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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. BioPHP was developed in December 2005 by Joseba Bikandi at the University of the Basque Country, Spain as an extension of GenePHP. GenePHP is one of the four projects currently forming BioPHP. Projects BioPHP is divided into four 'projects'. The GenePHP project has a similar structure to other Bio* projects, with a number of classes representing (amongst other things) DNA ... [...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] |
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 ... [...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] |
Open-source Software
Open-source software (OSS) is Software, computer software that is released under a Open-source license, license in which the copyright holder grants users the rights to use, study, change, and Software distribution, distribute the software and its source code to anyone and for any purpose. Open-source software may be developed in a collaborative, public manner. Open-source software is a prominent example of open collaboration, meaning any capable user is able to online collaboration, participate online in development, making the number of possible contributors indefinite. The ability to examine the code facilitates public trust in the software. Open-source software development can bring in diverse perspectives beyond those of a single company. A 2024 estimate of the value of open-source software to firms is $8.8 trillion, as firms would need to spend 3.5 times the amount they currently do without the use of open source software. Open-source code can be used for studying and a ... [...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] |
GNU GPL
The GNU General Public Licenses (GNU GPL or simply GPL) are a series of widely used free software licenses, or ''copyleft'' licenses, that guarantee end users the freedom to run, study, share, or modify the software. The GPL was the first copyleft license available for general use. It was originally written by Richard Stallman, the founder of the Free Software Foundation (FSF), for the GNU Project. The license grants the recipients of a computer program the rights of the Free Software Definition. The licenses in the GPL series are all copyleft licenses, which means that any derivative work must be distributed under the same or equivalent license terms. The GPL is more restrictive than the GNU Lesser General Public License, and even more distinct from the more widely used permissive software licenses such as BSD, MIT, and Apache. Historically, the GPL license family has been one of the most popular software licenses in the free and open-source software (FOSS) domain. Promi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Duplicate Code
In computer programming, duplicate code is a sequence of source code that occurs more than once, either within a program or across different programs owned or maintained by the same entity. Duplicate code is generally considered Code smell, undesirable for a number of reasons. A minimum requirement is usually applied to the quantity of code that must appear in a sequence for it to be considered duplicate rather than coincidentally similar. Sequences of duplicate code are sometimes known as code clones or just clones, the automated process of finding duplications in source code is called clone detection. Two code sequences may be duplicates of each other without being character-for-character identical, for example by being character-for-character identical only when white space characters and comments are ignored, or by being token (parser), token-for-token identical, or token-for-token identical with occasional variation. Even code sequences that are only functionally identical may b ... [...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] |
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] |
University Of The Basque Country
The University of the Basque Country (, ''EHU''; , ''UPV''; officially EHU) is a Spanish public university of the Basque Country (autonomous community), Basque Autonomous Community. Heir of the University of Deusto, University of Bilbao, initially it was made up of the Faculty of Economic and Business Sciences of Sarriko (1955), Medicine (1968) and Sciences (1968). Following the General Law of Education (1970), the Nautical School (1784), the School of Business Studies of Bilbao (1818) and the Technical Schools of Engineers (1897) joined in, until it grew into the complex of thirty centers that compose it presently. It has campuses over the three provinces of the autonomous community: Bizkaia Campus (in Leioa, Bilbao, Portugalete and Barakaldo), Gipuzkoa Campus (in San Sebastián and Eibar), and Alava Campus in Vitoria, Spain, Vitoria-Gasteiz. It stands out as the main research institution in the Basque Country, carrying out 90% of the basic research carried out in that territory ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Spain
Spain, or the Kingdom of Spain, is a country in Southern Europe, Southern and Western Europe with territories in North Africa. Featuring the Punta de Tarifa, southernmost point of continental Europe, it is the largest country in Southern Europe and the fourth-most populous European Union member state. Spanning across the majority of the Iberian Peninsula, its territory also includes the Canary Islands, in the Eastern Atlantic Ocean, the Balearic Islands, in the Western Mediterranean Sea, and the Autonomous communities of Spain#Autonomous cities, autonomous cities of Ceuta and Melilla, in mainland Africa. Peninsular Spain is bordered to the north by France, Andorra, and the Bay of Biscay; to the east and south by the Mediterranean Sea and Gibraltar; and to the west by Portugal and the Atlantic Ocean. Spain's capital and List of largest cities in Spain, largest city is Madrid, and other major List of metropolitan areas in Spain, urban areas include Barcelona, Valencia, Seville, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Perl
Perl is a high-level, general-purpose, interpreted, dynamic programming language. 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. Perl originally was not capitalized and the name was changed to being capitalized by the time Perl 4 was released. The latest release is Perl 5, first released in 1994. From 2000 to October 2019 a sixth version of Perl was in development; the sixth version's name was changed to Raku. Both languages continue to be developed independently by different development teams which liberally borrow ideas from each other. Perl borrows features from other programming languages including C, sh, AWK, and sed. It provides text processing facilities without the arbitrary data-length limits of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
