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List Of Open-source Bioinformatics Software
This is a list of computer software which is made for bioinformatics and released under open-source software licenses with articles in Wikipedia. See also * Comparison of software for molecular mechanics modeling * Earth BioGenome Project * List of sequence alignment software * List of open-source healthcare software * List of biomedical cybernetics software * List of freeware health software * List of genetic engineering software * List of molecular graphics systems * List of systems biology modelling software * List of proprietary bioinformatics software References External links Free Biology Software– Free Software Directory – Free Software Foundation {{DEFAULTSORT:Open source bioinformatics software Lists of bioinformatics software * Bioinformatics Open Open or OPEN may refer to: Music * Open (band), Australian pop/rock band * The Open (band), English indie rock band * ''Open'' (Blues Image album), 1969 * ''Open'' (Gerd Dudek, Buschi Niebergall, and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Software
Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications. The history of software is closely tied to the development of digital computers in the mid-20th century. Early programs were written in the machine language specific to the hardware. The introduction of high-level programming languages in 1958 allowed for more human-readable instructions, making software development easier and more portable across different computer architectures. Software in a programming language is run through a compiler or Interpreter (computing), interpreter to execution (computing), execute on the architecture's hardware. Over time, software has become complex, owing to developments in Computer network, networking, operating systems, and databases. Software can generally be categorized into two main types: # operating systems, which manage hardware resources and provide services for applicat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
The Apache Software Foundation
The Apache Software Foundation ( ; ASF) is an American nonprofit corporation (classified as a 501(c)(3) organization in the United States) to support a number of open-source software projects. The ASF was formed from a group of developers of the Apache HTTP Server, and incorporated on March 25, 1999. it includes approximately 1000 members. The Apache Software Foundation is a decentralized open source community of developers. The software they produce is distributed under the terms of the Apache License, a permissive open-source license for free and open-source software (FOSS). The Apache projects are characterized by a collaborative, consensus-based development process and an open and pragmatic software license, which is to say that it allows developers, who receive the software freely, to redistribute it under non-free terms. Each project is managed by a self-selected team of technical experts who are active contributors to the project. The ASF is a meritocracy, implying that ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MIT License
The MIT License is a permissive software license originating at the Massachusetts Institute of Technology (MIT) in the late 1980s. As a permissive license, it puts very few restrictions on reuse and therefore has high license compatibility. Unlike copyleft software licenses, the MIT License also permits reuse within proprietary software, provided that all copies of the software or its substantial portions include a copy of the terms of the MIT License and also a copyright notice. In 2015, the MIT License was the most popular software license on GitHub, and was still the most popular in 2025. Notable projects that use the MIT License include the X Window System, Ruby on Rails, Node.js, Lua (programming language), Lua, jQuery, .NET, Angular (web framework), Angular, and React (JavaScript library), React. License terms The MIT License has the identifier MIT in the SPDX License List. It is also known as the "#Ambiguity and variants, Expat License". It has the following terms: Co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BED (file Format)
The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented in the form of columns separated by spaces or tabs. This format was developed during the Human Genome Project and then adopted by other sequencing projects. As a result of this increasingly wide use, this format had already become a ''de facto'' standard in bioinformatics before a formal specification was written. One of the advantages of this format is the manipulation of coordinates instead of nucleotide sequences, which optimizes the power and computation time when comparing all or part of genomes. In addition, its simplicity makes it easy to manipulate and read (or parsing) coordinates or annotations using word processing and scripting languages such as Python, Ruby, or Perl or more specialized tools such as BEDTools. History The end of the 20th century saw the emergence of the first projects to sequence complete geno ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BSD Licenses
BSD licenses are a family of permissive free software licenses, imposing minimal restrictions on the use and distribution of covered software. This is in contrast to copyleft licenses, which have share-alike requirements. The original BSD license was used for its namesake, the Berkeley Software Distribution (BSD), a Unix-like operating system. The original version has since been revised, and its descendants are referred to as modified BSD licenses. BSD is both a license and a class of license (generally referred to as BSD-like). The modified BSD license (in wide use today) is very similar to the license originally used for the BSD version of Unix. The BSD license is a simple license that merely requires that all code retain the BSD license notice if redistributed in source code format, or reproduce the notice if redistributed in binary format. The BSD license (unlike some other licenses e.g. GPL) does not require that source code be distributed at all. Terms In addition to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Unix
