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Help Shape New Directions in Open Science: Vote for Your Favorite Innovation!

a globe of a word cloud related to open science

In the spirit of open science – a movement to make data and other information from scientific research available to everyone — the National Institutes of Health invites you to cast your vote and help us decide which of the projects competing for the Open Science Prize are the most innovative and most likely to have the greatest impact. Your vote plays a critical role in determining the three finalists for the ultimate selection of a grand prize winner of $230,000.00

In this competition, six finalist teams, composed of at least one U.S.-based and one international researcher, are using open data to improve human health. Open data refers to publicly-accessible data that is available for re-use by anyone.

While science is truly a global endeavor, often involving teams of scientists at institutions in different nations, funding for scientific research is typically tied to the country of origin. To overcome this, the National Institutes of Health and the UK-based Wellcome Trust, with additional funding from the Howard Hughes Medical Institute, have jointly created the Open Science Prize, an innovative effort showing how funding agencies can collaborate internationally.

The goal of this Prize is to stimulate the development of novel and ground-breaking tools and platforms to enable the reuse and repurposing of open digital research objects relevant to biomedical or health applications.  A Prize model is necessary to help accelerate the field of open biomedical research beyond what current funding mechanisms can achieve.  We also hope to demonstrate the huge potential value of Open Science approaches, and to generate excitement, momentum and further investment in the field.

The prize was first announced in 2015 and we invited solvers around the world to submit their ideas.  Out of a pool of 96 applicant teams, six finalists were selected and provided $80,000 to develop their ideas into prototypes.

Vote today! You can play a part in shaping the future of biomedical research. To vote, go to www.OpenSciencePrize.org, review the projects listed there (and also described below), and choose the three you would like to see advance to the final round of competition. Voting is open from December 1, 2016 until January 6, 2017 at 11:59 p.m. PST.  The 3 prototypes receiving the highest number of public votes will advance to a final round of review by a panel of science experts and judges from the National Institutes of Health and the Wellcome Trust  A single, grand prize winning team will receive an award of $230,000 jointly funded by the collaborators will be announced in March 2017.

You can learn more about each of the six finalist projects below (listed in no particular order):

Open Neuroimaging Laboratory: Advancing brain research by enabling collaborative annotation, discovery and analysis of brain imaging data

There is a massive volume of brain imaging data available on the internet, capturing different types of information such as brain anatomy, connectivity and function. This data represents an incredible effort of funding, data collection, processing and the goodwill of thousands of participants.  The development of a web-based application called BrainBox enables distributed collaboration around annotation, discovery and analysis of publicly available brain imaging data, generating insight on critical societal challenges such as mental disorders, but also on the structure of our cognition.  Collaborators can send information, make comments, and highlight particular locations on the images, and access can be restricted to allow collaborators to view the images without modifying them – using a functionality similar to Google Docs.

Open AQ: Providing real-time information on poor air quality by combining data from across the globe

Poor air quality is responsible for one out of eight deaths across the world, but the most polluted places in the world are not well-researched, hindering scientific progress. Accessible and timely air quality data is critical to advancing the scientific fight against air pollution and is essential for health research.  The OpenAQ platform collects data every 10 minutes and allows users to view stored data and compare locations.  To date, the OpenAQ community has collected 32,929,735 air quality measurements from 4,569 locations in 41 countries.  Data are aggregated from 55 government level and research-grade sources.

Real-Time Evolutionary Tracking for Pathogen Surveillance and Epidemiological Investigation:  Permitting analysis of emerging epidemics such as Ebola, MERS-CoV and Zika

The Nextstrain project is an app for tracking pathogen evolution in real time, critical in this era of high mobility. Contact tracing is the main way to fight a virus without a vaccine; sequencing the genomes of viruses such as Ebola can determine the shared mutations and phylogeny of each strain, allowing field epidemiologists a more nuanced way to trace contact. To facilitate treatment of active outbreaks of pathogens such as Zika, Nextstrain is able to show molecular epidemiology within days. It also is intended to be scalable and easy to interpret for teams on the ground. The project uses an online visualization platform where the outputs of statistical analyses can be used by public health officials for epidemiological insights within days of samples being taken from patients.

