BioPHP is a collection of

open-source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...

PHP PHP is a General-purpose programming language, general-purpose scripting language geared toward web development. It was originally created by Danish-Canadian programmer Rasmus Lerdorf in 1993 and released in 1995. The PHP reference implementati ...

code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other

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 combin ...

tools. BioRuby is released under the

GNU GPL The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the four freedoms to run, study, share, and modify the software. The license was the first copyleft for general ...

version 2 licence and is one of a number of Bio* projects, designed to reduce

code duplication 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 undesirable for a nu ...

. As an open source bioinformatics project, BioPHP is affiliated with the

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, ...

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 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 sup ...

and BioPython and BioRuby. BioPHP was developed in December 2005 by Joseba Bikandi at the

University of the Basque Country The University of the Basque Country ( eu, Euskal Herriko Unibertsitatea, ''EHU''; es, Universidad del País Vasco, ''UPV''; UPV/EHU) is a Spanish public university of the Basque Autonomous Community. Heir of the University of Bilbao, initially ...

Spain , image_flag = Bandera de España.svg , image_coat = Escudo de España (mazonado).svg , national_motto = '' Plus ultra'' ( Latin)(English: "Further Beyond") , national_anthem = (English: "Royal March") , ...

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 and protein sequences and sequence alignments. Each class is designed to be general enough to be useful in a number of BioPHP projects. Similarly, the Functions project aims to create a number of functions to perform tasks on class objects and reduce code duplication between projects. The Minitools and Tools projects aim to generate a set of PHP scripts for small, repetitive tasks; scripts in the Tools project generally have special requirements, such as interfacing with non-PHP scripts and/or code (written in, for instance,

Perl Perl is a family of two High-level programming language, high-level, General-purpose programming language, general-purpose, Interpreter (computing), interpreted, dynamic programming languages. "Perl" refers to Perl 5, but from 2000 to 2019 it ...

or C).

References

External links

*{{Official website, http://biophp.org/
An object-oriented BioPHPLee Katz's biophp
Free bioinformatics software

History

Projects

See also

References

External links