Aggregated Computational Toxicology online resource

Jun 2, 2016

The iCSS Chemistry Dashboard – The First Step in Building a Strong Chemistry Foundation for 21st Century Toxicology

Aggregated Computational Toxicology online resource, chemical research, Chemical Safety for Sustainability, computational toxicology, Endocrine Disruptor Screening Program, iCSS Dashboard, toxcast 1 Comment

By Antony Williams

Computational Chemist Antony Williams is the project lead for the iCSS Chemistry Dashboard

EPA has released the Interactive Chemical Safety for Sustainability Chemistry Dashboard—or the iCSS Chemistry Dashboard—a new web application to support scientists in chemical research.

The dashboard is a new app in the armory of computational toxicologists everywhere. It provides data on over 700,000 chemicals including access to nearly 10,000,000 experimental and predicted chemical properties via a website search. The data are downloadable at the click of a button and are even viewable on your smartphone or tablet. The data and an associated collection of additional resources have been brought together in one application.

The dashboard provides access to the rich and highly curated content that is contained within the Distributed Structure-Searchable Toxicity Database (DSSTox) which was first released in 2002. The data contained within the DSSTox database has been expanded over the years and now is available via an intuitive website for searching.

For this project, we focused our efforts on building a web application that allows the public to easily search our chemistry data. A number of dashboards and web applications have been built over the years including the Aggregated Computational Toxicology Resource, the ToxCast dashboard, and the Endocrine Disruptor Screening Program dashboard. We were able to take advantage of this previous work and improve the user experience for navigating the data. The resulting web application was released on April 1^st, no joke, for beta testing in the real world and to gather initial feedback from the community.

The new chemistry dashboard has been available for only a couple of months and is already garnering positive feedback from its users. New data, functionality, and capabilities are in development to provide regular updates to the application. Much like with Wikipedia’s “crowdsourced feedback”, the application’s users are able to inform us of any issues they see in the data at the individual chemical level to improve the data for all users. As crowdsourced collaboration is increasingly used in the curation of chemistry data, we expect the iCSS Chemistry Dashboard to become one of the primary platforms for environmental chemists and computational toxicologists around the world and form the chemistry foundation for EPA’s efforts in 21^st century toxicology.

About the Author: Antony (Tony) Williams is a computational chemist in the National Center for Computational Toxicology and the project leader for the iCSS Chemistry Dashboard. He is an analytical scientist and cheminformatician by training and was one of the original founders for the ChemSpider website. He is widely published with over 150 publications and books/book chapters.

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Apr 6, 2016

Tools for Building Disaster Resilient Communities

Aggregated Computational Toxicology online resource, Community Resiliency, Community-Based Water Resiliency, EPA Homeland Security Research, I-Waste 1 Comment

By Eli Walton

As a student in Connecticut, I witnessed first-hand the effects of major disasters like Hurricane Sandy and “Winter Storm Nemo,” the February 2013 blizzard. Downed trees and branches littered streets and green space, record snowfall rendered roadways impassable for residents and emergency services, and hundreds of thousands of people were left without power, sometimes for weeks. Having experienced these impacts, I am grateful to be part of EPA’s efforts to help communities better mitigate, prepare for, respond to, and recover from events like these.

Disaster responders in hazmat suits clean up

EPA Responds to the Deepwater Horizon Oil Spill in 2010.

Disasters—whether a hurricane, oil spill, or contamination event—can strike at any time, at any place, and can have devastating consequences for human health and the environment. They may make existing problems worse, like when the Joplin, Missouri tornado exposed people to toxic waste lingering from Joplin’s mining days. They also may create new environmental hazards, like when mold plagued homes and businesses flooded by Hurricane Sandy. While not all disasters can be prevented, the potential harms and risks they pose can be mitigated with the right tools and actions.

Researchers and scientists in EPA’s Homeland Security Research Program, along with collaborators across the Agency, are constantly developing and refining new tools for decision-makers. These tools, compiled in this inventory, serve a variety of purposes, including cleaning up contamination, managing waste and debris, and modeling watersheds. Individually, these tools address different issues that may arise when preparing for or responding to an event. Altogether, they can help communities become more resilient to disasters.

An American flag hangs above wreckage from a tornado.

Wreckage following a 2013 Tornado in Moore, Oklahoma.

