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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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Systems Biology
Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionist, reductionism) to biological research. This multifaceted research domain necessitates the collaborative efforts of chemists, biologists, mathematicians, physicists, and engineers to decipher the biology of intricate living systems by merging various quantitative molecular measurements with carefully constructed mathematical models. It represents a comprehensive method for comprehending the complex relationships within biological systems. In contrast to conventional biological studies that typically center on isolated elements, systems biology seeks to combine different biological data to create models that illustrate and elucidate the dynamic interactions with ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graph Drawing Software
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 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 vertices and 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 mental map. Graphical conventions Graphs are frequently drawn as node–l ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java Platform
Java is a set of computer software and specifications that provides a software platform for developing application software and deploying it in a cross-platform computing environment. Java is used in a wide variety of computing platforms from embedded devices and mobile phones to enterprise servers and supercomputers. Java applets, which are less common than standalone Java applications, were commonly run in secure, Sandbox (computer security), sandboxed environments to provide many features of native applications through being embedded in HTML pages. Writing in the Java (programming language), Java programming language is the primary way to produce code that will be deployed as Java byte code, byte code in a Java virtual machine (JVM); byte code compilers are also available for other languages, including Ada (programming language), Ada, JavaScript, Kotlin (programming language), Kotlin (Google's preferred Android language), Python (programming language), Python, and Ruby (p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mathematical And Theoretical Biology
Mathematical and theoretical biology, or biomathematics, is a branch of biology which employs theoretical analysis, mathematical models and abstractions of living organisms to investigate the principles that govern the structure, development and behavior of the systems, as opposed to experimental biology which deals with the conduction of experiments to test scientific theories. The field is sometimes called mathematical biology or biomathematics to stress the mathematical side, or theoretical biology to stress the biological side. Theoretical biology focuses more on the development of theoretical principles for biology while mathematical biology focuses on the use of mathematical tools to study biological systems, even though the two terms interchange; overlapping as Artificial Immune Systems of Amorphous Computation. Mathematical biology aims at the mathematical representation and modeling of biological processes, using techniques and tools of applied mathematics. It can ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Software
{{short description, none The list of bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ... 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 *S ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein–protein Interaction Prediction
Protein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical processes. ''Experimentally'', physical interactions between pairs of proteins can be inferred from a variety of techniques, including yeast two-hybrid screening, two-hybrid systems, Protein-fragment complementation assay, protein-fragment complementation assays (PCA), affinity purification/mass spectrometry, protein microarrays, fluorescence resonance energy transfer (FRET), and Microscale Thermophoresis (MST). Efforts to experimentally determine the interactome of numerous species are ongoing. Experimentally determined interactions usually provide the basis for ''computational methods' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JavaScript Library
A JavaScript library is a library of pre-written JavaScript code that allows for easier development of JavaScript-based applications, especially for AJAX and other web-centric technologies. They can be included in a website by embedding it directly in the HTML via a script tag. Libraries With the expanded demands for JavaScript, an easier means for programmers to develop such dynamic interfaces was needed. Thus, JavaScript libraries and JavaScript widget libraries were developed, allowing for developers to concentrate more upon more distinctive applications of Ajax. This has led to other companies and groups, such as Microsoft and Yahoo! developing their own JavaScript-based user interface libraries, which find their way into the web applications developed by these companies. Some JavaScript libraries allow for easier integration of JavaScript with other web development technologies, such as CSS, PHP, Ruby, and Java, while others provide utilities, often in the form of JavaScript ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JavaScript Framework
A web framework (WF) or web application framework (WAF) is a software framework that is designed to support the development of web applications including web services, web resources, and web APIs. Web frameworks provide a standard way to build and deploy web applications on the World Wide Web. Web frameworks aim to automate the overhead associated with common activities performed in web development. For example, many web frameworks provide libraries for database access, templating frameworks, and session management, and they often promote code reuse. Although they often target development of dynamic web sites, they are also applicable to static websites. History As the design of the World Wide Web was not inherently dynamic, early hypertext consisted of hand-coded HTML text files that were published on web servers. Any modifications to published pages needed to be performed by the pages' author. In 1993, the Common Gateway Interface (CGI) standard was introduced for interfa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Genomics
Computational genomics refers to the use of computational and statistical analysis to decipher biology from genome sequences and related data, including both DNA and RNA sequence as well as other "post-genomic" data (i.e., experimental data obtained with technologies that require the genome sequence, such as genomic DNA microarrays). These, in combination with computational and statistical approaches to understanding the function of the genes and statistical association analysis, this field is also often referred to as Computational and Statistical Genetics/genomics. As such, computational genomics may be regarded as a subset of bioinformatics and computational biology, but with a focus on using whole genomes (rather than individual genes) to understand the principles of how the DNA of a species controls its biology at the molecular level and beyond. With the current abundance of massive biological datasets, computational studies have become one of the most important means to biolog ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
JavaScript
JavaScript (), often abbreviated as JS, is a programming language and core technology of the World Wide Web, alongside HTML and CSS. Ninety-nine percent of websites use JavaScript on the client side for webpage behavior. Web browsers have a dedicated JavaScript engine that executes the client code. These engines are also utilized in some servers and a variety of apps. The most popular runtime system for non-browser usage is Node.js. JavaScript is a high-level, often just-in-time–compiled language that conforms to the ECMAScript standard. It has dynamic typing, prototype-based object-orientation, and first-class functions. It is multi-paradigm, supporting event-driven, functional, and imperative programming styles. It has application programming interfaces (APIs) for working with text, dates, regular expressions, standard data structures, and the Document Object Model (DOM). The ECMAScript standard does not include any input/output (I/O), such as netwo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
