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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] |
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] |
Ewan Birney
John Frederick William Birney (known as Ewan Birney) (born 6 December 1972) is joint director of EMBL's European Bioinformatics Institute (EMBL-EBI), in Hinxton, Cambridgeshire and deputy director general of the European Molecular Biology Laboratory (EMBL). He also serves as non-executive director of Genomics England, chair of the Global Alliance for Genomics and Health (GA4GH) and honorary professor of bioinformatics at the University of Cambridge. Birney has made significant contributions to genomics, through his development of innovative bioinformatics and computational biology tools. He previously served as an associate faculty member at the Wellcome Trust Sanger Institute. Education Birney was educated at Eton College as an Oppidan Scholar. Before going to university, Birney completed a gap year internship at Cold Spring Harbor Laboratory supervised by James Watson and Adrian Krainer. Birney completed his Bachelor of Arts degree in Biochemistry at the University of Oxfor ... [...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] |
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] |
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] |
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] |
BioPHP
BioPHP is a collection of open-source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools. BioRuby is released under the GNU GPL version 2 licence and is one of a number of Bio* projects, designed to reduce code duplication. As an open source bioinformatics project, BioPHP is affiliated with the Open Bioinformatics Foundation. History The BioPHP project grew out of GenePHP, which was started by Serge Gregorio in 2003. GenePHP was conceived as a PHP-based implementation of similar bioinformatics packages such as BioPerl and BioPython and 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 biol .... BioPHP was developed in December 2005 by Joseba Bikandi at the University of the Basque Country, Spain as an extens ... [...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] |
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] |
Perl
Perl is a family of two high-level, general-purpose, interpreted, dynamic programming languages. "Perl" refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned "sister language", Perl 6, before the latter's name was officially changed to Raku in October 2019. Though Perl is not officially an acronym, there are various backronyms in use, including "Practical Extraction and Reporting Language". Perl was developed by Larry Wall in 1987 as a general-purpose Unix scripting language to make report processing easier. Since then, it has undergone many changes and revisions. Raku, which began as a redesign of Perl 5 in 2000, eventually evolved into a separate language. Both languages continue to be developed independently by different development teams and liberally borrow ideas from each other. The Perl languages borrow features from other programming languages including C, sh, AWK, and sed; They provide text processing facilities without the arbitrary data-le ... [...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 it is usually noted in parentheses if they differ from the file format 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 NT, 95- 98, and 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 is the file's extension. Some file formats ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioconductor
Bioconductor is a Free software, free, Open-source software, open source and Open source software development, open development software project for the analysis and comprehension of Genome, genomic data generated by Wet laboratory, wet lab experiments in molecular biology. Bioconductor is based primarily on the statistics, statistical R (programming language), R programming language, but does contain contributions in other programming languages. It has two Software release life cycle, releases each year that follow the semiannual releases of R. At any one time there is a Software versioning, release version, which corresponds to the released version of R, and a Software versioning, development version, which corresponds to the development version of R. Most users will find the release version appropriate for their needs. In addition there are many genome annotation packages available that are mainly, but not solely, oriented towards different types of microarrays. While computati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
