[Source: Business Wire] - A model collaboration between academia and the healthcare community is benefiting Arizona communities and citizens, thanks to advanced analytics software from business analytics leader SAS. The Arizona Health Query database (AZHQ) is using SAS® software to integrate and analyze millions of anonymized healthcare records. Analyzing data over time and across health systems, researchers identify specific community health needs, inform public policy and, ultimately, lower costs.
Created by Arizona State University’s Center for Health Information and Research (CHiR), AZHQ consolidates health information from dozens of healthcare organizations in Arizona to form a community health data system. Previously, patient data was spread across different healthcare providers, which hindered effective research of community health issues. With more than 40 data partners, including the Arizona Health Care Cost Containment System (AHCCCS) – the state’s Medicaid system – that is no longer an issue.
“With the participation of many public and private healthcare data partners, we’re able to apply SAS data integration and analytics capabilities to track patients over time and location, and identify trends and patterns in healthcare within and across communities,” said Wade Bannister, creator of the AZHQ database and Associate Director for CHiR.
Researchers have also used AZHQ to analyze health disparities in Hispanic and non-Hispanic children, the evolution of Valley fever, asthma patterns in Arizona, and the efficacy of hospitals in serving the needy. It has also been used to conduct community health assessments.
A good example of how AZHQ is affecting community health is the program’s study of MRSA (Methicillin-Resistant Staphylococcus aureus), a staph infection that is resistant to antibiotics. By tracking the disease’s spread by zip code, researchers were able to postulate how and why it was spreading.
Since its inception, AZHQ has consolidated data on 9 million people and 200 million healthcare encounters, pulling data from more than 60 healthcare delivery institutions, including hospitals, insurers and employers. Patient privacy is paramount; AZHQ complies with HIPAA regulations and is regularly audited to ensure continuing compliance. AZHQ received the university’s President’s Medal for Social Embeddedness in 2005 and 2008.
SAS predictive analytics present an opportunity for cost savings, according to William Johnson, who founded AZHQ and directs CHiR. Using SAS, he and fellow researchers analyzed AHCCCS data to develop a model that predicts risk associated with future high-cost Medicaid users.
“By assessing risk factors and predicting costs of patient care years in advance, steps can be taken to alleviate costs through intervention and more informed budget decisions,” said Johnson.
“The breadth of data in the system makes it unique in the US,” said Johnson. “With the advanced research capabilities we have, we’re confident our partnership with the community impacts Arizona healthcare in a very positive way.”
Showing posts with label Bioinformatics. Show all posts
Showing posts with label Bioinformatics. Show all posts
Monday, January 5, 2009
Wednesday, November 12, 2008
Light-speed computer connection will slash the time it takes TGen-ASU to transfer huge amounts of genetic data
[Source: TGen] - Hot on the heels of a new supercomputer, plans for a new light-speed data line between the Translational Genomics Research Institute and Arizona State University could slash the time is takes to transfer genetic information.
Accelerating the flow of information could help speed discoveries that eventually could help produce treatments and cures for diseases such as Alzheimer's, autism, diabetes and various cancers.
Because of the huge amounts of data generated by TGen's experiments, it now take as long as 12 days using conventional cables to transmit 7 terabytes of information from a typical experiment 10 miles between TGen's downtown Phoenix labs and ASU's new Saguaro 2 supercomputer in Tempe.
But through a partnership between ASU and Obsidian Strategics Inc., an Edmonton, Alberta-based defense-intelligence contractor, the same voluminous data – the equivalent of 3.5 million iPod songs – soon could be transmitted in as short as 1 hour.
The difference is something called "dark fiber," unused fiber optic cables installed years ago throughout the nation in anticipation of future growth and development.
"The primary advantage of a link like this is it will allow us to move data faster from the instruments at TGen to the computation and storage at ASU," said Dan Stanzione, director of the High Performance Computing Initiative at ASU's Ira A. Fulton School of Engineering.
"This particularly applies to the next-gen sequencers," said Stanzione, referring to TGen's deployment of ever-faster tools for analyzing DNA in its quest to discover the causes, treatments and possible cures of various diseases.
Dr. Edward Suh, TGen's Chief Information Officer, said such capabilities will help expedite the translation of biomedical research from TGen labs into clinical drug treatments.
"The proposed high-speed data communication link, using Obsidian's network, will significantly reduce the time it takes to run complex data analyses and systems simulations on TGen's supercomputer systems," Suh said.
James Lowey, TGen's Director of High-Performance Biocomputing, said, "The high-speed link between TGen and ASU will enable TGen scientists to transfer data between their labs and the computational resources at ASU at an unprecedented rate, accelerating the pace of discovery.
"With the ever-increasing amount of data being generated by both proteomics and next-generation sequencing, it is critical to have state-of-the-art communications networks between locations where data is generated, and where it is analyzed," Lowey said. "Having this very high-speed link helps position TGen as being a leader in biomedical data analysis."
Stanzione said ASU still is looking for a partner to provide the fiber optic cable, but that a planned pilot dark-fiber link would be between ASU and TGen.
A single experimental run from DNA sequencers can generate 7 terabytes, or 7,000 gigabytes, of data, Stanzione said. Existing ASU-TGen connections can move about 30 gigabytes an hour, he said, meaning the transfer of scientific experimental information can take more than a week.
The proposed system using Obsidian Strategics technology is expected to hit 8,000 gigabytes per hour, or about 8 terabytes, reducing the time it takes to move data between TGen scientific instruments and the ASU supercomputer to as little as 1 hour, Stanzione said.
Reducing transmission time will be come more critical in the future, with TGen’s next generation sequencers easily producing as much as 30 terabytes of data, or the equivalent of an iPod with 15 million songs.
Obsidian Strategics is the leading developer of InfiniBand range extension, routing and encryption technology. ASU and Obsidian will join with others in a venture supported by the Canadian Consulate-Phoenix to advance the capabilities of the optical network, linking higher education facilities in Arizona, as well as in adjacent states.
Obsidian's Longbow technology leverages existing optical networks, and originally was designed to meet the demands of the U.S. Department of Defense’s next generation large data communications architecture.
Saguaro 2, the TGen-ASU supercomputer dedicated Oct. 3 at ASU's Barry M. Goldwater Center for Science and Engineering, is capable of 50 trillion mathematical operations per second.
Accelerating the flow of information could help speed discoveries that eventually could help produce treatments and cures for diseases such as Alzheimer's, autism, diabetes and various cancers.
Because of the huge amounts of data generated by TGen's experiments, it now take as long as 12 days using conventional cables to transmit 7 terabytes of information from a typical experiment 10 miles between TGen's downtown Phoenix labs and ASU's new Saguaro 2 supercomputer in Tempe.
But through a partnership between ASU and Obsidian Strategics Inc., an Edmonton, Alberta-based defense-intelligence contractor, the same voluminous data – the equivalent of 3.5 million iPod songs – soon could be transmitted in as short as 1 hour.
The difference is something called "dark fiber," unused fiber optic cables installed years ago throughout the nation in anticipation of future growth and development.
"The primary advantage of a link like this is it will allow us to move data faster from the instruments at TGen to the computation and storage at ASU," said Dan Stanzione, director of the High Performance Computing Initiative at ASU's Ira A. Fulton School of Engineering.
"This particularly applies to the next-gen sequencers," said Stanzione, referring to TGen's deployment of ever-faster tools for analyzing DNA in its quest to discover the causes, treatments and possible cures of various diseases.
Dr. Edward Suh, TGen's Chief Information Officer, said such capabilities will help expedite the translation of biomedical research from TGen labs into clinical drug treatments.
"The proposed high-speed data communication link, using Obsidian's network, will significantly reduce the time it takes to run complex data analyses and systems simulations on TGen's supercomputer systems," Suh said.
James Lowey, TGen's Director of High-Performance Biocomputing, said, "The high-speed link between TGen and ASU will enable TGen scientists to transfer data between their labs and the computational resources at ASU at an unprecedented rate, accelerating the pace of discovery.
"With the ever-increasing amount of data being generated by both proteomics and next-generation sequencing, it is critical to have state-of-the-art communications networks between locations where data is generated, and where it is analyzed," Lowey said. "Having this very high-speed link helps position TGen as being a leader in biomedical data analysis."
Stanzione said ASU still is looking for a partner to provide the fiber optic cable, but that a planned pilot dark-fiber link would be between ASU and TGen.
A single experimental run from DNA sequencers can generate 7 terabytes, or 7,000 gigabytes, of data, Stanzione said. Existing ASU-TGen connections can move about 30 gigabytes an hour, he said, meaning the transfer of scientific experimental information can take more than a week.
The proposed system using Obsidian Strategics technology is expected to hit 8,000 gigabytes per hour, or about 8 terabytes, reducing the time it takes to move data between TGen scientific instruments and the ASU supercomputer to as little as 1 hour, Stanzione said.
Reducing transmission time will be come more critical in the future, with TGen’s next generation sequencers easily producing as much as 30 terabytes of data, or the equivalent of an iPod with 15 million songs.
Obsidian Strategics is the leading developer of InfiniBand range extension, routing and encryption technology. ASU and Obsidian will join with others in a venture supported by the Canadian Consulate-Phoenix to advance the capabilities of the optical network, linking higher education facilities in Arizona, as well as in adjacent states.
Obsidian's Longbow technology leverages existing optical networks, and originally was designed to meet the demands of the U.S. Department of Defense’s next generation large data communications architecture.
Saguaro 2, the TGen-ASU supercomputer dedicated Oct. 3 at ASU's Barry M. Goldwater Center for Science and Engineering, is capable of 50 trillion mathematical operations per second.
