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Since its inception in October 2005, the BioPerl Wiki has become the goto (a good goto, that is) place for information on Bioperl development, documentation, installation and support. It's an experiment that worked--the main page has received over 600,000 hits.



The wiki is what it is because of the contributions of its users. We welcome and appreciate your edits. Please see our style guide for information. Below are some helpful MediaWiki editing links.

Module Documentation

There is a wiki page for every BioPerl module, if there is a newly created module we will need to add it to the site with our boilerplate template mentioned in the style guide. A listing of all pages in the Module namespace is available from Special:Allpages. We encourage the addition to these pages of snippets of code showing how to use these modules, workarounds, and pointers to other modules which are complementary. Comments and discussions about a module and its implementation should be localized to the discussion paired for each wiki page.

The Deobfuscator was written by Dave Messina as a browseable cgi interface to the modules. It comes (free!) with every distribution, and is also available here.

For other documentation options, please see Getting Started.

Editing Mediawiki

Some links to MediaWiki markup and Wikipedia editing help:

In addtion to direct editing the wiki pages via HTML in your web browser, you can download mediawiki pages and edit with local editors using the perl module WWW::Mediawiki::Client module - see the mvs client as part of the package.

Emacs users will find the wikipedia-mode very helpful. See this article for installation instructions.

Other BioPerl Media

In addition to the wiki, BioPerl has several other media choices for news, information and support.

  • The BioPerl mailing list is the place to send questions or ideas to a large group of experts (sign up here);
  • For a peek under the hood or gratuitous inbox dumping for the lonely, there is BioPerl guts, where all bug reports and Git commit messages go (sign up here);
  • See the blog for sporadically updated news;
  • The IRC on freenode.net/#bioperl is populated with friendly, helpful folk. The atmosphere is less formal than on the list;
  • For all BioPerl all the time, tune into BioPerl Twitter.


Help with Wiki Problems

To report a technical problem with the wiki (login/password problems, Database/Apache errors), please send an email to: support - AT - open-bio.org.

A list of wiki sysops is here.

Plugins and Extensions

We are happily using the Biblio.php extension from Martin Jambon to generate the bibliographic links on many pages. See the style guide for more information on using it.

We are also using the Winter extension for some scripting in our templates.

The GeSHi and GeSHiHighlight extension is used to generate pretty code markup for text that is enclosed in <perl></perl> blocks.

Information about plugins can be found at the Special:Version page including links to the installed Winter and RSS modules.


The BioPerl wiki uses Captcha to screen new users, through the ConfirmEdit MediaWiki extension. Rationale can be found on this page.

Happy Coding!

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