Avaki has co-authored a proposed standard for identifying biologically
significant data in life sciences applications.
The proposal, submitted to the Technical Architecture working group of
the Interoperable Informatics Infrastructure Consortium (I3C), is
co-authored by members from Whitehead/MIT Center for Genome Research,
Avaki, and Millennium Pharmaceuticals.
The Life Sciences Identifier
(LSID) defines a simple, standard way for any application to identify
and access biologically significant data, enabling researchers in life
sciences to make more effective use of applications and data to solve
important scientific problems, Avaki said. LSID is adapted from Avaki's
architecture for identifying Grid resources, as is the Secure Grid
Naming Protocol (SGNP), a proposed standard Avaki submitted to Global
Grid Forum earlier this year.
"Adoption of a naming protocol such as LSID, in concert with other
important architecture recommendations, enables I3C to accelerate the
development of interoperable life sciences applications," Avaki CEO
David Fish said in a statement.
LSID reduces the complexity of managing data in life sciences, where
researchers must sort through and analyze data from many sources in
order to advance their research, Avaki said. Nowhere is this problem
more pressing than in the early phases of drug discovery, the company
said.
"The pharmaceutical industry is experiencing an unprecedented level of
outsourcing, partnering, and corporate-academic collaboration, which
require a high volume of information sharing," Avaki said. "At the same
time, the amount and variety of data is staggering. LSID, and
applications based on it, makes it easier for companies to manage the
data and the collaborations required to move scientific discoveries
ahead by providing for scalable, secure, and migration-transparent
naming of biological data."
LSID was adapted from Avaki's Grid naming architecture and Millennium
Pharmaceuticals' MuID specification. Avaki's Grid software provides
wide-area access to processing, data, and application resources in a
single, uniform operating environment. The scalable, secure, and
migration-transparent naming of Grid resources is an important feature
on which the company based a proposed standard, the Secure Grid Naming
Protocol (SGNP), submitted to the Global Grid Forum earlier this year
for review and discussion.
"SGNP represents a protocol for naming a variety of resources managed by
Grids such as data, users, computers, applications, and queues, and can
be applied in other industries such as financial services and
engineering-intensive manufacturing," said Avaki founder and CTO Andrew
Grimshaw. "LSID represents one industry-specific application of the same
principles, addressing the problem of inconsistent naming of biological
data in life sciences. The submission of LSID shows that Avaki's naming
protocol is practical and versatile enough to address a wide range of
real-world challenges."
Platform Makes Equity Investment In Powerllel
Platform Computing announced a "significant equity investment" in
Powerllel Corp., a provider of advanced parallel processing software for
the financial services industry. Terms of the transaction were not
disclosed.
Powerllel develops advanced parallel computing software that distributes
and processes computationally intensive applications across multiple
systems to accelerate and improve the accuracy of results. "This will
enable financial services organizations to run mission-critical
financial applications, such as securities and portfolio pricing,
hedging, risk management, and end-of-day processing, unchanged in a Grid
computing infrastructure," Platform said. The investment is an expansion
of a strategic partnership announced by the two companies in January.
The companies have also entered into a multi-year strategic technology
and marketing alliance to develop integrated solutions for the financial
services industry. As part of the agreement, the firms will co-develop,
market and implement end-to-end parallel and distributed computing
systems for the financial services industry, providing faster, more
efficient solutions to a wide range of compute-intensive applications,
Platform said. Platform will also have a seat on Powerllel's Board of
Directors.
"Powerllel has a unique and exciting technology that supercharges
computationally-intensive applications, enabling them to run faster in a
Grid computing environment," Platform CEO Robert Gordon said in a
statement. "This provides financial services organizations with
compelling business advantages, including increased revenue from trading
operations and dramatically reduced computing time." Platform plans to
expand its solutions with Powerllel to other key verticals, such as life
sciences and manufacturing.
Plexxikon Chooses Sun Grid Technology to Power Drug Discovery
Platform
Sun Microsystems has been selected by drug discovery company Plexxikon
as its strategic technology partner, providing the life sciences company
with an end-to-end IT solution to help drive Plexxikon's efforts to
discover drugs faster, better and at a lower cost, the companies
announced.