Monday, November 3, 2008
Proposal to centralize UA information technology functions meets opposition
[Source: RENÉE SCHAFER HORTON, Tucson Citizen] - The message to University of Arizona President Robert N. Shelton and Provost Meredith Hay is loud and clear on the Transformation Plan Web site: Don't centralize UA's information technology functions.
"Transforming Technology Support Services" is the most controversial of the 75 proposals submitted to Hay Oct. 13 as the first step in UA's reorganization process - at least on the Web site.
The IT proposal, written by UA Information Technology Services CIO Michele Norin, had 64 comments as of Friday, including one from the director of the BIO5 Institute. Most of the other proposals had zero to five comments, although a proposal calling for the merger of the colleges of science and engineering had 14.
"We all absolutely hate this proposal," said anthropology Professor David Killick, one of the many critics who commented on Norin's proposal. "We aren't a corporation. Each of (our) departments and research facilities have very different computing needs. This is just an effort to save money, but in the long run it will make things worse, not better."
Shelton announced in mid-September that "business as usual" was no longer an option at UA in the face of declining state support. He said a major reorganization was necessary and asked deans and department heads to consult their constituencies and develop "white papers" listing consolidations, eliminations or reorganizations that would strengthen UA's mission while cutting costs.
The proposals are being vetted by a subcommittee of UA's Strategic Planning and Budgetary Advisory Committee, whhich will turn them over to Hay on Monday with recommendations of which should be scrapped, which implemented immediately and which need further development or refinement.
Complaints about Norin's proposal centered on a lack of constituent input and fear that centralizing IT functions will harm research and cost money.
According to Norin's proposal, the goal is to "transition a majority of technology personnel, equipment and operational budgets currently managed and performed within colleges, departments, and support units to the responsibility of the CIO, whereby management is centralized yet personnel are distributed."
Vicki Chandler, director of UA's BIO5 Institute, wrote that Norin's proposal "by and large … will be extremely detrimental to the activities of BIO5."
"I am genuinely concerned that the design, motive and rationale listed in the proposal lacks understanding of how our research-intensive units function and the essential role for IT in our research missions," Chandler wrote in the comments section on the Transformation Plan Web site. "This is exactly the type of proposal that will do major harm to our university's ability to continue to pursue big science."
Chris Segrin, head of the Department of Communications, recalled past efforts at centralizing IT services that cost his department "several thousand dollars" and wrote that he was concerned centralizing IT functions again could result in departments being charged outrageous sums from Norin's office for computer technician services.
"If one does not like (University Information Technology Services) fee structure or cannot afford it, what recourse does she or he have?" Segrin wrote. "In my view, the most likely effect of this plan would be an increase in revenue flowing into central administration, absent any clear plan for how that would translate into cost savings at the college, department, and end user level."
A handful of comments supported at least part of Norin's proposal, including Dianne Horgan, associate dean of the Graduate College.
"I came to UA from another (not so prestigious) university where something very similar was tried. I, and everyone else, fought it," Horgan wrote. "But three years later, I had to admit I'd been wrong. It worked, saved the university lots of money, and we ended up with far superior service."
Unlike the other proposals, Norin's did not describe the consultation process she used to come up with her proposal, a lapse a number of comments noted.
The proposal rubrics from Hay state that proposals should include information about "the processes of consultation with deans, heads, faculty, staff, appointed personnel, and students and the extent to which this proposal has the support of those affected."
Norin, through her administrative assistant, declined to comment on her proposal Friday.
"Transforming Technology Support Services" is the most controversial of the 75 proposals submitted to Hay Oct. 13 as the first step in UA's reorganization process - at least on the Web site.
The IT proposal, written by UA Information Technology Services CIO Michele Norin, had 64 comments as of Friday, including one from the director of the BIO5 Institute. Most of the other proposals had zero to five comments, although a proposal calling for the merger of the colleges of science and engineering had 14.
"We all absolutely hate this proposal," said anthropology Professor David Killick, one of the many critics who commented on Norin's proposal. "We aren't a corporation. Each of (our) departments and research facilities have very different computing needs. This is just an effort to save money, but in the long run it will make things worse, not better."
Shelton announced in mid-September that "business as usual" was no longer an option at UA in the face of declining state support. He said a major reorganization was necessary and asked deans and department heads to consult their constituencies and develop "white papers" listing consolidations, eliminations or reorganizations that would strengthen UA's mission while cutting costs.
The proposals are being vetted by a subcommittee of UA's Strategic Planning and Budgetary Advisory Committee, whhich will turn them over to Hay on Monday with recommendations of which should be scrapped, which implemented immediately and which need further development or refinement.
Complaints about Norin's proposal centered on a lack of constituent input and fear that centralizing IT functions will harm research and cost money.
According to Norin's proposal, the goal is to "transition a majority of technology personnel, equipment and operational budgets currently managed and performed within colleges, departments, and support units to the responsibility of the CIO, whereby management is centralized yet personnel are distributed."
Vicki Chandler, director of UA's BIO5 Institute, wrote that Norin's proposal "by and large … will be extremely detrimental to the activities of BIO5."
"I am genuinely concerned that the design, motive and rationale listed in the proposal lacks understanding of how our research-intensive units function and the essential role for IT in our research missions," Chandler wrote in the comments section on the Transformation Plan Web site. "This is exactly the type of proposal that will do major harm to our university's ability to continue to pursue big science."
Chris Segrin, head of the Department of Communications, recalled past efforts at centralizing IT services that cost his department "several thousand dollars" and wrote that he was concerned centralizing IT functions again could result in departments being charged outrageous sums from Norin's office for computer technician services.
"If one does not like (University Information Technology Services) fee structure or cannot afford it, what recourse does she or he have?" Segrin wrote. "In my view, the most likely effect of this plan would be an increase in revenue flowing into central administration, absent any clear plan for how that would translate into cost savings at the college, department, and end user level."
A handful of comments supported at least part of Norin's proposal, including Dianne Horgan, associate dean of the Graduate College.
"I came to UA from another (not so prestigious) university where something very similar was tried. I, and everyone else, fought it," Horgan wrote. "But three years later, I had to admit I'd been wrong. It worked, saved the university lots of money, and we ended up with far superior service."
Unlike the other proposals, Norin's did not describe the consultation process she used to come up with her proposal, a lapse a number of comments noted.
The proposal rubrics from Hay state that proposals should include information about "the processes of consultation with deans, heads, faculty, staff, appointed personnel, and students and the extent to which this proposal has the support of those affected."
Norin, through her administrative assistant, declined to comment on her proposal Friday.
ASU and Obsidian Collaboration Will Boost Bandwith Over Existing Optical Networks
[Source: BUSINESS WIRE] - Arizona State University (ASU) and Obsidian Strategics, the leading developer of InfiniBand range extension, routing and encryption technology, have announced a unique public-private partnership to explore faster, more efficient data server/transfer technologies for use at the ASU High Performance Computing Initiative (HPCI) facilities, on the ASU campus in downtown Tempe.
ASU and Obsidian will join with others to advance the capabilities of the optical network linking the higher education facilities in Arizona as well as to adjacent states. This enhanced network will establish:
-- a test bed from which to further explore/optimize high-bandwidth, low-latency switching, routing and encryption technologies and applications, pushing the limits of today's leading HPC solutions;
-- a real-world production environment capable of large-scale remote transfer of, or access to, research and scientific data sets along with geographically separated data replication (disaster tolerance for very large, valuable data sets).
ASU and others could utilize the network infrastructure in a variety of existing and new endeavors in the area of biomedical research, distributed access to large-scale computation and distributed large-scale storage, while Obsidian would work closely with researchers and network administrators to ensure the most advanced and appropriate features are developed, tested and implemented on the network.
"This partnership with Obsidian Strategics could provide ASU with bandwidth capacity that would rival any other State's current initiative, and provide Arizona with a distinct advantage in speed and capabilities," says Dr. Dan Stanzione, Director of the HPCI, at ASU. "ASU is very excited to be a part of this initiative that could well draw international attention to, and investment in, the growing Arizona bioscience and technology corridor."
Obsidian's Longbow products drive point-to-point optical connections that enable high-speed data transfer in minutes, in what would otherwise take hours, even days to pass from one researcher to another over current networking infrastructures.
"Arizona State University is committed to growing the infrastructure to support- our researchers," says Dr. Rick Shangraw, ASU's Vice President for Research and Economic Affairs. "The partnership with Obsidian places us at the cutting edge of high bandwidth computing at a time when this type of infrastructure is critical to building strong partnerships with our sponsors and collaborators."
Obsidian's Longbow solutions seamlessly stretch these connections over global distances - leveraging existing optical networks while preserving local link performance. The Longbow technology was designed to meet the mission critical demands of the Department of Defense's next generation Large Data communications architecture.
"The ASU-Obsidian partnership can showcase new ways to leverage regional optical networks, promoting more efficient utilization of large-scale computers and storage, reducing overall energy consumption, and massively improving remote access -- in a way that facilitates state-wide collaboration," says Dr. David Southwell, President of Obsidian Strategics.
This initiative is supported by the Canadian Consulate-Phoenix, which plays a key role in making strategic introductions across theState's universities, research facilities, local community, andcommercial companies. Adds Bill Halina, Obsidian's Chairman, "The Canadian Consulate has been a great help in making early inroads for us and it's up to all of us now to find creative solutions in funding and the support models to ensure growth of this initiative."
ASU and Obsidian will join with others to advance the capabilities of the optical network linking the higher education facilities in Arizona as well as to adjacent states. This enhanced network will establish:
-- a test bed from which to further explore/optimize high-bandwidth, low-latency switching, routing and encryption technologies and applications, pushing the limits of today's leading HPC solutions;
-- a real-world production environment capable of large-scale remote transfer of, or access to, research and scientific data sets along with geographically separated data replication (disaster tolerance for very large, valuable data sets).
