Online epidemic tracking tool wins Open Science Prize
Nextstrain.org synthesizes publicly available pathogen genomic data in near real-time to better understand the spread of epidemics such as Zika and Ebola.
A prototype online platform that uses real-time visualization and viral genome data to track the spread of global pathogens such as Ebola and Zika has been selected as the grand prize winner of the Open Science Prize.
The award is an international competition meant to foster innovative solutions in public health and biomedicine using open digital content.
An initiative of the National Institutes of Health, in collaboration with the Wellcome Trust and the Howard Hughes Medical Institute, the Open Science Prize has awarded $230,000 to Nextstrain.org, a website that gathers data from researchers worldwide, performs rapid phylogenetic analysis, and posts the results online.
Elizabeth Kittrie, strategic advisor for data and open science at NIH’s National Library of Medicine, notes that genome sequences of viral pathogens can provide valuable insights into the spread of epidemics. However, to be useful and actionable, samples have to be collected, analyzed and the results openly disseminated in near real-time, she contends.
Nextstrain.org ingests viral genome sequence data from openly available sources, conducts quick phylogenetic analyses to understand the ancestral relationships among those pathogens and displays the resulting phylogenetic “trees” on an interactive public website using real-time visualization, says Kittrie.
“Nextstrain had a tremendous public health impact by enhancing our ability to track diseases across international borders,” says Kittrie, who was the NIH lead for the Open Science Prize.
Also See: HHS, NIH to increase research access and transparency
According to Kittrie, without an online platform such as Nextstrain.org, researchers would be left with collecting genome sequence data for viral pathogens from “whatever kind of research they could glean from disparate databases and publications” made publically accessible long after an epidemic has subsided.
In those cases, she adds, the data is “very localized, and so researchers are not able to see the evolution of a virus over time and space,” often taking years to collect and synthesize the information.
The Nextstrain.org development team was led by Trevor Bedford of the Fred Hutchinson Cancer Research Center in Seattle and Richard Neher of Biozentrum at the University of Basel in Switzerland.
"Nextstrain.org aims to synthesize publicly available pathogen genomic data to arrive at an understanding of epidemic spread not available through traditional surveillance systems," said Bedford in a written statement.
"Our efforts with Nextstrain.org are only possible through open data sharing by others in the community. We've really enjoyed working with these teams in the field as they collect and share viral genome data,” added Neher.
According to NIH, the statistical analyses behind Nextstrain.org can be conducted in minutes, revealing patterns of geographic spread for the benefit of the global research community, which can query the database and examine the spread of disease by country, region, or type of strain.
“This tool exponentially advances our ability to track diseases in ways that we really couldn’t before, and is also a model of data sharing,” concludes Kittrie.
In the first phase of the competition, a panel of experts selected six multinational, interdisciplinary teams from an initial pool of 96 teams from 45 countries, who were each awarded $80,000 to build a prototype. Ultimately, the six teams were narrowed to three finalists with Nextstrain.org taking the top prize. The $230,000 award will be used by Nextstrain.org to fully develop their prototype.
The award is an international competition meant to foster innovative solutions in public health and biomedicine using open digital content.
An initiative of the National Institutes of Health, in collaboration with the Wellcome Trust and the Howard Hughes Medical Institute, the Open Science Prize has awarded $230,000 to Nextstrain.org, a website that gathers data from researchers worldwide, performs rapid phylogenetic analysis, and posts the results online.
Elizabeth Kittrie, strategic advisor for data and open science at NIH’s National Library of Medicine, notes that genome sequences of viral pathogens can provide valuable insights into the spread of epidemics. However, to be useful and actionable, samples have to be collected, analyzed and the results openly disseminated in near real-time, she contends.
Nextstrain.org ingests viral genome sequence data from openly available sources, conducts quick phylogenetic analyses to understand the ancestral relationships among those pathogens and displays the resulting phylogenetic “trees” on an interactive public website using real-time visualization, says Kittrie.
“Nextstrain had a tremendous public health impact by enhancing our ability to track diseases across international borders,” says Kittrie, who was the NIH lead for the Open Science Prize.
Also See: HHS, NIH to increase research access and transparencyAccording to Kittrie, without an online platform such as Nextstrain.org, researchers would be left with collecting genome sequence data for viral pathogens from “whatever kind of research they could glean from disparate databases and publications” made publically accessible long after an epidemic has subsided.
In those cases, she adds, the data is “very localized, and so researchers are not able to see the evolution of a virus over time and space,” often taking years to collect and synthesize the information.
The Nextstrain.org development team was led by Trevor Bedford of the Fred Hutchinson Cancer Research Center in Seattle and Richard Neher of Biozentrum at the University of Basel in Switzerland.
"Nextstrain.org aims to synthesize publicly available pathogen genomic data to arrive at an understanding of epidemic spread not available through traditional surveillance systems," said Bedford in a written statement.
"Our efforts with Nextstrain.org are only possible through open data sharing by others in the community. We've really enjoyed working with these teams in the field as they collect and share viral genome data,” added Neher.
According to NIH, the statistical analyses behind Nextstrain.org can be conducted in minutes, revealing patterns of geographic spread for the benefit of the global research community, which can query the database and examine the spread of disease by country, region, or type of strain.
“This tool exponentially advances our ability to track diseases in ways that we really couldn’t before, and is also a model of data sharing,” concludes Kittrie.
In the first phase of the competition, a panel of experts selected six multinational, interdisciplinary teams from an initial pool of 96 teams from 45 countries, who were each awarded $80,000 to build a prototype. Ultimately, the six teams were narrowed to three finalists with Nextstrain.org taking the top prize. The $230,000 award will be used by Nextstrain.org to fully develop their prototype.
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