OpenTrialsFDA: Enabling better access to drug approval packages submitted to and made available by the Food and Drug Administration

The OpenTrialsFDA app makes clinical trials data from the U.S. Food and Drug Administration (FDA) easier to find by making the contents of the drug approval packages publically available.  These review packages often contain information on clinical trials that have never been published in academic journals.  OpenTrialsFDA allows users to see the raw results of a study, such as unpublished data or data that seem more significant than they really are, in a way that is much more user-friendly and easier to navigate than the Drugs@FDA database of publicly available documents.

Fruit Fly Brain Observatory: Allowing researchers to better conduct modeling of mental and neurological diseases by connecting data related to the fly brain

Understanding human brain function and disease is arguably the biggest challenge in neuroscience. To help address this challenge, researchers turn to smaller but sufficiently complex brains from other organisms. The Fruit Fly Brain Observatory allows data from fruit fly brain scans to be used as models for investigating human neurological and psychological disorders. The Fruit Fly Brain Observatory also has integrated healthy and diseased models of the human brain for study. Using computational disease models, researchers can make targeted modifications that are difficult to perform in vivo with current genetic techniques. The platform is modular, so it will be extendable to mice, zebrafish, and other experimental animals. These capabilities have the potential to significantly accelerate the development of powerful new ways to predict the effects of pharmaceuticals upon neural circuit functions.

MyGene2: Accelerating Gene Discovery with Radically Open Data Sharing

Approximately 350 million people worldwide and over 30 million Americans have a rare disease. Most of these rare diseases are so-called Mendelian conditions, which means that mutation(s) in a single gene can cause disease.  Examples of such diseases are include sickle-cell anemia, Tay-Sachs disease, cystic fibrosis and xeroderma pigmentosa. Over 7,000 Mendelian conditions have been described, but to date, scientists have only linked half of those conditions to a specific gene. Consequently, close to 70 percent of families who undergo clinical testing lack a diagnosis.  MyGene2 is a website that makes it easy and free for families with Mendelian conditions to share health and genetic information with other families, clinicians and researchers worldwide in order to make a match.

 

CDC Addresses “Pioneer Gap” with Investment from their Innovation Fund!

In 2010, conversations with more than 70 staff at CDC identified a lack of early stage funding as a top barrier to innovation. To fill this “pioneer gap” the Office of the Associate Director for Science (OADS), Office of Technology and Innovation sponsors the Innovation Fund (iFund) to support CDC innovators of exceptional creativity who propose transformative, high impact approaches that address public health priorities.  The iFund supports the scaling and/or operationalization of tried and tested innovations. The program is designed for innovators who require support for continued growth and for assessing the likelihood that the innovation can achieve impact and/or viability at a larger scale.

Since its inception in 2011, the iFund has supported and financed over 60 mission-driven projects. Like the HHS Ventures Fund, teams pitch for up to $100,000 of support for a 15 month project timeframe.   This past December, OADS received over 82 proposals for consideration.

We are pleased to announce the teams selected for iFund support which includes one project co-funded with the HHS Ventures Fund. The selected individuals, projects, and CDC Centers, Institutes and Offices are listed below. Please join me in congratulating these teams!