ASU and others could utilize the network infrastructure in a variety of existing and new endeavors in the area of biomedical research, distributed access to large-scale computation and distributed large-scale storage, while Obsidian would work closely with researchers and network administrators to ensure the most advanced and appropriate features are developed, tested and implemented on the network.
"This partnership with Obsidian Strategics could provide ASU with bandwidth capacity that would rival any other State's current initiative, and provide Arizona with a distinct advantage in speed and capabilities," says Dr. Dan Stanzione, Director of the HPCI, at ASU. "ASU is very excited to be a part of this initiative that could well draw international attention to, and investment in, the growing Arizona bioscience and technology corridor."
Obsidian's Longbow products drive point-to-point optical connections that enable high-speed data transfer in minutes, in what would otherwise take hours, even days to pass from one researcher to another over current networking infrastructures.
"Arizona State University is committed to growing the infrastructure to support- our researchers," says Dr. Rick Shangraw, ASU's Vice President for Research and Economic Affairs. "The partnership with Obsidian places us at the cutting edge of high bandwidth computing at a time when this type of infrastructure is critical to building strong partnerships with our sponsors and collaborators."
Obsidian's Longbow solutions seamlessly stretch these connections over global distances - leveraging existing optical networks while preserving local link performance. The Longbow technology was designed to meet the mission critical demands of the Department of Defense's next generation Large Data communications architecture.
"The ASU-Obsidian partnership can showcase new ways to leverage regional optical networks, promoting more efficient utilization of large-scale computers and storage, reducing overall energy consumption, and massively improving remote access -- in a way that facilitates state-wide collaboration," says Dr. David Southwell, President of Obsidian Strategics.
This initiative is supported by the Canadian Consulate-Phoenix, which plays a key role in making strategic introductions across theState's universities, research facilities, local community, andcommercial companies. Adds Bill Halina, Obsidian's Chairman, "The Canadian Consulate has been a great help in making early inroads for us and it's up to all of us now to find creative solutions in funding and the support models to ensure growth of this initiative."
Wednesday, October 29, 2008
New Supercomputer Can Do 50 Trillion Operations Per Second
[Source: ScienceDaily] - In less time than the blink of an eye, the Translational Genomics Research Institute's new supercomputer at Arizona State University can do operations equal to every dollar in the recent Wall Street bailout.
That would be 700 billion computations in less than 1/60th of a second, says Dan Stanzione, director of the High Performance Computing Initiative at ASU's Ira A. Fulton School of Engineering.
The "Saguaro 2" supercomputer, housed on the first floor of ASU's Barry M. Goldwater Center for Science and Engineering, is capable of 50 trillion mathematical operations per second.
"That's the equivalent of taking a calculator and doing one operation per second, by hand, continuously for the next one and a half million years," Stanzione said.
Although the computing world changes daily, and measurements depend on numerous factors, Stanzione said, for some functions, ASU's new computer may be among the top five in the world.
TGen will need that speed as it continues its research into a variety of human diseases through the use of data-rich DNA sequencing, genotyping, microarrays and bioinformatics.
"This is really a remarkable testament," to the cooperative efforts of ASU and TGen, said Dr. Jeffrey Trent, President and Scientific Director of TGen, especially in a tight funding environment.
The new supercomputer will help TGen's efforts in translational biomedicine, developing new therapies targeted for individual patients suffering from Alzheimer's, autism, diabetes, coronary heart disease, melanoma, pancreatic cancer, prostate cancer, colon cancer, multiple myeloma, and breast cancer.
Dr. Edward Suh, TGen's Chief Information Officer, said a joint TGen-ASU computer support team is being assembled, and he urged the creation of more partnerships between TGen and ASU.
"I am confident this new supercomputer system will help the ASU and TGen scientists expedite their research, and accelerate innovation in biomedical and engineering research," Suh said. "It is my hope to see this supercomputer system, and a supporting informatics program which Dan and I are putting together, bring the ASU and TGen scientists closer than before for even greater success."
Saguaro 2 – a partially water-cooled set of 7-foot-tall black monolith computer racks, each with as many as 512 processor cores, and linked by ultra-high-speed Infiniband cables – was funded in part by a nearly $2 million grant in July by the National Institutes of Health. The grant was in response to a wide range of scientific activities proposed by TGen, the Ira A. Fulton School of Engineering, and ASU's BioDesign Institute.
The new system doubles the capabilities of ASU's High Performance Computing Initiative (HPCI). The system consists of Intel microprocessors, servers from Dell, storage from Data Direct Networks, and components from a number of other partners, including fiber optic cables from Phoenix-based Zarlink.
More importantly for TGen, the new system has 20 times the previous computational power available to TGen researchers, said James Lowey, director of TGen's High Performance Biocomputing Center.
The new supercomputer also adds to the storage capacity of the HPCI, bringing the total storage to 1.5 quadrillion bytes, or 1.5 petabytes -- or 15 followed by 14 zeroes (1,500,000,000,000,000). That's enough storage space to record nearly a quarter million DVD discs.
The HPCI storage will be used to store a vast array of data from TGen's sequencers and simulations, as well as other large datasets from ASU researchers, including a high resolution mapping of the moon to be performed in 2009 by NASA's Lunar Reconnaissance Orbiter.
"As we move in science into the nano scale of materials and molecular design and diagnostics, or into the macro scale of global climate or the motion of the galaxies, experimentation becomes more expensive and difficult, and simulation becomes invaluable," Stanzione said. "The speed of those simulations determine the speed of progress."
The computational speed of Saguaro 2 is especially critical to the work of TGen. "In 2009, more genome sequence data will be generated than all the words spoken by humans in all of history. Teasing meaningful understanding from this avalanche of data is also the role of HPC (high performance computing)," Stanzione said.
That would be 700 billion computations in less than 1/60th of a second, says Dan Stanzione, director of the High Performance Computing Initiative at ASU's Ira A. Fulton School of Engineering.
The "Saguaro 2" supercomputer, housed on the first floor of ASU's Barry M. Goldwater Center for Science and Engineering, is capable of 50 trillion mathematical operations per second.
"That's the equivalent of taking a calculator and doing one operation per second, by hand, continuously for the next one and a half million years," Stanzione said.
Although the computing world changes daily, and measurements depend on numerous factors, Stanzione said, for some functions, ASU's new computer may be among the top five in the world.
TGen will need that speed as it continues its research into a variety of human diseases through the use of data-rich DNA sequencing, genotyping, microarrays and bioinformatics.
"This is really a remarkable testament," to the cooperative efforts of ASU and TGen, said Dr. Jeffrey Trent, President and Scientific Director of TGen, especially in a tight funding environment.
The new supercomputer will help TGen's efforts in translational biomedicine, developing new therapies targeted for individual patients suffering from Alzheimer's, autism, diabetes, coronary heart disease, melanoma, pancreatic cancer, prostate cancer, colon cancer, multiple myeloma, and breast cancer.
Dr. Edward Suh, TGen's Chief Information Officer, said a joint TGen-ASU computer support team is being assembled, and he urged the creation of more partnerships between TGen and ASU.
"I am confident this new supercomputer system will help the ASU and TGen scientists expedite their research, and accelerate innovation in biomedical and engineering research," Suh said. "It is my hope to see this supercomputer system, and a supporting informatics program which Dan and I are putting together, bring the ASU and TGen scientists closer than before for even greater success."
Saguaro 2 – a partially water-cooled set of 7-foot-tall black monolith computer racks, each with as many as 512 processor cores, and linked by ultra-high-speed Infiniband cables – was funded in part by a nearly $2 million grant in July by the National Institutes of Health. The grant was in response to a wide range of scientific activities proposed by TGen, the Ira A. Fulton School of Engineering, and ASU's BioDesign Institute.
The new system doubles the capabilities of ASU's High Performance Computing Initiative (HPCI). The system consists of Intel microprocessors, servers from Dell, storage from Data Direct Networks, and components from a number of other partners, including fiber optic cables from Phoenix-based Zarlink.
More importantly for TGen, the new system has 20 times the previous computational power available to TGen researchers, said James Lowey, director of TGen's High Performance Biocomputing Center.
The new supercomputer also adds to the storage capacity of the HPCI, bringing the total storage to 1.5 quadrillion bytes, or 1.5 petabytes -- or 15 followed by 14 zeroes (1,500,000,000,000,000). That's enough storage space to record nearly a quarter million DVD discs.
The HPCI storage will be used to store a vast array of data from TGen's sequencers and simulations, as well as other large datasets from ASU researchers, including a high resolution mapping of the moon to be performed in 2009 by NASA's Lunar Reconnaissance Orbiter.
"As we move in science into the nano scale of materials and molecular design and diagnostics, or into the macro scale of global climate or the motion of the galaxies, experimentation becomes more expensive and difficult, and simulation becomes invaluable," Stanzione said. "The speed of those simulations determine the speed of progress."
The computational speed of Saguaro 2 is especially critical to the work of TGen. "In 2009, more genome sequence data will be generated than all the words spoken by humans in all of history. Teasing meaningful understanding from this avalanche of data is also the role of HPC (high performance computing)," Stanzione said.
Thursday, October 16, 2008
Computer science professor Richard Snodgrass will help lead a project with funding from the National Science Foundation.
[Source: La Monica Everett-Haynes, University Communications] - A project is underway to develop a system that would be able to detect and track even minute changes in electronic data systems that hold sensitive and private information.