For example, the Incident Waste Assessment & Tonnage Estimator (I-WASTE) can help with disaster preparedness and planning by identifying appropriate waste disposal technologies and facilities before they are needed. The Community-Based Water Resiliency Tool (CBWR) can help with emergency planning for an event that may affect water resources and can be used by utilities, officials, and concerned citizens alike. When environmental contamination arises, the Aggregated Computational Toxicology Online Resource (ACTOR) can be used to inform decisions based on chemical toxicity and the potential health effects of chemical exposures in the environment.

The tools in this inventory are just a sample of EPA’s resources, and much more work is underway across the Agency and with collaborators to help strengthen both individual and community disaster resilience.

About the Author: Eli Walton is a Student Services Contractor with the National Homeland Security Research Center in EPA’s Office of Research and Development.

Jun 26, 2013

EPA Scientists Presented Open Science at White House

Aggregated Computational Toxicology online resource, Champions of Change, chemical safety assessment, Chemical Safety for Sustainability research, computational toxicology, Distributed Structure-Searchable Toxicity Database, EPA scientists, innovation, National Center for Computational Toxicology, Open Science, open scientific data, toxicity forecaster, Toxicity Reference database 1 Comment

By Tina Bahadori

From weather forecasts, air quality advisories, and portable GPS navigation devices, to waterfowl migration, and the mapping of the human genome, the use of government and government-supported science and data have vastly improved our lives. They have also sparked countless new private businesses and industries leading to economic growth and opportunity for innovators and entrepreneurs in every region of the country.

Recognizing the power and potential of such Open Science, on June 20, 2013 the White House invited four EPA scientists—Drs. Richard Judson, Keith Houck, Matt Martin, and Ann Richard—to present research posters describing their efforts to provide public access to massive amounts of data from chemical safety studies. The scientists presented their posters after the White House’s “Champions of Change” award ceremony. The award ceremony recognized 13 Champions of Change for their efforts to provide the public access to innovative science.

In addition to the 13 Champions of Change, the White House selected 12 scientists (including the EPA researchers) to present posters describing their vision and commitment to Open Science.

EPA scientists at the White House poster session.

EPA scientists Ann Richard and Matt Martin at the White House poster session.

The select group of 25 was chosen from hundreds of nominations submitted to the White House’s request for innovative Open Science leaders. The White House event highlighted outstanding individuals, organizations, and research projects promoting and using open scientific data and publications to accelerate progress.

To exemplify Open Science work, the four EPA scientists presented how they are using advances in computational toxicology to provide open and accessible chemical safety data to help better protect human health and the environment. Each of the EPA scientists are working to harness the power of computer science and innovative new chemical safety assessment methods and tools to provide open, transparent public access to chemical information. For example:

Dr. Matt Martin leads a team of Agency scientists and partners who developed the Toxicity Reference database (ToxRefDB). ToxRefDB contains 30 years and $2 billion worth of pesticide registration studies. The database allows scientists and others to search and download thousands of toxicity testing results on hundreds of chemicals that were previously only available on paper or microfiche.
Dr. Ann Richard is the leader behind another open, accessible database, the Distributed Structure-Searchable Toxicity Database (DSSTox). DSSTox provides open-access to information on the physical and structural properties of chemicals and links this information to toxicity potential. This is key information for assessing the potential risk of chemicals to human health and the environment.
Dr. Richard Judson leads a team of scientists who developed the Aggregated Computational Toxicology online Resource (ACToR). ACToR is EPA’s online warehouse of all publicly available chemical data aggregated from more than 1,000 public sources on more than half a million chemicals. ACToR can be used to query a specific chemical and find available public hazard, exposure, and risk assessment data as well as previously unpublished studies related to cancer, reproductive, and developmental toxicity.
Dr. Keith Houck is the driving force behind EPA’s Toxicity Forecaster (ToxCast), a research program advancing the use of automated, rapid chemical tests (called “high-throughput screening assays”) to screen thousands of chemicals in more than 650 assays for toxicity potential. This includes the development of the ToxCast Database (ToxCastDB) which provides publicly accessible, searchable, and downloadable access to all the screening data generated by ToxCast.

These four scientists have led the effort to democratize access to knowledge and information and level the playing field for all those involved and interested in protecting public health and the environment. By doing so, they exemplify the spirit of Open Science celebrated by President Obama’s Champions of Change program.

About the Author: Tina Bahadori, Sc.D. is the National Program Director for EPA’s Chemical Safety for Sustainability research program. Learn more about her on EPA’s Science Matters: Meet our Scientists web page.