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XGMML
XGMML (the eXtensible Graph Markup and Modeling Language) is an XML application based on GML which is used for graph description. Technically, while GML is not related to XML nor SGML, XGMML is an XML application that is so designed that there's a 1:1 relation towards GML for trivial conversion between the two formats. Applications supporting XGMML * Cytoscape, an open source bioinformatics software platform for visualizing molecular interaction networks, loads and saves networks and node/edge attributes in XGMML * Biomax BioXM Knowledge Management Environment, a customizable knowledge management system for life sciences, supports export of semantic network A semantic network, or frame network is a knowledge base that represents semantic relations between concepts in a network. This is often used as a form of knowledge representation. It is a directed or undirected graph consisting of vertices, ... graphs as XGMML files * JNets, a network visualization and analysis too ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LOGML
An XML 1.0 based markup language for web server log reports, that allows automated data mining and report generation. LOGML is based on XGMML for graph description. See also *XGMML *List of markup languages This is a list of markup languages. This page directly lists markup languages that have not yet been assigned to more specific categories. However, many specific markup language are instead listed only under the narrower lists referenced below. Bu ... External links Cover Pages: Log Markup Language (LOGML) {{compu-lang-stub XML markup languages Computer file formats ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cytoscape
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases and searching in large networks. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged. Cytoscape also has a JavaScript-centric sister project nameCytoscape.jsthat can be used to analyse and visualise graphs in JavaScript environments, like a browser. History Cytoscape was originally created at the Institute of Systems Biology in Seattle in 2002. Now, it is developed by an international consortium of open source developers. Cytoscape was initially made public in July, 2002 (v0.8); the second release (v0.9) was in November, 2002, and v1.0 w ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Modeling Language
A modeling language is any artificial language that can be used to express information or knowledge or systems in a structure that is defined by a consistent set of rules. The rules are used for interpretation of the meaning of components in the structure. Overview A modeling language can be graphical or textual. * ''Graphical'' modeling languages use a diagram technique with named symbols that represent concepts and lines that connect the symbols and represent relationships and various other graphical notation to represent constraints. * ''Textual'' modeling languages may use standardized keywords accompanied by parameters or natural language terms and phrases to make computer-interpretable expressions. An example of a graphical modeling language and a corresponding textual modeling language is EXPRESS. Not all modeling languages are executable, and for those that are, the use of them doesn't necessarily mean that programmers are no longer required. On the contrary, executab ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graph Modelling Language
Graph Modeling Language (GML) is a hierarchical ASCII-based file format for describing graphs. It has been also named ''Graph Meta Language''. Example A simple graph in GML format: graph comment "This is a sample graph" directed 1 id 42 label "Hello, I am a graph" node [ id 1 label "node 1" thisIsASampleAttribute 42 node [ id 2 label "node 2" thisIsASampleAttribute 43 ] node [ id 3 label "node 3" thisIsASampleAttribute 44 ] edge [ source 1 target 2 label "Edge from node 1 to node 2" ] edge [ source 2 target 3 label "Edge from node 2 to node 3" ] edge source 3 target 1 label "Edge from node 3 to node 1" ] Applications supporting GML * Cytoscape, an open source bioinformatics software platform for visualizing molecular interaction networks, loads and save previously-constructed interaction networks in GML. * igraph, an open source network analysis library with interfaces to multiple programming languages. * Gephi, an open sour ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Standard Generalized Markup Language
The Standard Generalized Markup Language (SGML; ISO 8879:1986) is a standard for defining generalized markup languages for documents. ISO 8879 Annex A.1 states that generalized markup is "based on two postulates": * Declarative: Markup should describe a document's structure and other attributes rather than specify the processing that needs to be performed, because it is less likely to conflict with future developments. * Rigorous: In order to allow markup to take advantage of the techniques available for processing, markup should rigorously define objects like programs and databases. DocBook SGML and LinuxDoc are examples which used SGML tools. Standard versions SGML is an ISO standard: "ISO 8879:1986 Information processing – Text and office systems – Standard Generalized Markup Language (SGML)", of which there are three versions: * Original ''SGML'', which was accepted in October 1986, followed by a minor Technical Corrigendum. * ''SGML (ENR)'', in 1996, resul ... [...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] |
List Of Bioinformatics Software
The list of bioinformatics software tools can be split up according to the license used: *List of proprietary bioinformatics software *List of open-source bioinformatics software Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: *Sequence analysis software **List of sequence alignment software ** List of alignment visualization software ** Alignment-free sequence analysis **De novo sequence assemblers ** List of gene prediction software ** List of disorder prediction software ** List of Protein subcellular localization prediction tools **List of phylogenetics software **List of phylogenetic tree visualization software ** :Metagenomics_software *Structural biology software ** List of molecular graphics systems ** List of protein-ligand docking software **List of RNA structure prediction software ** List of software for protein model error verification ** List of protein secondary structure prediction programs ** List of protei ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biomax Informatics AG
Biomax Informatics is a Munich-based software company specializing in research software for bioinformatics. Biomax was founded in 1997 and has its roots in the Munich Information Center for Protein Sequences (MIPS). The company's customer base consists of companies and research organizations in the areas of drug discovery, diagnostics, fine chemicals, food and plant production. In addition to exclusive software tools, Biomax Informatics provides services and curated knowledge bases. In September 2007, Biomax Informatics acquired the Viscovery software business of the Austrian data mining specialist Eudaptics Software. Biomax Informatics and Sophic Systems Alliance Inc. (USA) participate in the Cancer Gene Data Curation Project with the National Cancer Institute (USA). This project maintains a public data set of cancer-related genes and drugs. This data set has been integrated with the NCI's ( cancer Bioinformatics Infrastructure Objects) domain model which is part of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Semantic Network
A semantic network, or frame network is a knowledge base that represents semantic relations between concepts in a network. This is often used as a form of knowledge representation. It is a directed or undirected graph consisting of vertices, which represent concepts, and edges, which represent semantic relations between concepts, mapping or connecting semantic fields. A semantic network may be instantiated as, for example, a graph database or a concept map. Typical standardized semantic networks are expressed as semantic triples. Semantic networks are used in natural language processing applications such as semantic parsing and word-sense disambiguation. Semantic networks can also be used as a method to analyze large texts and identify the main themes and topics (e.g., of social media posts), to reveal biases (e.g., in news coverage), or even to map an entire research field. History Examples of the use of semantic networks in logic, directed acyclic graphs as a mnemonic to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
XML Markup Languages
Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. The World Wide Web Consortium's XML 1.0 Specification of 1998 and several other related specifications—all of them free open standards—define XML. The design goals of XML emphasize simplicity, generality, and usability across the Internet. It is a textual data format with strong support via Unicode for different human languages. Although the design of XML focuses on documents, the language is widely used for the representation of arbitrary data structures such as those used in web services. Several schema systems exist to aid in the definition of XML-based languages, while programmers have developed many application programming interfaces (APIs) to aid the processing of XML data. Overview The main purpose of XML is serialization, i. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
