BioPHP Homepage - Mainframe

BioPHP: PHP for Biocomputing

Last updated: November 1, 2003 (Saturday)

Welcome Message

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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.

Sergio E. Gregorio, Jr.
Project Proponent

[ Project Objective ] [ What can BioPHP do? ] [ BioPHP Files ] [ Various Links ] [ My Resume ]

What's New?

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Cayte Lindner has submitted code for parsing KEGG GLYCAN data files. We'll be posting it here soon. (Oct 31, 2003)

Joel Dudley has begun work on modules related to Evolution and Phylogenetics. (Oct 31, 2003)

I'm back from my "hiatus" and itching to write code! But before that, I'm posting BioPHP 1.1 source code under development, particularly the parsers for KEGG files, PDB protein file, the Entrez Genome file, and other file formats (part 1) and (part 2), and the all-important include files, seq.inc.php, etc.inc.php, and seqdb.inc.php. Keep coming back to this site as I'll be posting a few more files later. Also, I'll try to package the different files as one downloadable GZ/ZIP file. - Serge (Oct 22, 2003)

Our site is slowly growing as shown by the latest stats from Sourceforge. (Oct 19, 2003)

Joseba Bikandi has written PHP code for Polymerase Chain Reaction (PCR) which you can find here. All we need to do now is find a way to plug them into BioPHP... (Sep 2003)

Finally, a site update after nearly 2 months! The www.biophp.net site is now up courtesy of Bravepages. (Aug 15, 2003)

We have four new members on board! Let's welcome Anton, Joseba, Joel, and Nileshwar. (Aug 2003)

Whoever said we can't take criticisms? Check out these sites (loudthinking.com and crummy.com) which take a critical/skeptical view of BioPHP and see if you agree or disagree. (Aug 15, 2003)

Don't forget to visit the Demo Scripts Page, the I/O Scripts Page, and the page on Known Bugs in BioPHP 1.0 (July 2003)

What is Bioinformatics?

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Bioinformatics is...

the application of information technology (IT) to the management of (usually large sets of) biological information, such as DNA, RNA, and protein sequence and structural data.
focused on information management (development of biological databases, DB interfaces, and query tools) and data mining (tools for detection of patterns in biological data).
a subset of "computational biology," which is the use of quantitative methods and techniques in modeling biological systems, e.g. simulation of biochemical and cellular processes, molecular motions and interactions, etc.
interdisciplinary and borrows heavily from the field of mathematics, computer science, linguistics, etc.
an valuable research tool because it generates "leads" or hypotheses that can then be tested experimentally.

What is PHP?

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PHP is...

a server-side HTML-embedded scripting language (unlike Javascript which is run on the "client-side").
capable of doing anything any other CGI program can do, such as collect form data, generate dynamic page content, send and receive cookies, etc.
known for its support for a wide range of databases.
relatively simple and easy to use (when compared to, say, Perl or Java).
capable of "talking" to other services using protocols such as IMPA, SNMP, NNTP, POP3, HTTP, etc.
has a large installation base and a vibrant developer community.
located at www.php.net (official home page).

Project Objective

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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 Members

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Project Administrator: Serge Gregorio, Jr.
Developers/Admin:
    Anton Bergheim
    Elpidio Latorilla, Germany
    Frankie Asseg, Germany
    Greg Tyrell, New South Wales, Australia
    Joel Dudley, Arizona, USA
    Joseba Bikandi, Spain
    Katherine Lindner, New England, USA
    Nico Stuurman, California, USA
    Nileshwar Dosooye, Tennessee, USA
    Rogelio Nocom, Manila, Philippines
    Sean Clark, Idaho, USA
    Serge Gregorio, Jr., Manila, Philippines
    Sujeevan Ratnasingham
Other Contributors:
    Brandon King, USA
    Dominik Gehl, France
    Jesus Castagnetto
    Stephan Montagnes
Bioinformatics Advisor:
    Allan Sioson, Virginia, USA

Click here for more information on the project.

What can BioPHP do?

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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:

read biological data in the GenBank, Swissprot, Fasta, and Clustal ALN formats
allows user to navigate data spread across several flat files.
can do simple sequence analysis tasks such as computing molecular weights, translating codons to amino residues, generating the charge, chemgrp, consensus strings, etc.
can look for patterns in sequences such as start and stop codons, mirrors and palindromes, and other more complex patterns (represented as regular expressions).
can digest a nucleic sequence using one or more restriction enzymes or endonucleases.
can interface with external programs such as Clustal, to align two or more nucleic or protein sequences

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

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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.

Version 1.0 code was written entirely by Serge Gregorio, Jr.

BioPHP (GenePHP) 1.0 Source Code:

Click on the

icon to view the source code online.

	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

You can download the source code from Sourceforge's download page.

BioPHP (GenePHP) 1.0 Documentation:

BioPHP Online Technical Reference

BioPHP How To - Installation and Quickstart

BioPHP (GenePHP) 1.0 Source Code:

You can download the source code from Sourceforge's download page.

BioPHP (GenePHP) 1.0 Documentation:

BioPHP source code is covered by the GNU General Public License (GPL) Version 2.