Press Release
February 11, 2002
First O'Reilly Bioinformatics Technology Conference Built Bioinformatics Bridges
Sebastopol, CA--Not even a rare snowfall in Tucson could quench the
enthusiasm of the nearly 700 programmers, scientists, developers, and
researchers participating in the first O'Reilly Bioinformatics
Technology Conference, held January 28-31, 2002 at the Westin La Paloma
Resort. "Bioinformatics is one of the next great revolutions in the
computer industry," asserts O'Reilly & Associates founder and president
Tim O'Reilly. "It pushes us forward on so many fronts, not just in the
raw biological science. It's an area where massive computing needs,
huge databases, and innovative web services are all pushed to their
limit. The conference's underlying theme was the importance of
collaboration, data sharing, and peer review, and the role of open
source software in keeping openness a key part of this new science."
While other bioinformatics conferences have focused on academic papers
and project results, an exceptionally receptive audience in Tucson
illustrated the thirst for knowledge of programming solutions to
biological science issues. "Bioinformatics is about combining the
collective wits of programmers and scientists to create tools that will
allow us to find our way through the enormous amounts of biological
data," says co-chair Lorrie LeJeune. "Yes, we have drafted a map of the
human genome. We can see that there are 'streets,' but we don't yet
know what planet we're on, much less the city we're in. Biological data
has maddening subtleties, complexities and redundancies--with better
tools, we can perform better analyses, which in turn will yield more
accurate conclusions. It's these conclusions that will ultimately
determine such things as treatments for diseases and drug therapies. We
planned this conference to help bioinformaticians 'read the maps'
because bioinformatics not only has amazing potential, it's already
changing our lives."
Notes conference co-chair Nathan Torkington, "Conferences are all about
the flow of information. Not only were bioinformatics software
developers giving information to the audience, but there was a
tremendous amount of communication between the leaders of different
groups." Wet lab researchers and programmers alike came together for
discussion and discovery. Every one of the six keynote addresses were
packed; a second session had to be added to Peter Schattner's wildly
popular "Perl & Bioperl" tutorial.
Participants heard from pioneers and up-and-coming innovators James
Ostell, Ewan Birney, Terry Gaasterland and Christopher Hogue. In his
closing keynote, Leroy Hood discussed how the Human Genome Project has
led to several paradigm changes in systems biology, and predictive and
preventive medicine. In his keynote, O'Reilly author Lincoln Stein
addressed the benefits of moving towards a cooperative, formal Web
services model for bioinformatics data providers to reduce the
fragmentation of bioinformatics protocols, technologies and standards.
In a separate session, Stein described the Distributed Sequence
Annotation System (DAS), an open source protocol and tool set for
exchanging annotations on genomic sequences. DAS allows a single
machine to gather information from multiple, geographically separated
annotation databases, collate the information, and display it to the
user in a single integrated view.
James Tisdall, conference tutorial leader and author of "Beginning Perl
for Bioinformatics," comments: "I think the most important result of
the conference is an enhanced dialogue between biologists and
programmers. Important open source infrastructure was not only
presented, but was also developed in the great 'hack-a-thon' that
resulted in a solid advance in the inter-operability of the major open
source biology projects. My only regret was that there were so many
interesting talks that I couldn't get to. But the most satisfying thing
to me was the high level of interest on the part of newcomers to the
bioinformatics field who were in attendance. This enthusiasm is bound
to be translated into some good science in the months and years ahead."
The hackathon Tisdall refers to was the conference's unofficial
kick-off, led by Ewan Birney, Ensembl project leader at the European
Bioinformatics Institute. Three days of high-tech biohacking was fueled
by the eye-popping hardware provided by Apple, and low-tech
person-to-person interaction. Explains Torkington, "In much the same
way as the invention of the web browser changed the way people accessed
information on the net, this project promises to change the way
bioinformaticians access sequence data on the net. Our vision is to
create a single client library that knows how to fetch sequences from a
variety of sources, removing the need for the end user to know *where*
everything is kept to focus on what they want to do with the
information."
While project design (bioperl, biojava, and biopython representatives
settling on the infrastructure's essential features and support
languages) was the goal for Tucson, the proof-of-concept
implementations were nearly completed as well. Several new technologies
are being developed as part of the hackathon work: BioFetch, a simple
web-based protocol for fetching sequence information, and BioSQL, a
standard interface to sequence information in a relational database.
Progress continues via email, and later this month the twenty-odd
developers will reunite in Cape Town, South Africa--headquarters of
co-sponsor Electric Genetics-where the client library project is
expected to be completed. The results of the hackathon will be free and
available to all. Birney will continue his public dialogue on
bioinformatics and open source by presenting a keynote address at
O'Reilly's Open Source Convention in San Diego this summer.
Other highlights of the conference include:
Bioinformatics.Org ran a specialized track within the conference, and
also revealed its first-ever Benjamin Franklin Award winner: Michael
Eisen of the Lawrence Berkeley National Laboratory. Following the award
presentation for promoting freedom and openness in bioinformatics,
Eisen delivered a laureate talk on the Public Library of Science
project.
Members of the Gene Ontology Consortium met at the end of
the O'Reilly Bioinformatics Technology Conference to provide
demonstrations and discussions of current annotation efforts of
consortium members and future development plans by users of GO.
Sponsors and exhibitors packed the exhibit hall for two days during
the conference, showcasing both the latest products and services, as
well as the efforts of bioinformatics community organizations.
Attendees warmed to O'Reilly's "green" commitment, appreciating the
recycled materials used to create the pen, writing tablet, t-shirt, and
messenger-style bag for the conference.
Concludes Tim O'Reilly, "The essence of what we do at O'Reilly
conferences is bring together a core group of the key developers for a
given technology and people who want to learn from them. But we also
try to frame the conference so that the attendees learn not just about
specific tools or techniques but big picture ideas." More bridges will
no doubt be crossed by the time the next O'Reilly Bioinformatics
Technology Conference rolls around in early 2003.
Online Resources:
About O'Reilly
O'Reilly Media spreads the knowledge of innovators through its books, online services, magazines, and conferences. Since 1978, O'Reilly Media has been a chronicler and catalyst of cutting-edge development, homing in on the technology trends that really matter and spurring their adoption by amplifying "faint signals" from the alpha geeks who are creating the future. An active participant in the technology community, the company has a long history of advocacy, meme-making, and evangelism.
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