University of Arizona computer science professor Richard T. Snodgrass and his colleagues have spent years working to strengthen safeguards for digital records.
The team of researchers from the UA and two other institutions has just received a joint grant from the National Science Foundation to advance their work, which is especially relevant given recent financial scandals and also because of recently mandated federal laws against white-collar crime.
"If I change a cell, the product would think the whole document is changed,” Snodgrass said, adding that the system would help users comply with regulations and also increase accountability within their respective practices.
“What we’re doing is taking those techniques to an individual cell level," he said. "This will help companies to be compliant with these laws and, just as important, help the public to know that these regulations are being followed.”
Snodgrass is a co-principal investigator on a three-year NSF grant totaling $870,000 that will allow researchers to develop and study a system of creating databases that are far more secure and advanced in tracking information changes, while retaining their high performance.
"Primarily, we’re creating new functionality to enable the database to do something it can’t do now, and to do it efficiently,” said Snodgrass, who specializes in tamper detection, database design, temporal databases and the science of computation.
The team is working to create a system that would be able to detect and track changes made, and to tie those changes to a single source – but without sacrificing performance for security. The project has implications for any business that uses a database to store information that is of a critical nature.
The grant – "III-COR Medium: Collaborative Research: Achieving Compliant Databases” – will be split among the UA, Stony Brook University and the University of Illinois at Urbana-Champaign.
The challenge, Snodgrass said, will be in making sure that the system is in compliance and, at the same time, prevents insiders “with super-user powers” from improperly changing the stored information.
All of this is increasingly important to ensure secure databases not only for best business practices, but also because of government mandates, Snodgrass said.
“Many laws are now on the books because of Enron and others,” said Snodgrass, who added that the UA’s grant amount is about $280,000.
“These laws say that changes to the financial record need to be monitored and that only certain people can make changes,” he said.
One such law is what is commonly known as the Sarbanes-Oxley Act – one that the U.S. Congress passed in 2002 after a series of financial scandals surfaced in companies like Enron, Tyco and WorldCom.
The act, as it reads, was created to “protect investors by improving the accuracy and reliability of corporate disclosures.” The federal law makes it illegal to destroy, alter or falsify records, among other things. It also called for the creation of an oversight board and strengthened sanctions against those who commit white-collar crimes.
“There are many products that help support these laws," Snodgrass said. "The problem is that those systems don’t work if you have a database like an Excel spreadsheet."
University of Arizona computer science professor Richard T. Snodgrass and his colleagues have spent years working to strengthen safeguards for digital records.
The team of researchers from the UA and two other institutions has just received a joint grant from the National Science Foundation to advance their work, which is especially relevant given recent financial scandals and also because of recently mandated federal laws against white-collar crime.
"If I change a cell, the product would think the whole document is changed,” Snodgrass said, adding that the system would help users comply with regulations and also increase accountability within their respective practices.
“What we’re doing is taking those techniques to an individual cell level," he said. "This will help companies to be compliant with these laws and, just as important, help the public to know that these regulations are being followed.”
Snodgrass is a co-principal investigator on a three-year NSF grant totaling $870,000 that will allow researchers to develop and study a system of creating databases that are far more secure and advanced in tracking information changes, while retaining their high performance.
"Primarily, we’re creating new functionality to enable the database to do something it can’t do now, and to do it efficiently,” said Snodgrass, who specializes in tamper detection, database design, temporal databases and the science of computation.
The team is working to create a system that would be able to detect and track changes made, and to tie those changes to a single source – but without sacrificing performance for security. The project has implications for any business that uses a database to store information that is of a critical nature.
The grant – "III-COR Medium: Collaborative Research: Achieving Compliant Databases” – will be split among the UA, Stony Brook University and the University of Illinois at Urbana-Champaign.
The challenge, Snodgrass said, will be in making sure that the system is in compliance and, at the same time, prevents insiders “with super-user powers” from improperly changing the stored information.
All of this is increasingly important to ensure secure databases not only for best business practices, but also because of government mandates, Snodgrass said.
“Many laws are now on the books because of Enron and others,” said Snodgrass, who added that the UA’s grant amount is about $280,000.
“These laws say that changes to the financial record need to be monitored and that only certain people can make changes,” he said.
One such law is what is commonly known as the Sarbanes-Oxley Act – one that the U.S. Congress passed in 2002 after a series of financial scandals surfaced in companies like Enron, Tyco and WorldCom.
The act, as it reads, was created to “protect investors by improving the accuracy and reliability of corporate disclosures.” The federal law makes it illegal to destroy, alter or falsify records, among other things. It also called for the creation of an oversight board and strengthened sanctions against those who commit white-collar crimes.
“There are many products that help support these laws," Snodgrass said. "The problem is that those systems don’t work if you have a database like an Excel spreadsheet."
Tuesday, September 23, 2008
TGen Researchers Publish New Multiplexed Sequence Approach
[Source: By a GenomeWeb staff reporter , GenomeWeb News] - In a paper appearing online in Nature Methods this weekend, a team of researchers from the Translational Genomics Research Institute described a new multiplexed, targeted re-sequencing strategy for assessing regions of the human genome more quickly and efficiently.
The team used PCR amplicons to create degenerate, indexed DNA barcodes targeting specific regions of the genome before sequencing them with the Illumina Genome Analyzer. The multiplexed approach, they say, is an effective way to uncover genetic variation in genes of interest — an approach intended to facilitate cost-efficient re-sequencing on genes involved in particular diseases and conditions.
“In many cases, rather than sequencing the whole genome for ten people, researchers would rather sequence a dozen genes for 1,000 people,” co-lead author John Pearson, head of TGen’s Bioinformatics Research Unit, said in a statement.
The researchers tested their approach by simultaneously sequencing Encyclopedia of DNA Elements, or ENCODE, regions from the genomes of numerous HapMap individuals. Using its targeted resequencing approach, the team was able to identify genetic variants not previously described for these regions.
“Although whole-genome sequencing may be the primary motivator for improvements in sequencing technology, it is clear that next-generation technologies are immediately useful for focused, hypothesis-driven sequencing of linkage peaks, groupings of candidate genes or sequencing the entire known coding region of the human genome,” the authors noted. “In this report, we developed per-individual indexing of pooled PCR amplicons to carry out targeted sequencing.”
In the future, they added, pooled amplicons may also be replaced by other sample-preparation strategies, including genome partitioning. “[V]ariant discovery through the re-sequencing of all candidate regions implicated in a disease across genomes of dozens, possibly hundreds, of individuals could be considerably accelerated by merging multiplex capture, indexing, and next-generation sequencing approaches in a single protocol.”
The team used PCR amplicons to create degenerate, indexed DNA barcodes targeting specific regions of the genome before sequencing them with the Illumina Genome Analyzer. The multiplexed approach, they say, is an effective way to uncover genetic variation in genes of interest — an approach intended to facilitate cost-efficient re-sequencing on genes involved in particular diseases and conditions.
“In many cases, rather than sequencing the whole genome for ten people, researchers would rather sequence a dozen genes for 1,000 people,” co-lead author John Pearson, head of TGen’s Bioinformatics Research Unit, said in a statement.
The researchers tested their approach by simultaneously sequencing Encyclopedia of DNA Elements, or ENCODE, regions from the genomes of numerous HapMap individuals. Using its targeted resequencing approach, the team was able to identify genetic variants not previously described for these regions.
“Although whole-genome sequencing may be the primary motivator for improvements in sequencing technology, it is clear that next-generation technologies are immediately useful for focused, hypothesis-driven sequencing of linkage peaks, groupings of candidate genes or sequencing the entire known coding region of the human genome,” the authors noted. “In this report, we developed per-individual indexing of pooled PCR amplicons to carry out targeted sequencing.”
In the future, they added, pooled amplicons may also be replaced by other sample-preparation strategies, including genome partitioning. “[V]ariant discovery through the re-sequencing of all candidate regions implicated in a disease across genomes of dozens, possibly hundreds, of individuals could be considerably accelerated by merging multiplex capture, indexing, and next-generation sequencing approaches in a single protocol.”
A National Science Foundation grant will allow the UA to establish a research center.
[Source: University Communications] - The National Science Foundation has awarded a five-year, $18.5 million grant to establish an engineering research center based at The University of Arizona.
The center, or ERC, will focus on removing one of the last bottlenecks in the Internet by developing optoelectronic technologies for high-bandwidth, low-cost, widespread access networks.
The UA and nine partner universities will collaborate as the Center for Integrated Access Networks, or CIAN, to create an advanced optical access network capable of delivering data more than a thousand times faster to users at lower cost than they now pay to connect to information data bases and communication networks.
"NSF is pleased to welcome The University of Arizona and its partner universities into the ERC program,” said Lynn Preston, NSF deputy division director and leader of the Engineering Research Center program.
“As the world increasingly relies on communications networks, we anticipate that CIAN will contribute the understanding and innovations needed to extend the reach and expand the capabilities of these networks. We expect this area of research to interest many pre-college students in the program and in engineering, and we look forward to CIAN graduates becoming leaders and innovators in the creation of future communications systems," Preston said.
"I am very enthusiastic about this ERC," said Leslie P. Tolbert, UA vice president for research, graduate studies and economic development. "The University is proud to be the lead institution in this important collaborative endeavor that is aimed at generating the edge network of the future."
Partner universities in CIAN include the University of California at San Diego (UCSD), the California Institute of Technology (Caltech), Stanford University, the University of Southern California (USC), University of California at Los Angeles (UCLA), University of California at Berkeley, Columbia University, Norfolk State University and Tuskegee University.
