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Gephi 0
Gephi ( ) is an open-source network theory, network analysis and network visualization, visualization software package written in Java on the NetBeans platform. History Initially developed by students of the University of Technology of Compiègne (UTC) in France, Gephi has been selected for the Google Summer of Code in 2009, 2010, 2011, 2012, and 2013. Its last version, 0.10.1 has been launched in 2023. Previous versions are 0.6.0 (2008), 0.7.0 (2010), 0.8.0 (2011), 0.8.1 (2012), 0.8.2 (2013), 0.9.0 (2015), 0.9.1 (2016) and 0.9.2 (2017). The Gephi Consortium, created in 2010, is a French non-profit corporation which supports development of future releases of Gephi. Members include SciencesPo, Linkfluence, WebAtlas, and Quid (encyclopedia), Quid. Gephi is also supported by a large community of users, structured on a discussion group and a forum and producing numerous blogposts, papers and tutorials. In November 2022, a lightweight web version of Gephi, Gephi lite, was announced. ...
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Java (programming Language)
Java is a High-level programming language, high-level, General-purpose programming language, general-purpose, Memory safety, memory-safe, object-oriented programming, object-oriented programming language. It is intended to let programmers ''write once, run anywhere'' (Write once, run anywhere, WORA), meaning that compiler, compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to Java bytecode, bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax (programming languages), syntax of Java is similar to C (programming language), C and C++, but has fewer low-level programming language, low-level facilities than either of them. The Java runtime provides dynamic capabilities (such as Reflective programming, reflection and runtime code modification) that are typically not available in traditional compiled languages. Java gained popularity sh ...
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Jadaliyya
''Jadaliyya'' (" dialectic") is an independent ezine founded in 2010 by the Arab Studies Institute (ASI) to cover the Arab World and the broader Middle East. It publishes articles in Arabic, French, English and Turkish, and is run primarily on a volunteer basis by an editorial team, and an expanding pool of contributors that includes academics, journalists, activists and artists. Overview ''Jadaliyya'' () is derived from the , meaning " dialectic." ''Jadaliyya's'' co-editors are unpaid volunteers and the magazine does not accept advertising. While most of ''Jadaliyya'' is either self-funded or funded by barter for "big projects," it has received grants from the Open Society Institute. According to ''Portal 9'': "The Arab uprisings, which gained momentum only a few months after ''Jadaliyya'' was established, firmly catapulted it to the forefront of critical debates and analysis of the Arab world." George Mason University professor Bassam Haddad, its founding editor, said t ...
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Graphviz
Graphviz (short for ''Graph Visualization Software'') is a package of open-source software, open-source tools initiated by AT&T Labs, AT&T Labs Research for Graph drawing, drawing graph (discrete mathematics), graphs (as in Vertex (graph theory), nodes and Edge (graph theory), edges, not as in bar charts) specified in DOT (graph description language), DOT language scripts having the file name extension "gv". It also provides libraries for software applications to use the tools. Graphviz is free software licensed under the Eclipse Public License. Tools ; dot : a Command-line interface, command-line tool to produce layered graph drawing, layered graph drawings in a variety of output formats, such as (PostScript, PDF, Scalable Vector Graphics, SVG, annotated text and so on). ; neato : useful for undirected graphs up to about 1000 nodes. "Spring system, Spring model" layout minimizes global energy. ; fdp : force-directed graph drawing similar to "spring model", but minimizes forc ...
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Graph-tool
graph-tool is a Python (programming language), Python module for manipulation and statistical analysis of Graph (discrete mathematics), graphs (AKA Network theory, networks). The core data structures and algorithms of graph-tool are implemented in C++, making extensive use of metaprogramming, based heavily on the Boost Graph Library. Many algorithms are implemented in parallel using OpenMP, which provides increased performance on Multi-core processor, multi-core architectures. Features * Creation and manipulation of Directed graph, directed or Graph (discrete mathematics), undirected graphs. * Association of arbitrary information to the vertices, edges or even the graph itself, by means of property maps. * Filter vertices and/or edges "on the fly", such that they appear to have been removed. * Support for DOT language, dot, Graph Modelling Language and GraphML formats. * Convenient and powerful graph drawing based on cairo (graphics), cairo or Graphviz. * Support for typical st ...
