[Bioperl-l] Press Release for Bioperl 1.0

Ewan Birney birney@ebi.ac.uk
Mon, 18 Mar 2002 19:01:58 +0000 (GMT)

This is a press release thing I am circulating for the 1.0 release. If
you know any journalists, or otherwise want to promote it, do forward this
text on.

I have to say, a warm, fuzzy feeling hits me as I think of where this all
started, back when Perl5 was a twinkle in Larry Wall's eye and Steve
Brenner was using this strange language called Perl to handle SCOP. 

We've come along way. We've got a long way to go. But it is certainly good

[PS *Everyone* owes jason beers for the last 2 weeks of his life]


   Bioperl 1.0 release.

   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


  For information on Bioperl generally, visit our web site at


  For information on OBF, visit http://open-bio.org

  For follow-up information by email, send an email to


Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420