The new center brings together leading researchers and world-class educators who will work to create "truly transformative systems that are of critical importance to the foundation of our national information infrastructure," said CIAN director Nasser Peyghambarian, UA professor of optical sciences and of materials science and engineering.
National Science Foundation funding for the new UA-based center is timely, Peyghambarian added, citing a recent study. Analysts at Nemertes Research, an Illinois-based firm that specializes in information technologies research, predict that demand for Internet access, especially in North America, will exceed existing Internet capacity within the next three to five years.
Failing to invest in new access infrastructure won't cause the Internet to collapse, the analysts said, but it will throttle innovation and "painlessly and invisibly leach competitiveness out of the economy."
"Our vision is to create the 'PC' equivalent of the optical access network," Peyghambarian said.
His analogy refers to the revolution in electronic computing.
Forty years ago, the first commercially successful supercomputer was the size of a room, cost more than a million dollars and performed five hundred million operations per second. Today's personal computers sit on desk tops, typically cost about a thousand dollars each and process more than a billion operations per second.
CIAN's goal over the next decade is to devise and adapt chip-scale optoelectronic integration technologies for an advanced optical access network capable of delivering data at 10 gigabits, or 10 billion operations per second, to single users "anywhere, at anytime," and at lower cost, Shaya Fainman, professor of electrical and computer engineering at UCSD and CIAN deputy director, said. The current data transfer rate is about 10 megabits, or 10 million operations per second.
In a unique approach, CIAN vertically integrates research from developing nanostructured photonic devices to demonstrating advanced network services.
USC Professor Alan Willner and Columbia Professor Keren Bergman will lead the system and networking research thrust of CIAN. Caltech Professor Axel Scherer and Berkeley Profesor Ming Wu will lead the subsystem integration research thrust. Berkeley Professor Connie Chang-Hasnain and UA College of Optical Sciences Professor Hyatt Gibbs will lead the photonic material and device research thrust.
UCSD Professor Joseph Ford and UA optical sciences Professor Franko Kueppers will lead the CIAN’s “Grand Challenge Testbed,” the center’s system integration and network demonstration platform. UA mathematics/optical sciences Professor Jerry Moloney will develop modeling and design tools for the integrated optoelectronic chips.
CIAN will serve industry through innovative systems research. Multi-billion-dollar communications, commerce, entertainment and health care industries will benefit. UA optical sciences Professor Robert Norwood will head CIAN's industrial collaboration and technology transfer program. This part of the program gives industry a voice in various functions of CIAN including guiding the selection of research projects, enabling technology transfer and participating in student education.
The center will educate students from diverse backgrounds by piloting novel, multi-level "super courses" and student recruitment and retention programs. "Education is a significant part of our NSF engineering research center," Peyghambarian said. "These students will be the skilled workforce who will lead the next-generation communications industry."
UA College of Engineering faculty members Kelly Potter, Joseph Simmons and Supapan Seraphin and Meredith Whitaker of UA optical sciences will lead the education and outreach activities of CIAN, while Kimberly Sierra-Cajas of UA optical sciences and Professor Arlene Maclin from Norfolk State University will lead the diversity enhancement program. The CIAN team will partner with minority-serving institutions such as Pima Community College, Norfolk State University and Tuskegee University and Native American tribes in Arizona, including the Pascua Yaqui Tribe, in student education and outreach programs.
Outreach programs will include middle schools, high schools, undergraduate and graduate programs. CIAN student training also will go beyond the United States.
"Students need to realize that they're not on an isolated island. Understanding how research is done in other cultures is very, very important to our field," Peyghambarian said. "So each student funded through the center will have at least one international research experience before graduation."
Research exchange programs are being arranged with universities and companies in Germany, Japan, Israel, Finland and elsewhere.
The center, or ERC, will focus on removing one of the last bottlenecks in the Internet by developing optoelectronic technologies for high-bandwidth, low-cost, widespread access networks.
The UA and nine partner universities will collaborate as the Center for Integrated Access Networks, or CIAN, to create an advanced optical access network capable of delivering data more than a thousand times faster to users at lower cost than they now pay to connect to information data bases and communication networks.
"NSF is pleased to welcome The University of Arizona and its partner universities into the ERC program,” said Lynn Preston, NSF deputy division director and leader of the Engineering Research Center program.
“As the world increasingly relies on communications networks, we anticipate that CIAN will contribute the understanding and innovations needed to extend the reach and expand the capabilities of these networks. We expect this area of research to interest many pre-college students in the program and in engineering, and we look forward to CIAN graduates becoming leaders and innovators in the creation of future communications systems," Preston said.
"I am very enthusiastic about this ERC," said Leslie P. Tolbert, UA vice president for research, graduate studies and economic development. "The University is proud to be the lead institution in this important collaborative endeavor that is aimed at generating the edge network of the future."
Partner universities in CIAN include the University of California at San Diego (UCSD), the California Institute of Technology (Caltech), Stanford University, the University of Southern California (USC), University of California at Los Angeles (UCLA), University of California at Berkeley, Columbia University, Norfolk State University and Tuskegee University.
The new center brings together leading researchers and world-class educators who will work to create "truly transformative systems that are of critical importance to the foundation of our national information infrastructure," said CIAN director Nasser Peyghambarian, UA professor of optical sciences and of materials science and engineering.
National Science Foundation funding for the new UA-based center is timely, Peyghambarian added, citing a recent study. Analysts at Nemertes Research, an Illinois-based firm that specializes in information technologies research, predict that demand for Internet access, especially in North America, will exceed existing Internet capacity within the next three to five years.
Failing to invest in new access infrastructure won't cause the Internet to collapse, the analysts said, but it will throttle innovation and "painlessly and invisibly leach competitiveness out of the economy."
"Our vision is to create the 'PC' equivalent of the optical access network," Peyghambarian said.
His analogy refers to the revolution in electronic computing.
Forty years ago, the first commercially successful supercomputer was the size of a room, cost more than a million dollars and performed five hundred million operations per second. Today's personal computers sit on desk tops, typically cost about a thousand dollars each and process more than a billion operations per second.
CIAN's goal over the next decade is to devise and adapt chip-scale optoelectronic integration technologies for an advanced optical access network capable of delivering data at 10 gigabits, or 10 billion operations per second, to single users "anywhere, at anytime," and at lower cost, Shaya Fainman, professor of electrical and computer engineering at UCSD and CIAN deputy director, said. The current data transfer rate is about 10 megabits, or 10 million operations per second.
In a unique approach, CIAN vertically integrates research from developing nanostructured photonic devices to demonstrating advanced network services.
USC Professor Alan Willner and Columbia Professor Keren Bergman will lead the system and networking research thrust of CIAN. Caltech Professor Axel Scherer and Berkeley Profesor Ming Wu will lead the subsystem integration research thrust. Berkeley Professor Connie Chang-Hasnain and UA College of Optical Sciences Professor Hyatt Gibbs will lead the photonic material and device research thrust.
UCSD Professor Joseph Ford and UA optical sciences Professor Franko Kueppers will lead the CIAN’s “Grand Challenge Testbed,” the center’s system integration and network demonstration platform. UA mathematics/optical sciences Professor Jerry Moloney will develop modeling and design tools for the integrated optoelectronic chips.
CIAN will serve industry through innovative systems research. Multi-billion-dollar communications, commerce, entertainment and health care industries will benefit. UA optical sciences Professor Robert Norwood will head CIAN's industrial collaboration and technology transfer program. This part of the program gives industry a voice in various functions of CIAN including guiding the selection of research projects, enabling technology transfer and participating in student education.
The center will educate students from diverse backgrounds by piloting novel, multi-level "super courses" and student recruitment and retention programs. "Education is a significant part of our NSF engineering research center," Peyghambarian said. "These students will be the skilled workforce who will lead the next-generation communications industry."
UA College of Engineering faculty members Kelly Potter, Joseph Simmons and Supapan Seraphin and Meredith Whitaker of UA optical sciences will lead the education and outreach activities of CIAN, while Kimberly Sierra-Cajas of UA optical sciences and Professor Arlene Maclin from Norfolk State University will lead the diversity enhancement program. The CIAN team will partner with minority-serving institutions such as Pima Community College, Norfolk State University and Tuskegee University and Native American tribes in Arizona, including the Pascua Yaqui Tribe, in student education and outreach programs.
Outreach programs will include middle schools, high schools, undergraduate and graduate programs. CIAN student training also will go beyond the United States.
"Students need to realize that they're not on an isolated island. Understanding how research is done in other cultures is very, very important to our field," Peyghambarian said. "So each student funded through the center will have at least one international research experience before graduation."
Research exchange programs are being arranged with universities and companies in Germany, Japan, Israel, Finland and elsewhere.
Monday, September 15, 2008
TGen investigators devise faster, cheaper way of analyzing the human genome
[Source: TGen] - Investigators at the Translational Genomics Research Institute (TGen) today announced a faster and less expensive way for scientists to find which genes might affect human health.
Using bar-codes, not unlike what shoppers find in grocery stores, TGen researchers found a way to index portions of the nearly 3-billion-base human genetic code, making it easier for scientists to zero in on the regions most likely to show variations in genetic traits.
The findings were published today in the online version of the journal Nature Methods. The study will be published in print in the journal's October edition.
Dr. David Craig, associate director of TGen's Neurogenomics Division, said the new method should cost only one-tenth, or less, of the current cost of sequencing genes commonly done to analyze Single Nucleotide Polymorphisms (SNPs), and in performing Genome-Wide Association (GWA) studies.
"Our goal is to find the genetic basis of disease," said Craig, the study's lead author. "It (the new method) provides us a way to immediately use next-generation sequencing technology for studying hundreds to thousands of individuals."
