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PathVisioRPC
PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible. PathVisio provides a basic set of features for pathway drawing, analysis and visualization. Additional features are available as plugins. : History PathVisio was created primarily at Maastricht University and Gladstone Institutes. The software is developed in Java and it's also used as part of the WikiPathways framework as an applet. Starting from version 3.0 (released in 2012) plugins are OSGi compliant and plugin directory describing them, was developed. In 2015 version 3.2 was released. This was the first signed version with a certificate issued by a certification authority. Many of the running issues introduced by java 1.7 and 1.8 with the new security rules were solved. Since 2013 a javascript version (PV ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PathVisioRPC
PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible. PathVisio provides a basic set of features for pathway drawing, analysis and visualization. Additional features are available as plugins. : History PathVisio was created primarily at Maastricht University and Gladstone Institutes. The software is developed in Java and it's also used as part of the WikiPathways framework as an applet. Starting from version 3.0 (released in 2012) plugins are OSGi compliant and plugin directory describing them, was developed. In 2015 version 3.2 was released. This was the first signed version with a certificate issued by a certification authority. Many of the running issues introduced by java 1.7 and 1.8 with the new security rules were solved. Since 2013 a javascript version (PV ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Java Platform
Java is a set of computer software and specifications developed by James Gosling at Sun Microsystems, which was later acquired by the Oracle Corporation, that provides a system 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, sandboxed environments to provide many features of native applications through being embedded in HTML pages. Writing in the Java programming language is the primary way to produce code that will be deployed as byte code in a Java virtual machine (JVM); byte code compilers are also available for other languages, including Ada, JavaScript, Python, and Ruby. In addition, several languages have been designed to run natively on the JVM, including Clojure, Groovy, and Scala. J ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Apache 2
APACHE II ("Acute Physiology and Chronic Health Evaluation II") is a severity-of-disease classification system, one of several ICU scoring systems. It is applied within 24 hours of admission of a patient to an intensive care unit (ICU): an integer score from 0 to 71 is computed based on several measurements; higher scores correspond to more severe disease and a higher risk of death. The first APACHE model was presented by Knaus et al. in 1981. Application APACHE II was designed to measure the severity of disease for adult patients admitted to intensive care units. It has not been validated for use in children or young people aged under 16. This scoring system is used in many ways which include: # Some procedures or some medicine is only given to patients with a certain APACHE II score # APACHE II score can be used to describe the morbidity of a patient when comparing the outcome with other patients. # Predicted mortalities are averaged for groups of patients in order to speci ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Pathway
A biological pathway is a series of interactions among molecules in a cell that leads to a certain product or a change in a cell. Such a pathway can trigger the assembly of new molecules, such as a fat or protein. Pathways can also turn genes on and off, or spur a cell to move.{{Cite web , url=https://www.genome.gov/about-genomics/fact-sheets/Biological-Pathways-Fact-Sheet , title = Biological Pathways Fact Sheet Some of the most common biological pathways are involved in metabolism, the regulation of gene expression and the transmission of signals. Pathways play a key role in advanced studies of genomics. Most common types of biological pathways: *Metabolic pathway *Genetic pathway *Signal transduction pathway Pathways databases * KEGG Pathway database is a popular pathway search database highly used by biologists. * WikiPathways is a community curated pathway database using the "wiki" concept. All pathways have an open license and can be freely used. * Reactome is a free and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Maastricht University
Maastricht University (abbreviated as UM; nl, Universiteit Maastricht) is a public research university in Maastricht, Netherlands. Founded in 1976, it is the second youngest of the thirteen Dutch universities. In 2021, 22,383 students studied at Maastricht University, 56% of whom were foreign students, with over 4,000 employees. About half of the bachelor's programmes are fully offered in English, while the other half is taught wholly or partly in Dutch. Most of the master's and doctoral programmes are in English. Besides traditional programmes, Maastricht University also has three honours liberal arts colleges: University College Maastricht and the Maastricht Science Programme in the same liberal arts tradition. The satellite University College Venlo opened in 2015. Maastricht University regularly ranks as one of Europe's leading universities. The university has been placed in the top 300 universities in the world by five major ranking tables. Maastricht University was at 88th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gladstone Institutes
