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BioPerl 1.0 Release
Submitted by Gary Van Domselaar; posted on Monday, March 18, 2002 (2 comments)
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Following is the press release by the Open Bio Foundation on the 1.0 Release of Bioperl:
The Bioperl project, the leading open source project for the use of Perl in bioinformatics has posted its 1.0 release. Bioperl provides a series of extensions to Perl for handling biological data, a field called bioinformatics. In recent years this field has exploded due to the massive data sets generated in molecular biology. The best known of these is the human genome project, which is an international collaboration to determine the DNA sequence of ourselves. This data is more than 100 New York phone books and storing and searching these massive datasets has become common place in modern biology. Bioperl is used to provide this computational infrastructure, in particular in the human genome project.
Bioperl was developed by a loose collaboration of individuals worldwide, similar to the open development ethos in Linux or Apache. There is no funding body behind it, all programming time is freely donated and decisions are made in an open forum by electronic mail. Both academics and commercial developers contribute to the project.
The Perl programming language is an ideal fit to bioinformatics, despite being originally designed for system administration. Most of the data generated is text-based. Even the DNA sequence itself is represented as long string of letters, and Perl's natural text handling means that otherwise complex problems can be simply solved. Bioperl was started in 1995, during the Perl4 heydays as young bioinformatics researchers started to share ideas about how to use this language in biology.
Since then the developer group has grown to 45 registered developers. In 1998 the project has found a permament home on the internet at bio.perl.org - the original machine hosting this system was in fact recovered from a dumpster to pressed into service in one developer's bedroom. The project received a hardware grant in 2000 and a centralised infrastructure grant from Sun in 2001. Network connectivity was donated by Wyeth in Boston, MA.
Bioperl has been used worldwide since 1998 but the project has always used conservative release numbering - for example, for the last 2 years, the stable release series was 0.7. By moving to 1.0, Bioperl is declaring that it is "feature complete" for sequence handling, the most common task in bioinformatics.
Bioperl is used in both small academic labs through to enterprise level computing in large pharmaceutical companies. Every large pharmaceutical company has used Bioperl at some point, and most are using it currently, some as part of their mission critical services. To manage the growth of Bioperl and the other Bio* projects (eg, BioJava), the Open Bioinformatics Foundation (OBF) was formed in 2001. OBF is registered non-profit organisation which owns the physical hardware and other assets of Bioperl and the other Bio projects (BioJava and BioPython).
For more information on Bioperl 1.0, read the release notes at
http://bio.perl.org/Core/Latest/Release-1.0.txt
For information on Bioperl generally, visit our web site at
http://bio.perl.org
For information on OBF, visit
http://open-bio.org
For follow-up information by email, send an email to
info[at]open-bio.org
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Anybody knows as I makes using bioperl to know the variants of a gene?
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Anybody knows as I makes using bioperl to know the variants of a gene?
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