John Pearson, the head of TGen's Bioinformatics Research Unit, said the new method would allow scientists worldwide to more easily tune their sequencing experiments, and conduct their experiments with greater speed.
"In many cases, rather than sequencing the whole genome for 10 people, researchers would rather sequence a dozen genes for 1,000 people," said Pearson, who contributed to the study.
TGen scientists adapted an exciting new technology known as "next generation sequencing" to allow samples to be run and analyzed using 15 well-characterized indexes.
"Moving forward, TGen scientists are now attempting to merge this indexing approach with sequence-capture methods currently under development in their laboratories, which would likely further improve the cost savings and speed," said Dr. Matthew Huentelman, an investigator in TGen's Neurogenomics Division, who also contributed to the study.
Depending on assumptions made in an experiment, the desired coverage -- and as a consequence, the cost -- can vary substantially, the study said, depending on whether the objective is:
Discovering genetic variants for genotyping by a separate method such as custom SNP genotyping.
Conducting polymorphism discovery and variant calling within one sequencing experiment.
Exhaustively resequencing for all common and rare variants.
The new method of analyzing human genetics should enable scientists at TGen and elsewhere to push ahead with key scientific research needed to prevent, diagnosis and treat a variety of diseases and conditions.
"Although whole-genome sequencing may be the primary motivator for improvements in sequencing technology," the study said, "it is clear that next-generation technologies are immediately useful for focused, hypothesis-driven sequencing of linkage peaks, groupings of candidate genes or sequencing the entire known coding sequence of the human genome."
Using bar-codes, not unlike what shoppers find in grocery stores, TGen researchers found a way to index portions of the nearly 3-billion-base human genetic code, making it easier for scientists to zero in on the regions most likely to show variations in genetic traits.
The findings were published today in the online version of the journal Nature Methods. The study will be published in print in the journal's October edition.
Dr. David Craig, associate director of TGen's Neurogenomics Division, said the new method should cost only one-tenth, or less, of the current cost of sequencing genes commonly done to analyze Single Nucleotide Polymorphisms (SNPs), and in performing Genome-Wide Association (GWA) studies.
"Our goal is to find the genetic basis of disease," said Craig, the study's lead author. "It (the new method) provides us a way to immediately use next-generation sequencing technology for studying hundreds to thousands of individuals."
John Pearson, the head of TGen's Bioinformatics Research Unit, said the new method would allow scientists worldwide to more easily tune their sequencing experiments, and conduct their experiments with greater speed.
"In many cases, rather than sequencing the whole genome for 10 people, researchers would rather sequence a dozen genes for 1,000 people," said Pearson, who contributed to the study.
TGen scientists adapted an exciting new technology known as "next generation sequencing" to allow samples to be run and analyzed using 15 well-characterized indexes.
"Moving forward, TGen scientists are now attempting to merge this indexing approach with sequence-capture methods currently under development in their laboratories, which would likely further improve the cost savings and speed," said Dr. Matthew Huentelman, an investigator in TGen's Neurogenomics Division, who also contributed to the study.
Depending on assumptions made in an experiment, the desired coverage -- and as a consequence, the cost -- can vary substantially, the study said, depending on whether the objective is:
Discovering genetic variants for genotyping by a separate method such as custom SNP genotyping.
Conducting polymorphism discovery and variant calling within one sequencing experiment.
Exhaustively resequencing for all common and rare variants.
The new method of analyzing human genetics should enable scientists at TGen and elsewhere to push ahead with key scientific research needed to prevent, diagnosis and treat a variety of diseases and conditions.
"Although whole-genome sequencing may be the primary motivator for improvements in sequencing technology," the study said, "it is clear that next-generation technologies are immediately useful for focused, hypothesis-driven sequencing of linkage peaks, groupings of candidate genes or sequencing the entire known coding sequence of the human genome."
Monday, September 8, 2008
Neural nanomachines project funded by NIH's EUREKA program
[Source: Nanowerk News] - Fueled by a new initiative at the National Institutes of Health called the EUREKA program, two Arizona State University (ASU) teams have received million-dollar grants to pursue the next frontiers in biomedical research.
EUREKA, an acronym for Exceptional, Unconventional Research Enabling Knowledge Acceleration, is intended to boost exceptionally innovative research.
Biodesign Institute researcher John Chaput and Ira A. Fulton School of Engineering associate professor Rudy Diaz each have received $1.2 million research grants from the new, high-impact NIH program. The EUREKA program represents the NIH’s increased emphasis on supporting unconventional, paradigm-shifting research.
“EUREKA projects promise remarkable outcomes that could revolutionize science,” says Elias Zerhouni, NIH’s director. “The program reflects NIH’s commitment to supporting potentially transformative research, even if it carries a greater-than-usual degree of scientific risk.”
Adds ASU President Michael Crow: “The National Institute of Health’s decision to fund these key biomedical research projects not only speaks to the intellectual merits of ASU’s outstanding proposals, but also confirms ASU’s success in attracting federal investment in bold, high-risk, high-impact research central to our mission.”
Chaput and Diaz’s projects were two of 38 proposals deemed exceptional. This is an impressive showing for ASU, and it demonstrates the university’s ability to compete with the best and brightest scientists from across the nation.
“The EUREKA competition provided a unique forum for our Biodesign team to develop a transformative platform that represents a convergence of chemistry, biology and informatics,” says John Chaput, a Biodesign Institute researcher and ASU assistant professor in the Department of Chemistry and Biochemistry.
Neural nanomachines
Research to be led by Diaz will focus on assembling nanomachines designed to deliver electrical signals to neurons on command. Applications of the technology would include bio-sensing and delivery devices that could be used to detect and treat a variety of human neurological disorders.
Diaz, an associate professor in the Department of Electrical Engineering and the Center for Nanophotonics in ASU’s Ira A. Fulton School of Engineering, will work professors Thomas Moore and Hao Yan in the Department of Chemistry and Biochemistry. Yan also works in the Center for Single Molecule Biophysics in the Biodesign Institute.
The team’s goal is to gain new insights into the pathological obstruction of neural signals and the development of new and more precise neural-stimulation technology.
With existing technology, viewing the “microscopic dynamics” of what is occurring in the human body at a cellular level “is like observing human activity on Earth from an orbiting satellite,” Diaz says.
Even with the development of laser tweezers and nanoelectrodes, “most of our cellular bio-chemistry knowledge is still extracted from circumstantial evidence,” Diaz says.
The method Diaz’s team proposes would permit “direct interaction with cells at the local level.” That would be achieved with a nanoscale structure that could be injected into the body, targeted to attach itself to certain clusters of cells and then controlled by chemical reactions triggered by light delivered either through the skin or via microscopic optical fibers.
The team will molecularly assemble a nanodevice that is best described as a remotely powered and remotely controlled pacemaker.
It will be built on a DNA chassis that includes antennas for receiving power and commands from the outside world, and batteries to store and deliver that power.
The antennas are built of Noble metal nanospheres that take advantage of the plasmon resonance to amplify and focus light with nanometer precision.
Artificial electrocytes – electric organ cells that work like batteries, such as those that naturally occur in fish such as electric eels – will be constructed from liposomes (fat cells) that will have ion pumps and ion gate molecules incorporated into their lipid membranes.
The whole structure will have to be encapsulated in a DNA “cage” to prevent the components from being short-circuited by the body’s fluids.
Under the correct wavelength of light, the power-receiving antennae would amplify the incident light to drive the electric charging of the artificial electrocyte.
The structure would include a set of plasmonic antennae. These are microscopic metal nanostructures that behave as antennae in the presence of photons (light) the way metal antennas behave in the presence of radio waves.
The antennas would be tuned to a different wavelength and coupled to the ion gates in the membranes to serve as light-activated switches to perform a “gate-opening” process that triggers the discharge of the artificial electrocyte chain, thus delivering an electrical impulse that can stimulate neurons.
The group hopes to prove the functionality of each component independently and to demonstrate that the entire assembly works as designed.
These nanostructures could lead to advanced neuro-imaging sensors operating at the cellular scale. Such nanosensors delivered to their targets by chemical tags, or during surgical intervention, could reveal new details about the transmission of neural signals and of their pathological interruption.
The light-powered artificial electrocyte could become a critical tool for improving microsurgery, and advancing the understanding of cellular biology.
Discovering ‘hidden’ proteins
During his four-year research project, Chaput will lead a Biodesign Institute team on a project that plans to search the human genome for regions of DNA that contain important, but as of yet unidentified genetic information.
If successful, Chaput’s project may confirm the possible existence of novel protein-coding regions that remain hidden in the shadows of the classic proteome. Determining how and when such proteins are made could have a major impact in diseases, such as cancer, by helping us to understand how cellular function is deposited in our genomes.
Within the code of life, three polymers – DNA, RNA and proteins – provide nearly all of the information content. Each is made from a slightly different set of chemical building blocks, and the exact sequence of these blocks within each chain carries out the instructions of the genetic code. Fifty years ago, Francis Crick, co-discoverer of the DNA double helix, first postulated the “central dogma” of molecular biology, where DNA information is transcribed to make RNA, and RNA is translated to make proteins.
The bounty of the Human Genome Project has identified nearly 25,000 genes. It’s estimated that the human body could make more than a million different proteins, the majority of which remain to be discovered. This entourage of proteins, the proteome, is ultimately responsible for everything good or bad that is related to human health and disease.
Chaput’s team, which includes fellow Biodesign colleagues Sudhir Kumar and Bertram Jacobs, has produced tantalizing clues that suggest there may be many proteins hidden within the DNA sequences of our genome. Together, they will combine their expertise in molecular and cellular biology, bioinformatics and virology to uncover how and when such proteins are made.
