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 and view the source code, design documents, or content of the product. The open source model is a decentrali ...

PHP PHP is a general-purpose scripting language geared towards web development. It was originally created by Danish-Canadian programmer Rasmus Lerdorf in 1993 and released in 1995. The PHP reference implementation is now produced by the PHP Group. ...

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

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, ...

tools. BioRuby is released under the

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 ...

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 n ...

. 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 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 ...

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 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, initial ...

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 Eur ...

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 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 ...

or C).

References

External links

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

History

Projects

See also

References

External links