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BioJava 5 Module Layout
BioJava is an open-source software project dedicated to provide Java tools to process biological data.VS Matha and P Kangueane, 2009, ''Bioinformatics: a concept-based introduction'', 2009. p26 BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a huge range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application ... [...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 de ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Database
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for museum collections etc.) Databases are important tools in assisting scientists to analyze and explain a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Class (computer Programming)
In object-oriented programming, a class is an extensible program-code-template for creating objects, providing initial values for state (member variables) and implementations of behavior (member functions or methods). In many languages, the class name is used as the name for the class (the template itself), the name for the default constructor of the class (a subroutine that creates objects), and as the type of objects generated by instantiating the class; these distinct concepts are easily conflated. Although, to the point of conflation, one could argue that is a feature inherent in a language because of its polymorphic nature and why these languages are so powerful, dynamic and adaptable for use compared to languages without polymorphism present. Thus they can model dynamic systems (i.e. the real world, machine learning, AI) more easily. When an object is created by a constructor of the class, the resulting object is called an instance of the class, and the member variable ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioJava 5 Module Layout
BioJava is an open-source software project dedicated to provide Java tools to process biological data.VS Matha and P Kangueane, 2009, ''Bioinformatics: a concept-based introduction'', 2009. p26 BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a huge range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Apache Maven
Maven is a build automation tool used primarily for Java projects. Maven can also be used to build and manage projects written in C#, Ruby, Scala, and other languages. The Maven project is hosted by the Apache Software Foundation, where it was formerly part of the Jakarta Project. Maven addresses two aspects of building software: how software is built and its dependencies. Unlike earlier tools like Apache Ant, it uses conventions for the build procedure. Only exceptions need to be specified. An XML file describes the software project being built, its dependencies on other external modules and components, the build order, directories, and required plug-ins. It comes with pre-defined targets for performing certain well-defined tasks such as compilation of code and its packaging. Maven dynamically downloads Java libraries and Maven plug-ins from one or more repositories such as the Maven 2 Central Repository, and stores them in a local cache. This local cache of downloaded ar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Crystallographic Information File
Crystallographic Information File (CIF) is a standard text file format for representing crystallographic information, promulgated by the International Union of Crystallography (IUCr). CIF was developed by the IUCr Working Party on Crystallographic Information in an effort sponsored by the IUCr Commission on Crystallographic Data and the IUCr Commission on Journals. The file format was initially published by Hall, Allen, and Brown and has since been revised, most recently versions 1.1 and 2.0. Full specifications for the format are available at the IUCr website. Many computer programs for molecular viewing are compatible with this format, including Jmol. Closely related is mmCIF, macromolecular CIF, which is intended as an alternative to the Protein Data Bank (PDB) format. It is now the default format used by the Protein Data Bank. Also closely related is Crystallographic Information Framework, a broader system of exchange protocols based on data dictionaries and relational r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Anonymous Function
In computer programming, an anonymous function (function literal, lambda abstraction, lambda function, lambda expression or block) is a function definition that is not bound to an identifier. Anonymous functions are often arguments being passed to higher-order functions or used for constructing the result of a higher-order function that needs to return a function. If the function is only used once, or a limited number of times, an anonymous function may be syntactically lighter than using a named function. Anonymous functions are ubiquitous in functional programming languages and other languages with first-class functions, where they fulfil the same role for the function type as literals do for other data types. Anonymous functions originate in the work of Alonzo Church in his invention of the lambda calculus, in which all functions are anonymous, in 1936, before electronic computers. In several programming languages, anonymous functions are introduced using the keyword ''la ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Apache Commons
The Apache Commons is a project of the Apache Software Foundation, formerly under the Jakarta Project. The purpose of the Commons is to provide reusable, open source Java software. The Commons is composed of three parts: proper, sandbox, and dormant. Commons Proper The Commons Proper is dedicated to creating and maintaining reusable Java components. The Commons Proper is a place for collaboration and sharing, where developers from throughout the Apache community can work together on projects to be shared by Apache projects and Apache users. Commons developers will make an effort to ensure that their components have minimal dependencies on other software libraries In computer science, a library is a collection of non-volatile resources used by computer programs, often for software development. These may include configuration data, documentation, help data, message templates, pre-written code and subro ..., so that these components can be deployed easily. In addition, Comm ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GitHub
GitHub, Inc. () is an Internet hosting service for software development and version control using Git. It provides the distributed version control of Git plus access control, bug tracking, software feature requests, task management, continuous integration, and wikis for every project. Headquartered in California, it has been a subsidiary of Microsoft since 2018. It is commonly used to host open source software development projects. As of June 2022, GitHub reported having over 83 million developers and more than 200 million repositories, including at least 28 million public repositories. It is the largest source code host . History GitHub.com Development of the GitHub.com platform began on October 19, 2007. The site was launched in April 2008 by Tom Preston-Werner, Chris Wanstrath, P. J. Hyett and Scott Chacon after it had been made available for a few months prior as a beta release. GitHub has an annual keynote called GitHub Universe. Org ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rcsb
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. History Two forces c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioRuby
BioRuby is a collection of open-source Ruby code, comprising classes for computational molecular biology and bioinformatics. It contains classes for DNA and protein sequence analysis, sequence alignment, biological database parsing, structural biology and other bioinformatics tasks. BioRuby is released under the GNU GPL version 2 or Ruby licence and is one of a number of Bio* projects, designed to reduce code duplication. In 2011, the BioRuby project introduced the Biogem software plugin system, with two or three new plugins added every month. BioRuby is managed via the BioRuby website and GitHub repository. History BioRuby The BioRuby project was first started in 2000 by Toshiaki Katayama as a Ruby implementation of similar bioinformatics packages such as BioPerl and BioPython. The initial release of version 0.1 was frequently updated by contributors both informally and at organised “hackathon” events; in June 2005, BioRuby was funded by IPA as an Exploratory Software Proj ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioPerl
BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project. Background BioPerl is an active open source software project supported by the Open Bioinformatics Foundation. The first set of Perl codes of BioPerl was created by Tim Hubbard and Jong Bhak at MRC Centre Cambridge, where the first genome sequencing was carried out by Fred Sanger. MRC Centre was one of the hubs and birth places of modern bioinformatics as it had a large quantity of DNA sequences and 3D protein structures. Hubbard was using the th_lib.pl Perl library, which contained many useful Perl subroutines for bioinformatics. Bhak, Hubbard's first PhD student, created jong_lib.pl. Bhak merged the two Perl subroutine libraries into Bio.pl. The name BioPerl was coined jointly by Bhak and Steven Brenner at the Centre for Protein Engineering (CPE). In 1995, Brenner organized a BioPerl session at the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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