“We have developed a combined experimental-bioinformatics approach that allows us to quickly search entire genomes for sequences that enhance the translation of a downstream gene,” Chaput says. “By determining the identity and location of these motifs, it should be possible to determine when specific genes are being made and possibly discover new genes that contribute to our proteome. Since many of these genes will likely be made by non-traditional methods, this technology will also allow us to investigate new mechanisms of protein translation.”
The motifs they hope to identify help recruit ribosomes, the protein translation machinery of the cell, to the correct translation start site on the RNA message. By identifying these landing sites, the team can use bioinformatics to learn where these motifs are located in the genome.
This information will enable Chaput’s team to create an annotated map of the human genome showing all possible locations where protein translation could occur.
EUREKA, an acronym for Exceptional, Unconventional Research Enabling Knowledge Acceleration, is intended to boost exceptionally innovative research.
Biodesign Institute researcher John Chaput and Ira A. Fulton School of Engineering associate professor Rudy Diaz each have received $1.2 million research grants from the new, high-impact NIH program. The EUREKA program represents the NIH’s increased emphasis on supporting unconventional, paradigm-shifting research.
“EUREKA projects promise remarkable outcomes that could revolutionize science,” says Elias Zerhouni, NIH’s director. “The program reflects NIH’s commitment to supporting potentially transformative research, even if it carries a greater-than-usual degree of scientific risk.”
Adds ASU President Michael Crow: “The National Institute of Health’s decision to fund these key biomedical research projects not only speaks to the intellectual merits of ASU’s outstanding proposals, but also confirms ASU’s success in attracting federal investment in bold, high-risk, high-impact research central to our mission.”
Chaput and Diaz’s projects were two of 38 proposals deemed exceptional. This is an impressive showing for ASU, and it demonstrates the university’s ability to compete with the best and brightest scientists from across the nation.
“The EUREKA competition provided a unique forum for our Biodesign team to develop a transformative platform that represents a convergence of chemistry, biology and informatics,” says John Chaput, a Biodesign Institute researcher and ASU assistant professor in the Department of Chemistry and Biochemistry.
Neural nanomachines
Research to be led by Diaz will focus on assembling nanomachines designed to deliver electrical signals to neurons on command. Applications of the technology would include bio-sensing and delivery devices that could be used to detect and treat a variety of human neurological disorders.
Diaz, an associate professor in the Department of Electrical Engineering and the Center for Nanophotonics in ASU’s Ira A. Fulton School of Engineering, will work professors Thomas Moore and Hao Yan in the Department of Chemistry and Biochemistry. Yan also works in the Center for Single Molecule Biophysics in the Biodesign Institute.
The team’s goal is to gain new insights into the pathological obstruction of neural signals and the development of new and more precise neural-stimulation technology.
With existing technology, viewing the “microscopic dynamics” of what is occurring in the human body at a cellular level “is like observing human activity on Earth from an orbiting satellite,” Diaz says.
Even with the development of laser tweezers and nanoelectrodes, “most of our cellular bio-chemistry knowledge is still extracted from circumstantial evidence,” Diaz says.
The method Diaz’s team proposes would permit “direct interaction with cells at the local level.” That would be achieved with a nanoscale structure that could be injected into the body, targeted to attach itself to certain clusters of cells and then controlled by chemical reactions triggered by light delivered either through the skin or via microscopic optical fibers.
The team will molecularly assemble a nanodevice that is best described as a remotely powered and remotely controlled pacemaker.
It will be built on a DNA chassis that includes antennas for receiving power and commands from the outside world, and batteries to store and deliver that power.
The antennas are built of Noble metal nanospheres that take advantage of the plasmon resonance to amplify and focus light with nanometer precision.
Artificial electrocytes – electric organ cells that work like batteries, such as those that naturally occur in fish such as electric eels – will be constructed from liposomes (fat cells) that will have ion pumps and ion gate molecules incorporated into their lipid membranes.
The whole structure will have to be encapsulated in a DNA “cage” to prevent the components from being short-circuited by the body’s fluids.
Under the correct wavelength of light, the power-receiving antennae would amplify the incident light to drive the electric charging of the artificial electrocyte.
The structure would include a set of plasmonic antennae. These are microscopic metal nanostructures that behave as antennae in the presence of photons (light) the way metal antennas behave in the presence of radio waves.
The antennas would be tuned to a different wavelength and coupled to the ion gates in the membranes to serve as light-activated switches to perform a “gate-opening” process that triggers the discharge of the artificial electrocyte chain, thus delivering an electrical impulse that can stimulate neurons.
The group hopes to prove the functionality of each component independently and to demonstrate that the entire assembly works as designed.
These nanostructures could lead to advanced neuro-imaging sensors operating at the cellular scale. Such nanosensors delivered to their targets by chemical tags, or during surgical intervention, could reveal new details about the transmission of neural signals and of their pathological interruption.
The light-powered artificial electrocyte could become a critical tool for improving microsurgery, and advancing the understanding of cellular biology.
Discovering ‘hidden’ proteins
During his four-year research project, Chaput will lead a Biodesign Institute team on a project that plans to search the human genome for regions of DNA that contain important, but as of yet unidentified genetic information.
If successful, Chaput’s project may confirm the possible existence of novel protein-coding regions that remain hidden in the shadows of the classic proteome. Determining how and when such proteins are made could have a major impact in diseases, such as cancer, by helping us to understand how cellular function is deposited in our genomes.
Within the code of life, three polymers – DNA, RNA and proteins – provide nearly all of the information content. Each is made from a slightly different set of chemical building blocks, and the exact sequence of these blocks within each chain carries out the instructions of the genetic code. Fifty years ago, Francis Crick, co-discoverer of the DNA double helix, first postulated the “central dogma” of molecular biology, where DNA information is transcribed to make RNA, and RNA is translated to make proteins.
The bounty of the Human Genome Project has identified nearly 25,000 genes. It’s estimated that the human body could make more than a million different proteins, the majority of which remain to be discovered. This entourage of proteins, the proteome, is ultimately responsible for everything good or bad that is related to human health and disease.
Chaput’s team, which includes fellow Biodesign colleagues Sudhir Kumar and Bertram Jacobs, has produced tantalizing clues that suggest there may be many proteins hidden within the DNA sequences of our genome. Together, they will combine their expertise in molecular and cellular biology, bioinformatics and virology to uncover how and when such proteins are made.
“We have developed a combined experimental-bioinformatics approach that allows us to quickly search entire genomes for sequences that enhance the translation of a downstream gene,” Chaput says. “By determining the identity and location of these motifs, it should be possible to determine when specific genes are being made and possibly discover new genes that contribute to our proteome. Since many of these genes will likely be made by non-traditional methods, this technology will also allow us to investigate new mechanisms of protein translation.”
The motifs they hope to identify help recruit ribosomes, the protein translation machinery of the cell, to the correct translation start site on the RNA message. By identifying these landing sites, the team can use bioinformatics to learn where these motifs are located in the genome.
This information will enable Chaput’s team to create an annotated map of the human genome showing all possible locations where protein translation could occur.
Monday, May 19, 2008
More Universities Hasten Bioinformatics Discoveries Using High-Performance SGI Solutions
[Source: PRNewswire-FirstCall/] - SGIC high-performance compute (HPC) systems have long been a fixture in universities throughout the world, speeding time to discovery across a wide range of disciplines.
SGI shared-memory servers can be found in university research facilities throughout the world, but a new trend is prompting universities to migrate from smaller systems that serve individual departments to larger clusters and shared-memory systems capable of meeting the needs of many departments and disciplines. This trend is saving IT administrators the cost and time of managing multiple small systems, and it offers a new generation of researchers the kind of HPC resources they need to tackle ever-larger bioinformatics problems.
Universities are choosing SGI systems to meet the demanding challenges of bioinformatics for several reasons.
The SGI server architecture offers the ability to scale compute power by adding processors as needed, without a forklift upgrade.
SGI systems meet the need for both shared memory and cluster computing environments to maximize application performance and enhance workflows.
Both shared memory and cluster capabilities can be combined to create a seamless, hybrid environment.
"Over the last several years, a number of universities have begun purchasing larger SGI Altix multiprocessor systems and have added IT departments to manage their use within the central data center," said Deepak Thakkar, Ph.D. higher education and research solutions manager, SGI. "Many researchers and departments then use grant monies and university matching funds to purchase processors on these large systems. Their purchased processors are always there for their needs, and occasionally, depending on the volume from other departments, IT managers can make more processors available to specific projects."
Recent examples of this trend include Michigan State University, Universite de Montreal, and the University of Arizona, all which are using SGI Altix systems for cutting edge bioinformatics research.
Michigan State University -- Gene Mutation Research
Michigan State University (MSU) has used an SGI(R) Altix(R) XE1300 cluster with 1,024 cores since September 2007. Evolutionary biologist Barry Williams, assistant professor, Zoology and Microbiology and Molecular Genomics, purchased 16 cores of the SGI Altix XE system to identify which forces of nature, such as natural selection or changes in population size, cause changes in DNA to accumulate over time, as well as those forces that prevent new mutations that arise in natural populations. When Williams sees mutations that seem to have some effect on genotype, he makes those mutations in many different strains of yeasts, and puts them in different environments to verify their potential effects. Williams works primarily with easily manipulated single-cell yeast microbes.
While he has done work on the university's existing SGI(R) Altix(R) 3700 HPC system at MSU, installed some two years ago, Williams considers the number of projects he can run in parallel on the new SGI Altix XE cluster as a boon to his research.
