BioPHP: PHP for Biocomputing
Last updated: November 1, 2003 (Saturday)
You have reached the new home of the BioPHP Project. This project is sponsored by Joseba Bikandi of in-silico.com. The project aims to extend the PHP scripting language so it can be used for biology, in general, and bioinformatics, in particular. The project currently has 14 members, and 7,000+ lines of source code. Among other features, its code can read GenBank and Swissprot data files.
The project is still (and always) a work in progress. We are currently building a model for biological data that falls within the scope of the project. Work is also underway to write code that can read other files such as the Kegg Ligand and Biopathways, Prosite, and PDB. We would like to encourage people to join and contribute to the project, be it in the computing side or in the biology side. Finally, I would like to thank all the members for their efforts and sacrifices.
E. Gregorio, Jr.
[ Project Objective ] [ What can BioPHP do? ] [ BioPHP Files ] [ Various Links ] [ My Resume ]
|What is Bioinformatics?||top|
|What is PHP?||top|
The BioPHP Project is a non-profit, open source software project that aims to extend the PHP scripting language so it can be used to develop bioinformatics applications. BioPHP per se is NOT a bioinformatics application. Rather, it is a collection of tools to help PHP developers write bioinformatics applications more rapidly than if they had to start from scratch using "vanilla PHP".
Project Administrator: Serge Gregorio, Jr.
Click here for more information on the project.
|What can BioPHP do?||top|
Before answering this question, it is better to ask, "What is BioPHP meant to do?" BioPHP, as we conceived it, is primarily a tool for developing web-based bioinformatics applications. While PHP can be used to write non-web scripts, we believe PHP's strength lies in the web. We envision BioPHP to be the "GLUE" that binds local and remote bioinformatics applications and databases together. The figure entitled BioPHP's Place in the Universe illustrates this.
Back to what it can do at the moment. Below is a short list of features of BioPHP (GenePHP) release 1.0:
You may want to take a look at a preliminary design for BioPHP.
To the question, "Why build BioPHP when there is BioPerl, BioJava, BioPython, etc.?" Our answer to this question is another question, "Why have PHP in the first place when there is Perl, Java, Python, etc.?", or "Why can't we just have ONE universal programming language?" When you've got an answer to these questions, please let me know.
|The BioPHP Files||top|
BioPHP (GenePHP) 1.0 was developed and tested on a PC running Windows 98, Apache
1.3.20, and PHP 4.0.6. It should work on Unix too.
BioPHP (GenePHP) 1.0 Source Code:
|seq.php - (short for "Sequence") contains code for the Seq Class.|
|seqdb.php - (short for "Sequence Database") contains code for the SeqDB Class.|
|resten.php - (short for "Restriction Enzyme") contains code for the RestEn Class.|
|seqalign.php - (short for "sequence alignment") contains code for the SeqAlign Class.|
|etc.php - (short for "et cetera") contains miscellaneous code|
BioPHP Online Technical Reference
BioPHP How To - Installation and Quickstart
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Copyright © 2003 by Sergio Gregorio, Jr.