"It’s a scenario that keeps politicians awake at night: A deadly form of avian flu mutates, spreads from birds to humans and sets off a global pandemic.
If — some say when — that scenario becomes a reality, it would fall to health professionals and researchers to come up with measures to combat it and treat patients. Perhaps more important, researchers are looking for safeguards that would prevent a pandemic from happening in the first place.
That’s where IT in the form of bioinformatics plays a major role.
Bioinformatics is the collection, organization and analysis of large amounts of biological data through the use of computers, networks and databases. A number of projects under way demonstrate the direction the field is taking and its continued importance in health care and homeland security."
Chicago Tribune Bioterror detectors go high-tech
"Government analysts have begun scanning the U.S. daily for the first signs of a bioterror attack by monitoring enormous databases that include over-the-counter drug sales and common ailments reported in hospital emergency rooms."
"Although supporters of the effort, including top Bush administration officials, believe stepped-up surveillance is crucial, critics say the concept is largely untested and likely to impose new burdens on an already over-stretched public health system."redux [10.28.04]
Nature: Science Update Pharmacy data reveals impact of smoking ban
"Prompted by the US anthrax attacks of October 2001, most of the new surveillance systems are designed to pick up early warning signs of a bioterror attack, such as a hike in fevers or rashes. They use sophisticated algorithms to filter computerized health data for unusual peaks.
But the systems are untested as yet by bioterror agents - so researchers are teasing other information from them. "These data have all sorts of uses," says Julie Paulin, an expert in preventive medicine at the Walter Reed Army Institute of Research in Silver Spring, Maryland."redux [04.17.03]
Stanford Medical Informatics Preprint Archive A Modular Framework for Automated Space-Time Surveillance Analysis of Public Health Data
"Public health surveillance is changing in response to concerns about bioterrorism, which have increased the pressure for early detection of epidemics. Rapid detection necessitates following multiple non-specific indicators, accounting for spatial structure, and quickly characterizing aberrancies. A single analytic method cannot meet these requirements, but there is no existing framework for the interoperation of surveillance methods. In this paper, we present such a framework and report on a preliminary implementation. Our framework consists of a decomposition of the surveillance analysis task into sub-tasks, and an ontology of surveillance analysis methods, which automate the sub-tasks. As an initial implementation, we use methods developed according to this framework to analyze 911 dispatch data from San Francisco."redux [01.22.03]
The New York Times U.S. Is Deploying a Monitor System for Germ Attacks
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"To help protect against the threat of bioterrorism, the Bush administration on Wednesday will start deploying a national system of environmental monitors that is intended to tell within 24 hours whether anthrax, smallpox and other deadly germs have been released into the air, senior administration officials said today.
The system uses advanced data analysis that officials said had been quietly adapted since the Sept. 11 attacks and tested over the past nine months. It will adapt many of the Environmental Protection Agency's 3,000 air quality monitoring stations throughout the country to register unusual quantities of a wide range of pathogens that cause diseases that incapacitate and kill."redux [11.25.02]
Wired News Global Network Battles Bioterror
"The Albuquerque physician-turned-researcher just returned from a trip to the NATO Summit in Prague, where he hoped to persuade President Bush and the other 19 member nations that a global health surveillance network is the best way to protect people from manufactured disease."
""The current system is exquisitely designed to fail," Zelicoff said."redux [10.31.02]
Stanford Medical Informatics Preprint Archive Knowledge-Based Bioterrorism Surveillance
"An epidemic resulting from an act of bioterrorism could be catastrophic. However, if an epidemic can be detected and characterized early on, prompt public health intervention may mitigate its impact. Current surveillance approaches do not perform well in terms of rapid epidemic detection or epidemic monitoring. One reason for this shortcoming is their failure to bring existing knowledge and data to bear on the problem in a coherent manner. Knowledge-based methods can integrate surveillance data and knowledge, and allow for careful evaluation of problem-solving methods. This paper presents an argument for knowledge-based surveillance, describes a prototype of BioSTORM, a system for real-time epidemic surveillance, and shows an initial evaluation of this system applied to a simulated epidemic from a bioterrorism attack."redux [02.18.02]
Informatics Review Medical Informatics Takes Center Stage with Bush Bioterrorism Agenda
"President George W. Bush, the National Homeland Defense Secretary, Tom Ridge, and Health and Human Services Secretary, Tommy Thompson visited the University of Pittsburgh (UP) yesterday to review one of the advanced developments in medical informatics - a collaboration of the University's Center for Biomedical Informatics and Carnegie Mellon University. The project, known as the Real-Time Outbreak and Disease Surveillance system (RODS), is an early warning system for outbreaks of disease designed to obtain and analyze existing sources of data in real time."RODS Laboratory Realtime Outbreak Detection System (RODS)
"The Real-time Outbreak and Disease Surveillance (RODS) system is a prototype public health surveillance system. RODS collects and analyzes relevant data automatically and in real-time, including emergency room registration data, microbiology culture results, reports of radiographs, and laboratory orders. RODS provides tools that (1) help detect the presence of a disease outbreak, and (2) support the characterization of that outbreak by a public health official. These tools include case definitions, automatic detection algorithms that can be attached to specific data streams, and data analytic tools that support temporal and spatial data analysis and visualization."redux [06.29.01]
EurekAlert GIS, bioinformatics collaborations offer promising new perspectives
"The merits of linking two fields seemingly as disparate as geographic information systems (GIS) and bioinformatics might not seem obvious, but Virginia Tech's recent symposium linking the twoaeand its roster of renowned participants from both fieldsaehas raised expectations "Applications of GIS to Bioinformatics" was the first major public forum to cross-pollinate the disciplines, helping to fortify a relatively new, yet highly promising investigative area."
""As a result of new dialog between the fields, as we've had at this conference, we are gaining an important mechanistic link between individual-level processes tracked by genomics and proteomics and population-level outcomes tracked by GIS and epidemiology. This will allow us to do a far better job of monitoring, quantifying, and predicting human-health consequences associated with the environment. The potential payoff in related fields such as those looking at climate change, emerging and resurgent infectious diseases, and environmental health is enormous.""Applications of GIS to Bioinformatics Symposium Proceedings
"The meeting brings together researchers in two of the most dynamic analytical technologies-GIS and bioinformatics. The value of GIS analytical systems and data structures to bioinformatics are only now being recognized. Similarly, the methodologies used in bioinformatics can inform GIS scholars of new approaches to pattern recognition and analysis. The purpose of the symposium is to explore the potentials for using GIS as an analytical methodology in bioinformatics and to understand the opportunities bioinformatics presents to the GIS research community. The symposium, the first to focus on the interface between these two research areas, will afford scholars the opportunity to establish new research directions in both fields of investigation."
“Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.”BIOINFORMATICS IN THE 21st CENTURY
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