"It's not unusual for one analysis running on one processor to take several days to a week. We have 6,000 genes that make up the yeast genome that we want to analyze, and each one can take a day. Without the Altix cluster this just becomes impossible," said Williams, who also conducts artificial life research on the SGI system. "The artificial life evolves autonomous computer programs in silico -- we do this to make general predictions about the evolutionary process that we can next test in the yeasts. The beauty of artificial life research is that you can repeat the experiment of evolution with the exact same starting conditions and let evolution take place again and again. I have 16 processors on the systems, so at any one time I can run 16 completely different worlds in parallel. They all start at the same point; they all have the same genetic diversity; they all start with the same individuals and the same conditions, but simultaneously, 16 times, I can let them evolve for millions upon millions of generations."
Many other MSU departments including Nuclear Physics, Mathematics and Chemistry will also be harnessing the power of the SGI system (see separate release, April 29, 2008).
Universite de Montreal -- World's Largest Heart Simulation Model with 2 Billion Elements
In the quest to discover how the mechanisms of heart disease work, researchers at the Universite de Montreal (UdM) ran the largest mathematical simulation of a heart ever assembled -- a 2 billion element model -- on a high-performance SGI(R) Altix(R) 4700 system with 1.2TB of memory. (See separate release January 15, 2008) The SGI Altix is believed to be the largest shared memory computing system in Canada
Until recently, the largest heart models in the world had at most a few million elements.
Dr. Mark Potse and Dr Alain Vinet, both affiliated with the Research Center of Sacre-Coeur Hospital and the Biomedical Engineering department at UdM, began running 100 to 120 million-point models as part of their heart disease research. Potse and Vinet regularly use 60 of the 768 Intel(R) Itanium(R) 2 processors running on the SGI Altix which, as part of the Quebec Network for High-Performance Computing (RQCHP), is shared by many researchers from across Canada since it's unveiling in February 2007.
In October last year, Potse and Vinet had the opportunity to run their custom electrocardiography (ECG) code using the entire SGI Altix system with all 786 processors and all 1.2TB of shared memory. Originally written by them on an earlier SGI system and ported to the SGI Altix system's Linux(R) environment in 2003, the ECG code made the leap from 120 million points to 2 billion with ease.
"This was a test to see if the simulation works and to determine that, if we have a much bigger machine, our software will be able to run more efficiently," said Potse. "This capability is really for the future when we can use this size of machine on a regular basis, but with the Altix system we have made the heart model of the future today."
The new UdM model is up to 1,000 times more detailed than previous models, enabling new scientific discoveries that would never be possible via observation alone.
University of Arizona -- Maize Sequencing Research
The University Information Technology Services (UITS) at the University of Arizona (UA)) purchased two SGI Altix 4700 systems with a total of 1.2TB of memory over a year ago. Instead of departments purchasing processors before installation, the UA allows professors and researchers to add processors to the scalable SGI compute environment. The systems are a university-wide resource available to any department in need of HPC, which includes a number of ongoing and new bioinformatics projects.
Research Professor Cari Soderlund heads the Arizona Genomics Computational Laboratory (AGCoL) that is currently working on the computational aspects of sequencing 30,000 genes for maize. In order to determine the sequence of genes, subsequences of about 800 base pairs (bp) are generated. To reconstruct the original gene sequence, the sub sequences are analyzed to determine the overlapping sub-sequences. For the 700,000 sequences, the global shared memory of the SGI Altix system will accelerate data generation and analysis.
"As our lab is often processing large datasets, the speedup from the SGI Altix system should increase the turn-around time between the generation of biological data and computational analysis," said Soderlund, who recently began porting her project to the SGI Altix system. "It would also allow for more experimentation of parameters and algorithms for larger datasets."
"The Altix 4700 has been our workhorse for the past year and is used by researchers throughout campus, including life sciences," said Dr. Michael Bruck, Assistant Director of Research Computing at the UA's UITS, which coordinates central research computer resources on campus. "The Altix is meeting and exceeding our expectations."
SGI Altix systems empower research at many prestigious universities, including UC Riverside, Purdue University, Stony Brook University, University of Utah, Technische Universitat Dresden (TU Dresden), University of Sao Paulo and U.S. Air Force Academy.
"With many universities deploying both shared memory systems and clusters such as the SGI Altix servers and Altix XE clusters, we are now seeing jobs scheduled based upon the architecture that best suits their computing needs-an entirely seamless process for the researchers," added Thakkar. "SGI systems are being rapidly adopted not only for bioinformatics, but for all disciplines ranging from astronomy to zoology."
Thursday, December 20, 2007
Biodiversity Informatics Initiative Underway
[Source: Bio5] - Two recently recruited scientists from UC Davis, Michael Sanderson, PhD, and Michelle McMahon, PhD, are jump-starting the new Biodiversity Informatics initiative at The University of Arizona (UA).
The initiative is building on existing UA strengths in biology and informatics. As it develops, the initiative will 1) provide nationally unique research and training programs, 2) establish a framework for meeting the expanding bioinformatics needs at the UA, and 3) complement the informatics programs at other institutions in the State. Funding for the initiative comes from the UA BIO5 Institute, College of Science and College of Agriculture and Life Sciences.
Dr. Sanderson, a professor in the Department of Ecology and Evolutionary Biology (EEB) and a BIO5 member, is spearheading the development of the research and training program, focusing on the Sonoran Desert. Dr. McMahon, a research assistant professor in the Department of Plant Sciences, runs the UA Herbarium.
With more than 380,000 specimens, it is the largest herbarium in the arid southwest and unique in having the largest collection in the world of plants from Arizona and Sonora, Mexico. It is one of several outstanding UA natural history collections.Plans also include competitively funded pilot projects to stimulate interactions between UA information scientists and biological researchers, and establishing a graduate interdisciplinary training program. For example, EEB is hiring postdoctoral level curators that will begin this fall; the new positions are part of a renewed investment in the UA natural history collections.
“The new curator positions are exciting because they will bring in people who are interested in combining rich resources in natural history collections with modern technology and cutting edge scientific questions,” says Dr. McMahon.
Why Informatics?
One common theme across all scientific activities and operations that support biological research and medical care is the need to share data efficiently and effectively. Yet, the data are not often in a form that is suitable for straightforward storage and application using simple data analysis tools such as statistical methods, data mining approaches or visualization. Some of these data are too voluminous to easily comprehend and manipulate unless presented in clustered, visual and other forms (e.g. image data that are digitized for analysis are often too complex to effectively analyze).
Advanced technology is required for the management of this scientific knowledge; thus it is imperative that biologists collecting and interpreting these data are interfacing with information technologists working at the cutting-edge of knowledge management.
What is Biodiversity Informatics?
Distinguished from typical “bioinformatics”, which emphasizes depth in genomic and post-genomic information mainly in model organisms and humans, “biodiversity informatics” focuses on breadth—attributes of large collections of disparate species at scales ranging from populations to geographic regions to entire biotas, and ultimately the entire phylogenetic tree of life. Biodiversity informatics uses the power of computational and information technologies to organize and analyze biological data from research collections, experiments, remote sensing, modeling, database searches and instrumentation – to deliver answers to users throughout the world. Today, the Internet and World Wide Web are powerful tools for linking and utilizing the extraordinary assets of natural history institutions.
The initiative is building on existing UA strengths in biology and informatics. As it develops, the initiative will 1) provide nationally unique research and training programs, 2) establish a framework for meeting the expanding bioinformatics needs at the UA, and 3) complement the informatics programs at other institutions in the State. Funding for the initiative comes from the UA BIO5 Institute, College of Science and College of Agriculture and Life Sciences.
Dr. Sanderson, a professor in the Department of Ecology and Evolutionary Biology (EEB) and a BIO5 member, is spearheading the development of the research and training program, focusing on the Sonoran Desert. Dr. McMahon, a research assistant professor in the Department of Plant Sciences, runs the UA Herbarium.
With more than 380,000 specimens, it is the largest herbarium in the arid southwest and unique in having the largest collection in the world of plants from Arizona and Sonora, Mexico. It is one of several outstanding UA natural history collections.Plans also include competitively funded pilot projects to stimulate interactions between UA information scientists and biological researchers, and establishing a graduate interdisciplinary training program. For example, EEB is hiring postdoctoral level curators that will begin this fall; the new positions are part of a renewed investment in the UA natural history collections.
“The new curator positions are exciting because they will bring in people who are interested in combining rich resources in natural history collections with modern technology and cutting edge scientific questions,” says Dr. McMahon.
Why Informatics?
One common theme across all scientific activities and operations that support biological research and medical care is the need to share data efficiently and effectively. Yet, the data are not often in a form that is suitable for straightforward storage and application using simple data analysis tools such as statistical methods, data mining approaches or visualization. Some of these data are too voluminous to easily comprehend and manipulate unless presented in clustered, visual and other forms (e.g. image data that are digitized for analysis are often too complex to effectively analyze).
Advanced technology is required for the management of this scientific knowledge; thus it is imperative that biologists collecting and interpreting these data are interfacing with information technologists working at the cutting-edge of knowledge management.
What is Biodiversity Informatics?
Distinguished from typical “bioinformatics”, which emphasizes depth in genomic and post-genomic information mainly in model organisms and humans, “biodiversity informatics” focuses on breadth—attributes of large collections of disparate species at scales ranging from populations to geographic regions to entire biotas, and ultimately the entire phylogenetic tree of life. Biodiversity informatics uses the power of computational and information technologies to organize and analyze biological data from research collections, experiments, remote sensing, modeling, database searches and instrumentation – to deliver answers to users throughout the world. Today, the Internet and World Wide Web are powerful tools for linking and utilizing the extraordinary assets of natural history institutions.
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