 

iFund awardees for CDC

iFund Awardees
Bottom Row (L to R): Heather Scobie, Eugene Lam, Matthew Maenner, Paula Braun.
Top Row: Diane Jackson and Greg Zarus

 

Development of a portable multi-sensor device to conduct remote, periodic air sampling for investigating city-wide air pollution complaints

Project Members

  • Greg Zarus, Agency for Toxic Substances and Disease Registries, CDC
  • Diane Jackson, Agency for Toxic Substances and Disease Registries, CDC
  • Lynn Wilder, Agency for Toxic Substances and Disease Registries, CDC
  • Custodio Muianga, Agency for Toxic Substances and Disease Registries, CDC

Project Sponsor

  • Ileana Arias, Division Director, Agency for Toxic Substances and Disease Registries, CDC

Field validation of new assay for the detection of measles and rubella infection and immunity

Project Members

  • Eugene Lam, Center for Global Health, CDC
  • Heather Scobie, Center for Global Health, CDC
  • Paul Rota, Office of Infectious Disease, CDC

Project Sponsor

  • Jordan Tappero, Division Director, Center for Global Health, CDC

Use of an innovative screening assay to improve maternal and child health (MCH)

Project Members

  • Bharat Parekh, Center for Global Health, CDC
  • Yetunde Fakile, Office of Infectious Disease, CDC
  • Ernest Yufenyuy, Center for Global Health, CDC
  • Diana Martin, Center for Global Health, CDC
  • Tun Ye, Center for Global Health, CDC
  • Mary Kamb, Office of Infectious Disease, CDC

Project Sponsor

  • Kevin Karem, Assoc. Dir. of Lab Science, Center for Global Health, CDC

Use of malaria parasite-specific metabolites as biomarkers for development of a sensitive, low-cost, rapid, simple and field deployable non-invasive diagnostic for malaria infection

Project Members

  • Ya Ping Shi, Center for Global Health, CDC
  • Sheila Sergent, Center for Global Health, CDC
  • Xichun Zhou, Center for Global Health, CDC
  • Scott Angus, Center for Global Health, CDC
  • Gus Dinovo, Office of Infectious Disease, CDC

Project Sponsor

  •  Larry Slutsker, Division Director, Center for Global Health, CDC

Inexpensive counterfeit drug identification device (CoDI)

Project Members

  • Mike Green, Center for Global Health, CDC
  • Isabel Swamidoss, Center for Global Health, CDC
  • Babita Ganguly, Center for Global Health, CDC
  • Maria Paul,

Project Sponsor

  • Larry Slutsker, Division Director, Center for Global Health, CDC

Reinventing autism surveillance with machine learning

Project Members

  • Matthew Maenner, National Center for Birth Defects and Developmental Disabilities,
  • Chad Heilig, Office of Public Health Scientific Services, CDC
  • Scott Lee, Office of Public Health Scientific Services, CDC
  • Nicole Dowling, Office of Noncommunicable Disease, Injury and Environmental Health, CDC
  • Maureen Durkin,

Project Sponsor

  • Colleen Boyle, Director,  National Center for Birth Defects and Developmental Disabilities, CDC

Identification of metabolic conjugates to detect opioid exposure

Project Members

  • Melissa Carter, National Center for Environmental Health, CDC
  • Samantha Isenberg, National Center for Environmental Health, CDC
  • Thomas Mathews, National Center for Environmental Health, CDC
  • Rebecca Shaner, National Center for Environmental Health, CDC

Project Sponsor

  • Jerry Thomas, Medical Officer, National Center for Environmental Health, CDC

Death-on-FHIR: Using new technologies to help improve the accuracy of mortality data and support real-time surveillance

Project Members

  • Paula Braun, National Center for Health Statistics, CDC
  • Mark Braunstein (Georgia Tech)
  • Glenn Copeland, Michigan
  • Michelle Williamson, National Center for Health Statistics, CDC
  • Hetty Khan, National Center for Health Statistics, CDC

Project Sponsor

  • Delton Atkinson, Health Statistician, National Center for Health Statistics, CDC

 Mini baghouse technology to control silica dust at fracking sites

Project Members

  • Eric Esswein, National Institute for Occupational Safety and Health, CDC
  • Arthur Miller, National Institute for Occupational Safety and Health, CDC

Project Sponsor

  • Jennifer Lincoln, Health Scientist, National Institute for Occupational Safety and Health, CDC

International Prize Winners Demonstrate the Future of Open Science

Open Science Winners Infographic-01

The finalists of the first international Open Science Prize competition were announced today.  The Open Science Prize is a collaborative effort between the National Institutes of Health, UK-based Wellcome Trust, and the Howard Hughes Medical Institute designed to encourage and recognize the development of new tools, products, and services that use open digital content to help solve pressing public health and biomedical research challenges.