"Our drug discovery platform is based on highly integrated technologies
that incorporate a heavy computational element. Sun's Grid Engine
technology allows us to more efficiently utilize the various
technologies and applications needed to power that platform," Plexxikon
senior vice president of research Michael Milburn said in a
statement.
Sun said it will provide a "complete, reliable and massively scalable"
IT solution based on Sun Grid Engine and the Sun Open Net Environment
(Sun ONE), powered by Sun Fire servers, to help Plexxikon more
efficiently run and manage its highly integrated drug discovery
platform.
"This competitive win further validates the scalability and flexibility
of our Sun ONE architecture and Grid technologies to efficiently handle
the vast volumes of highly complex data characteristic of today's life
science companies," Howard Asher, global director of Sun's life science
group, said in a statement. "Demonstrating ease of integration and
world-class performance with our software partners, we provided
Plexxikon with a solution that could deliver high reliability,
availability and serviceability features and a data management platform
capable of processing data on a massive scale. Working with Plexxikon,
we hope to help the life sciences industry create a better, more
productive drug discovery process."
Fujitsu's Snelling merges OGSA with Unicore
Upon reading the new Globus-IBM Open Grid Services Architecture (OGSA)
vision for the convergence of Grid computing with Web services, David
Snelling of Fujitsu Laboratories of Europe noticed that "the synergy
between OGSA and Unicore was quite high."
Unicore is an open source, Grid environment targeted at distributed use
of supercomputer facilities, Snelling said in a message posted to the
Global Grid Forum's OGSI working group email list.
"My first reading of OGSA and the GS Specification indicated that the
synergy between OGSA and Unicore was quite high," Snelling wrote.
"Therefore, as a tool to understanding OGSA better and to test this
hypothesis, I set out to develop an OGSA-compliant implementation of
Unicore."
Snelling used a Unicore servlet framework and The Mind Electric's Web
Services platform GLUE to create a hosting environment for GridServices.
The GridService implemented allows a user to run an application
advertised by a Unicore site. The application accepts an input file,
runs, and produces an output file. The source and destination of these
files can be anywhere in the Unicore Grid.
Snelling said he hopes the implementation will "yield interesting fruit
in the process of developing an Open Grid Systems Architecture."
The "OGSA Demonstrator" and README file can be found at
http://www.unicore.org/downloads.htm.
Buyya Takes University Of Melbourne Post
Rajkumar Buyya, who has been involved in the research and development of
Grid technologies since 1999, has become a faculty member and director
of research activities of the Grid Computing and Distributed Systems
(GRIDS) Laboratory within the Department of Computer Science and
Software Engineering at the University of Melbourne, Australia.
Before joining the University of Melbourne, he was a doctoral candidate
(Australian Government Research Scholar) at Monash University. He
submitted his Ph.D. thesis on "Economic-based Distributed Resource
Management and Scheduling for Grid Computing" in April.
Buyya will present results of his Ph.D. thesis at the Grid
Computing Planet Conference & Expo next week. Buyya said the work
has "created enormous commercial interest." Sun Microsystems, for
example, has donated equipment and offered grants "to enable
continuation of our Grid research, as they believe that our research
will take Sun and other current technologies to the next application
level," Buyya said. Sun grants also played a major role in the
establishment of the GRIDS
Laboratory, Australia's first fully dedicated research laboratory,
he said.
"The GRIDS Lab is rapidly growing and I recently received some more
grants to hire more researchers," Buyya said.
The GRIDS lab's major thrust is the design and development of
next-generation computing systems and applications that aggregate or
lease services of distributed resources depending on their availability,
capability, performance, cost, and users' quality-of-service
requirements.
Buyya was one of the contributors, with David Abramson and Jon Giddy, to
the design and development of a Grid resource broker called Nimrod-G
that has the ability to schedule large-scale computational and data
intensive applications such as drug design on world-wide distributed
resources. He developed a Grid modeling and simulation environment
called the GridSim Toolkit in collaboration with Manzur Mushed of the
Gippsland School of Computing and IT at Monash. He also developed the
Virtual Laboratory environment for distributed molecular modeling for
drug design on the Grid in collaboration with Kim Branson of WEHI.
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