Unix (, ; trademarked as UNIX) is a family of multitasking, multi-user computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, and others. Initially intended for use inside the Bell System, AT&T licensed Unix to outside parties in the late 1970s, leading to a variety of both academic and commercial Unix variants from vendors including University of California, Berkeley ( BSD), Microsoft (Xenix), Sun Microsystems ( SunOS/ Solaris), HP/ HPE ( HP-UX), and IBM ( AIX). The early versions of Unix—which are retrospectively referred to as " Research Unix"—ran on computers such as the PDP-11 and VAX; Unix was commonly used on minicomputers and mainframes from the 1970s onwards. It distinguished itself from its predecessors as the first portable operating system: almost the entire operating system is written in the C programming language (in 1973), which allows U ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Qt (software)
Qt ( pronounced "cute") is a cross-platform application development framework for creating graphical user interfaces as well as Cross-platform software, cross-platform applications that run on various software and hardware platforms such as Linux, Windows, macOS, Android (operating system), Android or embedded systems with little or no change in the underlying codebase while still being a native application with native capabilities and speed. Qt is currently being developed by The Qt Company, a publicly listed company, and the Qt Project under open-source governance, involving individual developers and organizations working to advance Qt. Qt is available under both commercial licenses and open-source GNU General Public License, GPL 2.0, GPL 3.0, and GNU Lesser General Public License, LGPL 3.0 licenses. Purposes and abilities Qt is used for developing graphical user interfaces (GUIs) and multi-platform application software, applications that run on all major Desktop computer ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Avogadro (software)
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture. Features * Molecule builder-editor for Microsoft Windows, Windows, Linux, Unix, and macOS. * All source code is licensed under the GNU General Public License (GPL) version 2. * Supported languages include: Chinese language, Chinese, English language, English, French language, French, German language, German, Italian language, Italian, Russian language, Russian, Spanish language, Spanish, and Polish language, Polish. * Supports thread (computer science), multi-threaded Rendering (computer graphics), rendering and computation. * Plugin architecture for developers, including rendering, interactive tools, commands, and Python (programming language), Python scripts. * OpenBabel import of files, input generation for multiple computational chemistry packages, X-ray c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scripps Research
Scripps Research is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California, the institute has over 170 laboratories employing 2,100 scientists, technicians, graduate students, and administrative and other staff. The institute holds over 1,100 patents, has produced 11 FDA-approved therapeutics, and has generated over 50 spin-off companies. The Scripps Research graduate program is ranked 9th nationally in the biological sciences, 6th for organic chemistry, and 6th for biochemistry. In 2022, their Jupiter, Florida, campus became a part of the University of Florida. Jupiter-based graduate students remain part of the Scripps Research graduate program. History Scripps Research began with the Scripps Metabolic Clinic, founded near the current site in the La Jolla area of San Diego in 1924 by philanthropist Ellen Browning Scripps, who was inspired by the discovery of insulin. In 1946, t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SGI IRIX
IRIX (, ) is a discontinued operating system developed by Silicon Graphics (SGI) to run on the company's proprietary MIPS workstations and servers. It is based on UNIX System V with BSD extensions. In IRIX, SGI originated the XFS file system and the industry-standard OpenGL graphics API. History SGI originated the IRIX name in the 1988 release 3.0 of the operating system for the SGI IRIS 4D series of workstations and servers. Previous releases are identified only by the release number prefixed by "4D1-", such as "4D1-2.2". The "4D1-" prefix continued to be used in official documentation to prefix IRIX release numbers. Prior to the IRIS 4D, SGI bundled the GL2 operating system, based on UniSoft UniPlus System V Unix, and using the proprietary MEX (Multiple EXposure) windowing system. IRIX 3.x is based on UNIX System V Release 3 with 4.3BSD enhancements, and incorporates the 4Sight windowing system, based on NeWS and IRIS GL. SGI's own Extent File System (EFS) replaces the S ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mac OS X
macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. Within the market of Desktop computer, desktop and laptop computers, it is the Usage share of operating systems#Desktop and laptop computers, second most widely used desktop OS, after Microsoft Windows and ahead of all Linux distributions, including ChromeOS and SteamOS. , the most recent release of macOS is MacOS Sequoia, macOS 15 Sequoia, the 21st major version of macOS. Mac OS X succeeded classic Mac OS, the primary Mac operating systems, Macintosh operating system from 1984 to 2001. Its underlying architecture came from NeXT's NeXTSTEP, as a result of NeXT#1997–2006: Acquisition by Apple, Apple's acquisition of NeXT, which also brought Steve Jobs back to Apple. The first desktop version, Mac OS X 10.0, was released on March 24, 2001. Mac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
AutoDock
AutoDock is a molecular modeling simulation software. It is especially effective for protein-ligand docking. AutoDock 4 is available under the GNU General Public License. AutoDock is one of the most cited docking software applications in the research community. It is used by the FightAIDS@Home and OpenPandemics - COVID-19 projects run at World Community Grid, to search for antivirals against HIV/AIDS and COVID-19. In February 2007, a search of the ISI Citation Index showed more than 1,100 publications had been cited using the primary AutoDock method papers. As of 2009, this number surpassed 1,200. AutoDock Vina is a successor of AutoDock, significantly improved in terms of accuracy and performance. It is available under the Apache license. Both AutoDock and Vina are currently maintained by Scripps Research, specifically the Center for Computational Structural Biology (CCSB) led by Dr. Arthur J. Olson AutoDock is widely used and played a role in the development of the first cl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
