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BioJava
BioJava is an open-source software project dedicated to providing Java tools for processing 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 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 applicatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioJava 5 Module Layout
BioJava is an open-source software project dedicated to providing Java tools for processing 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 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] |
BioPython
Biopython is an Open-source software, open-source collection of non-commercial Python (programming language), Python tools for computational biology and bioinformatics.Refer to the Biopython website for othepapers describing Biopython and a list of over one hundrepublications using/citing Biopython It contains classes to represent biological sequences and Bioinformatics#Genome annotation, sequence annotations, and it is able to read and write to a variety of file formats. It also allows for a programmatic means of accessing online Biological database, databases of biological information, such as those at National Center for Biotechnology Information, NCBI. Separate modules extend Biopython's capabilities to sequence alignment, protein structure, population genetics, phylogenetics, sequence motifs, and machine learning. Biopython is one of a number of Bio* projects designed to reduce Duplicate code, code duplication in computational biology. History Biopython development began i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...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] |
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, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...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 birthplaces 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] |
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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of File Formats
This is a list of file formats used by computers, organized by type. Filename extension is usually noted in parentheses if they differ from the file format's name or abbreviation. Many operating systems do not limit filenames to one extension shorter than 4 characters, as was common with some operating systems that supported the File Allocation Table (FAT) file system. Examples of operating systems that do not impose this limit include Unix-like systems, and Microsoft Windows Windows NT, NT, Windows 95, 95-Windows 98, 98, and Windows Me, ME which have no three character limit on extensions for 32-bit or 64-bit applications on file systems other than pre-Windows 95 and Windows NT 3.5 versions of the FAT file system. Some filenames are given extensions longer than three characters. While MS-DOS and NT always treat the suffix after the last period in a file's name as its extension, in UNIX-like systems, the final period does not necessarily mean that the text after the last period i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Class (computer Programming)
In object-oriented programming, a class defines the shared aspects of objects created from the class. The capabilities of a class differ between programming languages, but generally the shared aspects consist of state ( variables) and behavior ( methods) that are each either associated with a particular object or with all objects of that class. Object state can differ between each instance of the class whereas the class state is shared by all of them. The object methods include access to the object state (via an implicit or explicit parameter that references the object) whereas class methods do not. If the language supports inheritance, a class can be defined based on another class with all of its state and behavior plus additional state and behavior that further specializes the class. The specialized class is a ''sub-class'', and the class it is based on is its ''superclass''. Attributes Object lifecycle As an instance of a class, an object is constructed from a class via '' ... [...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 arti ... [...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. mmCIF Closely related is mmCIF, macromolecular CIF, which is intended as an successor 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 relation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Anonymous Function
In computer programming, an anonymous function (function literal, 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 ''lambda'', and anonymous functions are often ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