Gladstone Institutes is an independent, non-profit biomedical research organization whose focus is to better understand, prevent, treat and cure cardiovascular, viral and neurological conditions such as heart failure, HIV/AIDS and Alzheimer's disease. Its researchers study these diseases using techniques of basic and translational science. Another focus at Gladstone is building on the development of induced pluripotent stem cell technology by one of its investigators, 2012 Nobel Laureate Shinya Yamanaka, to improve drug discovery, personalized medicine and tissue regeneration. Founded in 1979, Gladstone is academically affiliated with the University of California, San Francisco (UCSF), and located adjacent to UCSF's Mission Bay campus. The organization comprises five major institutes, as well as multiple centers focused on various areas of research. The current president of the institute is Deepak Srivastava. History Gladstone Institutes was founded in 1979 as a research and ... [...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] |
WikiPathways
WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways. Any registered WikiPathways user can contribute, and anybody can become a registered user. Contributions are monitored by a group of admins, but the bulk of peer review, editorial curation, and maintenance is the responsibility of the user community. WikiPathways is built using MediaWiki software, a custom graphical pathway editing tool ( PathVisio) and integrated BridgeDb databases covering major gene, protein, and metabolite systems. Pathway content Each article at WikiPathways is dedicated to a particular pathway. Many types of molecular pathways are covered, including metabolic, signaling, regulatory, etc. and the supported species include human, mouse, zebrafish, fruit fly, C. elegans, yeast, rice and arabidopsis, as well as bacteria and plant species. Using a search feature, one can locate a particular pathway by name, by the genes and proteins it contains, or b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OSGi
OSGi is an open specification and open source project under the Eclipse Foundation. It is a continuation of the work done by the OSGi Alliance (formerly known as the Open Services Gateway initiative), which was an open standards organization for computer software founded in March 1999. The foundation originally specified and maintained the OSGi standard. The alliance transferred its work to the Eclipse Foundation at the end of 2020. The OSGi specification describes a modular system and a service platform for the Java programming language that implements a complete and dynamic component model, something that does not exist in standalone Java or VM environments. It has a service-oriented architecture based on micro services each implemented as an extended Java class file archive ( JAR (file format)). Description OSGi is built around a service-oriented architecture. Applications or components, come in the form of bundles for deployment, can be remotely installed, started, stop ... [...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] |
Free Bioinformatics Software
Free may refer to: Concept * Freedom, having the ability to do something, without having to obey anyone/anything * Freethought, a position that beliefs should be formed only on the basis of logic, reason, and empiricism * Emancipate, to procure political rights, as for a disenfranchised group * Free will, control exercised by rational agents over their actions and decisions * Free of charge, also known as gratis. See Gratis vs libre. Computing * Free (programming), a function that releases dynamically allocated memory for reuse * Free format, a file format which can be used without restrictions * Free software, software usable and distributable with few restrictions and no payment * Freeware, a broader class of software available at no cost Mathematics * Free object ** Free abelian group ** Free algebra ** Free group ** Free module ** Free semigroup * Free variable People * Free (surname) * Free (rapper) (born 1968), or Free Marie, American rapper and media pers ... [...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. Particularly from the year 2000 onwards, the concept has been used widely in biology in a variety of contexts. The Human Genome Project is an example of applied systems thinking in biology which has led to new, collaborative ways of working on problems in the biological field of genetics. One of the aims of systems biology is to model and discover emergent property, emergent properties, properties of cell (biology), cells, tissue (biology), tissues and organisms functioning as a system whose theoretical description is only possible using techniques of systems biology. These typically involve metabolic networks or cell ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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