Help | Home

BioPHP - Info

Project types
Structure of functions
Structure of minitools
New code projects
Our panel of selected developers the start
BioPHP license

Introduction A wiki is a type of website that allows users to add and edit content and is especially suited for constructive collaborative authoring. BioPHP uses a Wiki service to allow this kind of collaboration, so that PHP code for biocomputing may be developed. As edition of PHP code may easily generated errors, only registered users are allowed to edit PHP code. Registered users with no-activity during 2 months are deleted. The original code which started the project is available as a reference, and the codes are regularly updated by a panel of selected developers or by the author who originaly submitted the project. Before editing and changing a code project, please try its functionality in a website. Project types Four types of projects are available at the moment:
  • GenePHP: Originally conceived by S. Gregorio as a rewrite or translation of BioPerl into PHP, it nevertheless contains some peculiar ideas of its authors. From the estructure point of view, five classes has been created, and each one contains many functions with potential to be used in many different PHP projects. New classes may be added to the list on request.
  • Functions: one or more related PHP functions are included in each project. The basic idea is to generate code that may be included in other application.
  • Minitools: the basic idea is to generate a set of complete copy and paste scripts for small tasks. A fully functional program will be often available. It will be the reference for both new and skilled developers, and although they are fully functional, they have been modified to avoid overusage of computational power in our server. Users willing to get the complete functionality ofthose minitools must copy them to a PHP enable webserver. Check here how to easily install a webserver with apache/PHP in your computer.
  • Tools: Those will be multipage scripts, scripts with special requeriments, as for example images, or programs with a PHP program used as a interface of a non-PHP script (perl, C...). Code will not be editable, but a form may be used to contact the author.
Structure of functions Each project may include an unique function or a set of related ones. We encourage developers to explain the different parts of the code, so that it will be easily understand by other users. Before adding new functions to bioPHP, search carefully other projects to avoid their duplication. Structure of minitools Minitools are one page complete scripts developed for simple task for training and demonstration. They may be also used by new users without programming skills for computation. In order to homogenize internal structure of minitools, we encourage users to keep a common basic structure in all minitools. A maximum of four different parts for each minitool is proposed, although this basic structure is open to changes when necessary:
  • a form: for input of data
  • the script: we encourage developers to consider "the script" as the basic structure of the program, and to use functions for specific tasks. This global structure will allow to easily copy functions to be used in other scripts.
  • the functions: they will be used to perform basic calculations. It is convenient to use very descriptive function names, and their behaviour may be explained in the top of each function when necessary.
  • additional information, as for example references concerning the procedures.
Please try to create simple scripts, and avoid unnecessary graphical representations. Our panel of selected developers may remove the unnecessary information. New code projects New projects for functions and minitools may be added to BioPHP by registered users. For minitools, no demo programs will be available until the program is reviewed by our panel of selected developers. Our panel of selected developers Some developers are allowed to update or delete code projects. When updating a code project, original code associated to each project will be updated with the last modified code, so that the list of recent changes associated to each project will be deleted and restarted. For minitools, a demo script will be generated which limits CPU usage but maintains when possible the functionality of the minitool. There are two ways to become a selected developer:
  • Users especially active may be invited to become selected developers. This selection process is semiautomatic: activity of developers is recorder, and the system informs the webmaster about the more active ones. This activity is checked before invitation to join us.
  • Users willing to be selected must contact us and request changing their status from normal developer to a selected one. Let us know as much information as possible about your skills, and within a few days you will get a response. An active user is more likely to be included in our panel of selected developers. the start This project was started in December 2005 by Dr. Joseba Bikandi, a lecturer in the Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, The University of the Basque Country, Vitoria-Gasteiz, Spain. Joseba has developed several PHP scripts for simulation of molecular biology techniques, and a website has been developped with those scripts at The aim of Joseba is to make available most of the source code running at his site throw Simultaneously, is open to code from other users as described above. BioPHP license Code published at is covered by the GNU General Public License (GPL) Version 2. All code submitted to will be covered by this License. All information included in this page may be changed to increase the efficiency of the system.