara, California. __TOC__ Notebook interface Wolfram Mathematica (called ''Mathematica'' by some of its users) is split into two parts: the kernel and the front end. The kernel interprets expressions (Wolfram Language code) and returns result expressions, which can then be displayed by the front end. The origin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Python (programming Language)
Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is dynamically-typed and garbage-collected. It supports multiple programming paradigms, including structured (particularly procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC programming language and first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000 and introduced new features such as list comprehensions, cycle-detecting garbage collection, reference counting, and Unicode support. Python 3.0, released in 2008, was a major revision that is not completely backward-compatible with earlier versions. Python 2 was discontinued with version 2.7.18 in 2020. Python consistently ranks as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java (programming Language)
Java is a high-level, class-based, object-oriented programming language that is designed to have as few implementation dependencies as possible. It is a general-purpose programming language intended to let programmers ''write once, run anywhere'' ( WORA), meaning that compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax of Java is similar to C and C++, but has fewer low-level facilities than either of them. The Java runtime provides dynamic capabilities (such as reflection and runtime code modification) that are typically not available in traditional compiled languages. , Java was one of the most popular programming languages in use according to GitHub, particularly for client–server web applications, with a reported 9 million developers. Java was originally developed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
C Programming Language
''The C Programming Language'' (sometimes termed ''K&R'', after its authors' initials) is a computer programming book written by Brian Kernighan and Dennis Ritchie, the latter of whom originally designed and implemented the language, as well as co-designed the Unix operating system with which development of the language was closely intertwined. The book was central to the development and popularization of the C programming language and is still widely read and used today. Because the book was co-authored by the original language designer, and because the first edition of the book served for many years as the ''de facto'' standard for the language, the book was regarded by many to be the authoritative reference on C. History C was created by Dennis Ritchie at Bell Labs in the early 1970s as an augmented version of Ken Thompson's B. Another Bell Labs employee, Brian Kernighan, had written the first C tutorial, and he persuaded Ritchie to coauthor a book on the language. Ker ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized software development model that encourages open collaboration. A main principle of open-source software development is peer production, with products such as source code, blueprints, and documentation freely available to the public. The open-source movement in software began as a response to the limitations of proprietary code. The model is used for projects such as in open-source appropriate technology, and open-source drug discovery. Open source promotes universal access via an open-source or free license to a product's design or blueprint, and universal redistribution of that design or blueprint. Before the phrase ''open source'' became widely adopted, developers and producers have used a variety of other terms. ''Open source'' gained ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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