Six innovative proposals were selected as finalists.  Each of the finalist teams will receive $80,000 for development of a prototype by December 1, 2016.  The six proposals and their associated teams were chosen from an initial pool of 96 submissions representing 450 innovators from 45 countries across 5 continents.  Each proposal selected as a finalist represents an original approach to either synthesizing available data to create new knowledge or creating platforms that allow for the integration of such knowledge.  The six finalist proposals are described in detail on the Open Science Prize website.

The Open Science Prize finalists were announced at the 7th annual Health Datapalooza conference in Washington, DC.  The announcement was made by Phil Bourne, the Associate Director for Data Science at the National Institutes of Health and Clare Matterson, Director of Strategy at the Wellcome Trust.  A grand prize winner, to be selected from amongst the six finalists, will be announced in early 2017.  The grand prize winner will receive $230,000 to advance their winning project.

In order to qualify, each finalist team was required to be an international partnership, composed of at least two or more individuals or entities of which at least one is based in the United States and another is based in another country.  The fascinating stories of how these partnerships formed and what they have proposed provide important and inspiring examples of the power of open science.  These stories demonstrate how open science can enable interdisciplinary teams from across the globe to work together to creatively advance public health and biomedical research.

The following are brief summaries of the six proposals selected as finalists:

  • Open AQ: Real-Time Air Quality Data – This proposal was inspired by an initial open air quality project undertaken in Mongolia, which demonstrated the positive effect that air quality data can have on a community by enabling transparency and the ability to make data-driven comparisons.  Poor air quality is responsible for one out of eight deaths worldwide.  Impressed by the potential benefits of scaling the Mongolia project up to the global scale, the team proposes to devise a platform for making all of the world’s air quality data available to the global public in one open-source and open data platform.
  • Real-Time Evolutionary Tracking for Pathogen Surveillance and Epidemiological Investigation – This proposal stemmed from a conversation at a conference in California between an expert from the Max Planck Institute for Experimental Biology in Germany and an expert from the Fred Hutchinson Research Center in Seattle, Washington. The two proposed to expand their existing platform, focused on exposing flu viruses, to track other emerging diseases such as the Ebola and Zika viruses.  The project will use an online visualization platform where the outputs of statistical analyses can be used by public health officials for epidemiological insights within days of samples being taken from patients.
  • Open Neuroimaging Laboratory – This is a collaborative effort between researchers in the United States, Germany, and France and was inspired by the successful results of an online game, Eyewire, that has led to the discovery of several new neural pathways in the brain.  These researchers asked, “What if we could utilize gaming principles to engage citizens across the world to work collaboratively to help us map a still largely unchartered territory: the human brain?”  Their proposal aims to do exactly that.
  • OpenTrialsFDA – This proposal was inspired by a former FDA reviewer. Publicly available U.S. Food and Drug Administration drug approval packages often contain important information on clinical trials that are never published in academic journals. However, despite their high value, these FDA documents are notoriously difficult to access, aggregate, and search. As a consequence, they are rarely used by clinicians and researchers.  This project proposes to advance understanding of clinical trials by building a platform to make this publicly available, but difficult to find, FDA drug approval package information more readily available and combine it with knowledge being generated about clinical trials by Open Knowledge International, a UK-based organization.
  • Fruit Fly Brain Observatory – This proposal is designed to help pool data from different labs around the world and allow scientists with a variety of backgrounds, from computer science to neuroscience, to work together in advanced modeling.  Using computational disease models, researchers can make targeted modifications that are difficult to perform in vivo with current genetic techniques.  The urgency to develop such a platform comes from one of the lead investigators whose own family is affected by Alzheimer/Dementia and Parkinson’s Disease.
  • MyGene2: Accelerating Gene Discovery with Radically Open Data Sharing– This proposal was inspired by families of patients who suffer from rare disease disorders and want a tool to facilitate their ability to share health and genetic information.  The sharing of information through such an open platform could enable the rapid identification of matching cases, which could help speed up diagnosis and transform the process of gene discovery.

