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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 Pro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioJava
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 d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BioJS
BioJS is an open-source project for bioinformatics data on the web. Its goal is to develop an open-source library of JavaScript components to visualise biological data. BioJS develops and maintains small building blocks (components) which can be reused by others. For a discovery of available components, BioJS maintains registry. History The first version of BioJS was released in 2012 by John Gomez. It was developed as a JavaScript library of web components to represent biological data in web applications. Version 2.0 included a complete redesign of the library and was released in 2014 as a Google Summer of Code project led by Manuel Corpas and developed by David Dao and Sebastian Wilzbach. Since then over 100 people contributed to the project. Currently more than 150 components are available in the BioJS registry. Selected list of published components * DAG Viewer * DNA Content Viewer * FeatureViewer * HeatMapViewer * Intermine analysis * Intermine endpoints * KEGGViewer * PPI- ... [...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 In ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open Bioinformatics Foundation
The Open Bioinformatics Foundation is a non-profit, volunteer-run organization focused on supporting open source programming in bioinformatics. The mission of the foundation is to support the development of open source toolkits for bioinformatics, organise developer-centric hackathon events and generally assist in the development and promotion of open source software development in the life sciences. The foundation also organises and runs the annual Bioinformatics Open Source Conference, a satellite meeting of the Intelligent Systems for Molecular Biology conference. The foundation participates in the Google Summer of Code, acting as an umbrella organisation for individual bioinformatics-related projects. The Open Bioinformatics Foundation was started in 2001, arising from the BioJava, BioPerl and BioPython projects. A formal membership for the foundation was created in 2005. In October 2012, the foundation began an association with Software in the Public Interest (SPI), a US-base ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences, such as calculating the distance cost between strings in a natural language or in financial data. Interpretation If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity between amino acids occupying a parti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Google Summer Of Code
The Google Summer of Code, often abbreviated to GSoC, is an international annual program in which Google awards stipends to contributors who successfully complete a free and open-source software coding project during the summer. , the program is open to anyone aged 18 or over, no longer just students and recent graduates. It was first held from May to August 2005. Participants get paid to write software, with the amount of their stipend depending on the purchasing power parity of the country where they are located. Project ideas are listed by host organizations involved in open-source software development, though students can also propose their own project ideas. The idea for the Summer of Code came directly from Google's founders, Sergey Brin and Larry Page. From 2007 until 2009 Leslie Hawthorn, who has been involved in the project since 2006, was the program manager. From 2010 until 2015, Carol Smith was the program manager. In 2016, Stephanie Taylor took over management of the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ruby (programming Language)
Ruby is an interpreted, high-level, general-purpose programming language which supports multiple programming paradigms. It was designed with an emphasis on programming productivity and simplicity. In Ruby, everything is an object, including primitive data types. It was developed in the mid-1990s by Yukihiro "Matz" Matsumoto in Japan. Ruby is dynamically typed and uses garbage collection and just-in-time compilation. It supports multiple programming paradigms, including procedural, object-oriented, and functional programming. According to the creator, Ruby was influenced by Perl, Smalltalk, Eiffel, Ada, BASIC, Java and Lisp. History Early concept Matsumoto has said that Ruby was conceived in 1993. In a 1999 post to the ''ruby-talk'' mailing list, he describes some of his early ideas about the language: Matsumoto describes the design of Ruby as being like a simple Lisp language at its core, with an object system like that of Smalltalk, blocks inspired by higher-o ... [...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. Organizational ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