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Cytoscape
Cytoscape is an Open-source software, open source bioinformatics software platform for Visualization (graphic), visualizing Metabolic network modelling, molecular interaction networks and integrating with gene expression profiles and other state data. Additional features are available as plug-in (computing), 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 (programming language), 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 develo ...
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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 sou ...
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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 assoc ...
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Dot Language
DOT is a Graph (discrete mathematics), graph description language, developed as a part of the Graphviz project. DOT graphs are typically stored as Computer file, files with the .gv or .dot filename extension — .gv is preferred, to avoid confusion with the .dot extension used by versions of Microsoft Word before 2007. dot is also the name of the main program to process DOT files in the Graphviz package. Various programs can process DOT files. Some, such as ''dot'', ''neato'', ''twopi'', ''circo'', ''fdp'', and ''sfdp'', can read a DOT file and render it in graphical form. Others, such as ''gvpr'', ''gc'', ''acyclic'', ''ccomps'', ''sccmap'', and ''tred'', read DOT files and perform calculations on the represented graph. Finally, others, such as ''lefty'', ''dotty'', and ''grappa'', provide an interactive interface. The GVedit tool combines a text editor and a non-interactive viewer. Most programs are part of the Graphviz package or use it internally. DOT is historically an acron ...
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Social Network Analysis Software
Social network analysis (SNA) software is software which facilitates quantitative analysis of behavior, quantitative or qualitative research, qualitative social network analysis, analysis of social networks, by describing features of a network either through numerical or Graph drawing, visual representation. Overview Networks can consist of anything from families, project teams, classrooms, sports teams, legislatures, Nation states, nation-states, disease vectors, membership on Social networking service, networking websites like Twitter or Facebook, or even the Internet. Networks can consist of direct linkages between nodes or indirect linkages based upon shared attributes, shared attendance at events, or common affiliations. Network features can be at the level of individual node (graph theory), nodes, dyad (sociology), dyads, triad (relationship), triads, ties and/or edges, or the entire network. For example, node-level features can include network phenomena such as betweenness ...
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Graph (data Structure)
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 vertices for an undirected graph or a set of ordered pairs for a directed graph. These pairs are known as ''edges'' (also called ''links'' or ''lines''), and for a directed graph are also known as ''edges'' but also sometimes ''arrows'' or ''arcs''. The vertices may be part of the graph structure, or may be external entities represented by integer indices or references. A graph data structure may also associate to each edge some ''edge value'', such as a symbolic label or a numeric attribute (cost, capacity, length, etc.). Operations The basic operations provided by a graph data structure ''G'' usually include:See, e.g. , Sec ...
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Graph Theory
In mathematics and computer science, graph theory is the study of ''graph (discrete mathematics), graphs'', which are mathematical structures used to model pairwise relations between objects. A graph in this context is made up of ''Vertex (graph theory), vertices'' (also called ''nodes'' or ''points'') which are connected by ''Glossary of graph theory terms#edge, edges'' (also called ''arcs'', ''links'' or ''lines''). A distinction is made between undirected graphs, where edges link two vertices symmetrically, and directed graphs, where edges link two vertices asymmetrically. Graphs are one of the principal objects of study in discrete mathematics. Definitions Definitions in graph theory vary. The following are some of the more basic ways of defining graphs and related mathematical structures. Graph In one restricted but very common sense of the term, a graph is an ordered pair G=(V,E) comprising: * V, a Set (mathematics), set of vertices (also called nodes or points); * ...
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Graph Drawing
Graph drawing is an area of mathematics and computer science combining methods from geometric graph theory and information visualization to derive two-dimensional depictions of graph (discrete mathematics), graphs arising from applications such as social network analysis, cartography, linguistics, and bioinformatics. A drawing of a graph or network diagram is a pictorial representation of the vertex (graph theory), vertices and edge (graph theory), edges of a graph. This drawing should not be confused with the graph itself: very different layouts can correspond to the same graph., p. 6. In the abstract, all that matters is which pairs of vertices are connected by edges. In the concrete, however, the arrangement of these vertices and edges within a drawing affects its understandability, usability, fabrication cost, and aesthetics. The problem gets worse if the graph changes over time by adding and deleting edges (dynamic graph drawing) and the goal is to preserve the user's men ...
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