You can learn more about the Open Science Prize, the submitted proposals, and the innovators’ stories here.

The Open Science Prize was a first-ever international challenge effort funded jointly by the NIH and UK-based Wellcome Trust. It highlights the kinds of advancements in global public health and biomedical research that could be developed through further funding of open science.

Biomedical research is in the midst of a paradigm shift. Several factors are facilitating the global sharing of knowledge and the development of international partnerships.  These factors include: advances in information technology, reduced cost of data storage, open government policies being adopted by many countries across the globe, and public access mandates that require the sharing of funded research publications as well as the underlying data.  The existing paradigm of an investigator toiling alone is increasingly being replaced by a more collaborative approach to research that is driven by uses and re-uses of data.

The volume of digital information generated by biomedical research, often referred to as big data, is growing at a rapidly increasing pace. Researchers’ ability to derive knowledge from data is hindered by their ability to find, access, and use it. The goal of the Open Science Prize is to support the development and prototyping of services, tools, and platforms to overcome these hurdles to ensure data can be used to advance discovery and spur innovation.

Tools like the ones we are seeing through the Open Science Prize are enabling new types of research, new types of knowledge, new types of collaboration, and new ways of thinking.  They represent the tip of the iceberg in terms of what is, and what could be created, using open digital content.   We are excited about the power of open science, and look forward to tracking these teams as they build their prototypes over the next nine months.

The public will be invited to view these prototypes in early December and to cast their vote for their favorite using an online tool.  Your vote will help us to select the winning innovation for this contest!

The Open Science Prize is made possible through a collaboration between NIH and the Wellcome Trust. The Howard Hughes Medical Institute is also contributing funds to Wellcome Trust for the effort. The NIH effort is part of the Big Data to Knowledge (BD2K) Initiative, launched in December 2013 as a trans-NIH program with funding from all 27 institutes and centers as well as the NIH Common Fund.

This is a cross-post from Data Science at NIH.

What’s that Pill? New Challenge Aims to Help You Visually Identify Prescription Pills

Can you identify a pill by its shape, color, and markings? Chances are you can’t, but you know of times when it would be useful. You could use your smartphone to take a picture of a mystery pill and almost immediately see what it most likely could be. The National Library of Medicine (NLM), part of the National Institutes of Health, would like all of us to be able to more easily identify pills. And it is working on a fix, starting with prescription pills. NLM recently launched its Pill Image Recognition Challenge (Federal Register Notice, Submission Instructions). The Challenge asks any and all innovators to design algorithms and software that can effectively match lower-quality photos – like those we take with smartphones – with high-quality publicly-available images in the NLM RxIMAGE database. Today’s RxIMAGE has images and descriptions of about 4,000 prescription pills. NLM hopes that the satisfaction of addressing this easily stated problem, along with monetary awards, will entice experts and students working in fields as diverse as image recognition and data analytics to participate. NLM researchers plan to use Challenge submissions and potentially work with Challenge participants to build a software system and an Application Programming Interface (API) underlying a consumer-facing smartphone app for image recognition of prescription pills. The NLM Pill Image Recognition Project team thinks that people who pick up refills of prescriptions for generic drugs for themselves or family members would benefit from using such an app. A refill can be made by a different manufacturer and can have different color, shape, or markings. That can be confusing, but the app could help confirm what the refill is for. We look forward to seeing how the Pill Image Recognition Challenge can leverage the RxIMAGE database to produce tools for such public benefit.

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HHS Competes, an HHS IDEA Lab program, supports the use of prizes, challenges, and crowdsourcing to more effectively leverage the intelligence of the crowd to solve our nation’s toughest problems.  Learn more.