Contacts: Bernard Moret, (505) 277.5699
Stephanie Forrest, (505) 277.7104
Steve Carr, (505) 277.1821
September 17, 2003
UNM TO COLLABORATE ON TWO INFORMATION TECHNOLOGY RESEARCH
AWARDS THROUGH THE NATIONAL SCIENCE FOUNDATION
The University of New Mexico will collaborate with a number of institutions on two separate
Information Technology Research (ITR) “large” (over $5 million) awards announced by the
National Science Foundation today. The grants, totaling more than $24 million, are two of only
eight awarded from an initial field of 70.
This is the second year in a row UNM is the lead institution on a large ITR grant, last year's
was the SEEK project led by Biology Professor William Michener. UNM joins Carnegie
Mellon University, MIT, Cal-Berkeley, Cal-San Diego and the University of Florida as one of
the six institutions ever to be the lead institution on more than one large ITR grant in the
four-year history of the program.
UNM leads on the $11.6 million, 13-institution effort to develop computational tools to explore
evolutionary relationships among all species of living organisms forming the “Tree of Life.”
Spearheaded by Project Director Bernard Moret, professor of computer science in the School of
Engineering (SOE), the main collaborative institutions also include Florida State University,
UC Berkeley, UC San Diego and the University of Texas-Austin.
“This is an ambitious project to assemble an evolutionary Tree of Life that includes all known
plants and animals,” said Terry Yates, UNM Vice Provost for Research. “It will provide a
predictive and comparative framework for all fundamental and applied biology. This will
basically provide the infrastructure to allow us to pursue a variety of projects that benefit
society such as new drug discoveries, identify merging diseases and predict outbreaks, to
discover new life forms, to improve global agriculture and many other things we couldn’t do
previously because we didn’t know how these organisms were related. Developing a
comprehensive understanding of life’s history will advance all biology and provide enormous
benefits to society.
“Assembly of a comprehensive Tree of Life is like putting a man on the moon in terms of the
scope of the project. Among other things this effort of humans and resources. In addition,
there’s a lot of computational challenges to handle in the assembly of roughly 1.7 million
organisms.”
Constructing the “Tree of Life” poses one of the most complex biological problems and
represents challenges much greater than sequencing the human genome. Almost two million
species of organisms have been discovered and described, yet it is estimated that tens of
millions remain to be discovered. Some 60 to 70 thousand species have been studied in some
detail, but the resulting data are far from complete, so relatively little is known about
phylogenetic relationships of Earth's species or among the major branches of the Tree.
“Reconstructing the Tree of Life is extremely important -- we will get a better picture of how
life has evolved on earth, a better understanding of where we come from as humans, and a
sense of where life may be headed, on a very long time scale,” said Moret. “Among the many
consequences of obtaining an accurate reconstruction of the Tree, our understanding of the
relationships between the genetic code and cell functions will expand enormously, thus
accelerating the pace of biomedical discoveries.”
The relationships in the Tree of Life can be determined by comparing DNA sequences, the
encoded blueprint determining the characteristics of each organism. The relative similarities
between DNA sequences among different organisms allow scientists to predict the relationships
of these organisms to their common ancestors.
The end result is a map that describes species by their relationships to their close common
ancestors and to their more distant relations, much like a family tree. The map will depict the
evolutionary relationships of Earth's taxonomic diversity -- including living and extinct forms -over the past 3.5 billion years of its existence. Developing this map has long been a high
priority for biologists, but doing so requires an extraordinary computational effort.
“The computational problem is extremely difficult,” said David A. Bader, co-investigator on
the project and UNM professor of computer science. “Even with entirely novel solutions
methods, an enormous amount of computational power will be required to construct the first
version of such a tree.”
The focus of the initiative is to establish a national resource to move the research community
closer to realization of the Tree of Life. This resource will serve as an incubator to promote the
development of new ideas for this enormously challenging computational task and to create a
forum where experimentalists, computational biologists, and computer scientists share data,
compare methods, and analyze results, thereby speeding up tool development while also
sustaining current biological research projects.
“In order to assemble a Tree of Life we are going to need two different things. One is a lot of
data on existing species,” said Moret. “We don't have nearly enough yet. Then, we're going to
need computational methods and computational power to take the data and make sense out of
it.”
“Thus the goal of our ITR project is to provide the computational infrastructure -- including
algorithms, software, machines, and databases -- to support the analysis once more data have
been
collected,” added Moret. “We will do analyses all along the way, of course, but a full-scale
attempt at reconstructing the Tree of Life will not take place for many years yet: just coming up
with methods and platforms to operate at that scale will take us at least five years, not to
mention that collecting enough
data to support the reconstruction will require the efforts of teams of biologists all over the
world for many years.”
The resource will be composed of a large computational platform, a collection of interoperable
high-performance software for phylogenetic analysis, and a large database of datasets (both real
and simulated) and their analyses. The platform will be Internet accessible by developers,
researchers and educators. The software, freely available in source form, will be usable on
scales varying from laptops to supercomputers and will be packaged to be compatible with
current popular tools.
“We are very excited about this opportunity,” said Fran Berman, Director of the San Diego
Supercomputer Center at UC San Diego. “It gives us a chance to stretch the bounds of
technology to enable new science. Scientists in many fields are now confronted with large data
resources and so require new kinds of tools to help them sort and understand their data. We will
be working on developing critical cyberinfrastructure with the Tree of Life project.”
This project will bring together researchers from many areas and foster new collaboration and
styles
of research in computational biology; moreover, the interaction of algorithm design, database
management, large scale modeling, and biology will give fresh impetus and directions to each
area. The project also aims to increase public understanding of evolutionary relationships,
genomics and bioinformatics through informal education programs at its museum partners, the
American Museum of Natural History, the Peabody Museum at Yale University and the Jepson
Herbaria at UC Berkeley.
An additional large ITR award funded this year involves UNM Computer Science Professor
Stephanie Forrest. She is co-principal investigator on a $12.5 million ITR award titled,
“Sensitive Information in a Wired World,” led by Stanford University Professor Dan Boneh.
This project seeks to develop methods for data mining that respect and protect individual rights,
but
allow law enforcement and legitimate users to mine massive data sets. The research team will
also
develop database tools that enforce privacy policies while managing sensitive data and release
tools for end-users to prevent identity theft via spoofed or malicious websites.
“The idea behind the project is that more and more of our personal data and sensitive
information live on the Internet and are shipped around and accessed by many intermediate
parties,” said Forrest. “The question is how to protect that data. Traditional approaches to
computer security focus on narrow technical concerns and this project takes a broader view,
taking into account how technical
solutions interact with legal and other social institutions.
“The research we’ll be conducting at UNM focuses on two aspects. In the past we have studied
biologically inspired methods for computer security. My role in the project is to think about
biologically inspired methods for protecting data. In particular, one of the projects we’ll be
working on involves privacy enhancing databases. The idea is to protect the privacy of personal
information stored in databases, while still allowing legitimate activities such as
epidemiological studies or searches for
potential terrorists.”
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