computational toxicology

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

By Antony Williams

photo of 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 1st, 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 21st 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.

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

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When Robots and Metabolism Collide: EPA and Partners Announce Transform Tox Testing Challenge Semi-Finalists

By Kevin Kuhn

When I tell my friends about chemical high-throughput screening and the Transform Tox Testing Challenge, I always start with the robot. Why? Because people love robots.

Tox 21 robot at work

Robot in action at the National Center for Advancing Translational Sciences (NCATS) where it is housed.

The Robot, i.e. the ultra-high-throughput robotic screening system (pictured) is just one example of a suite of automated systems designed to test and screen chemicals. The system identifies chemicals’ potential for trouble faster and cheaper than ever before, and without the need to test on animals.

Thanks to these automated systems and Tox21 (a cooperative effort uniting EPA, the National Institutes of Health (NIH), and the Food and Drug Administration), we have run thousands and thousands of experiments to see how chemicals affect cells, their processes, and the proteins that do the work. It truly is some amazing research.

Of course, it wouldn’t be research if the system was perfect. Here’s the rub: cells used in EPA’s current lab tests do not typically break down or metabolize chemicals like they would in the body. This means that these tests may overlook chemicals that could be metabolized into a more toxic form. We need a robot-friendly way of making our lab tests act more like the human body when evaluating chemicals’ toxicity.

To find a solution, EPA, NIH’s National Center for Advancing Translational Sciences (NCATS), and the National Toxicology Program, headquartered at the National Institute of Environmental Health Sciences, launched the Transform Tox Testing Challenge in January.

Now we are thrilled to announce that we are awarding a total of $100,000 to ten semi-finalists for their amazing ideas. Descriptions of these promising proposals are available here. The semi-finalists have brought the best of modern technological approaches to bear on the problem, and we couldn’t be more excited about the ideas.

Right now these proposals are simply ideas on paper, but thanks to the challenge prize money, these solvers will have the opportunity to develop their plans into working prototypes and enter Stage 2 of the competition. EPA will host a workshop for the semi-finalists in July so that they can meet one another, learn more about our great set of screening systems, and potentially combine their talents to strengthen their Stage 2 entries.

With the possibility of solving this problem on the horizon, we’re one step closer to improving toxicity testing and protecting human health better than ever before. And, to be honest, that is even cooler than the robot.
For more information:


About the Author: Kevin Kuhn, Ph.D. is an advisor to the Chief Innovation Officer in the U.S. Environmental Protection Agency’s Office of Research and Development and  manages the Pathfinder Innovation Projects – a competition that provides seed funding for EPA research scientists to pursue high-risk, high-reward research. Learn more about EPA Innovation at:

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

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This Week in EPA Science

By Kacey FitzpatrickBike with Recap wheels

It’s Bike to Work Day! Did you ride your bike to work? Way to go! Now you can sit back, relax, and catch up on the latest in EPA science.

And if you didn’t bike to work—that’s okay, I didn’t either. But you can still enjoy the Recap.

Supporting Undergraduate Research
For more than 30 years, EPA has been supporting and encouraging undergraduates in environmental-related fields through the Greater Research Opportunities (GRO) Fellowship program. EPA just announced that GRO fellowships were awarded to 34 students who are majoring in environmental science, engineering, mathematics, and technology all across the nation. Read more about the fellowships in the blog GROing Above and Beyond.

Chemical Safety Research
EPA researchers are using new technology to improve computational exposure science, which helps create a more complete picture of how and in what amounts chemicals enter our bodies. Learn more about this research in the Science Matters article Improved Methods for Estimating Chemical Exposure.

Science to Achieve Results
Do you want to study how air pollution contributes to the development of cardiovascular disease? Then check out our latest Science to Achieve Results funding opportunity. You can learn more by looking at the Long-term Exposure to Air Pollution and Development of Cardiovascular Disease research grants page.

National Wetland Condition Assessment
This month EPA released the National Wetland Condition Assessment, a collaborative survey of our Nation’s wetlands. The survey examined the chemical, physical, and biological integrity of wetlands through a set of commonly used and widely accepted indicators. Learn more about the assessment here.

Stormwater Management in Response to Climate Change Impact
EPA and NOAA have led workshops and other community efforts across the Chesapeake Bay and Great Lakes regions to discuss how projected land use and climate change could impact local water conditions. This week EPA released a final report containing findings from these workshops. Read more in the report Stormwater Management in Response to Climate Change Impacts: Lessons from the Chesapeake Bay and Great Lakes Regions.

About the Author: Kacey Fitzpatrick is a student contractor and writer working with the science communication team in EPA’s Office of Research and Development. She is a regular contributor to It All Starts with Science and the founding writer of “The Research Recap.”

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

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Events to Watch for in May

By Michaela Burns

May is the best month—yes I said it. It’s the month before summer vacation, it’s the month where the weather gets warmer, and it’s the month of my birthday. Here are some public meetings and webinars EPA is hosting this month.

Look out for these events!

Children’s Center Monthly Webinar
Wednesday, May 11th 1:00 p.m. ET

paper cutouts of kids and a houseUp first is the EPA and National Institute of Environmental Health Sciences (NIEHS) Children’s Center Webinar series. This month’s topic is on the exposome, the measure of exposures in an individual lifetime and how those exposures affect their health. This webinar is bringing together leading experts in this field—Dr. Elaine Faustman from University of Washington, Dr. Roy Gerona from University of California, San Francisco, and Dr. Stephen Rappaport from University of California, Berkeley. After the presentations, Dr. Yuxia Cui of NIEHS will moderate a discussion.
Register now to be a part of the conversation.

Harmful Algal Blooms
Wednesday, May 18th 3:00 p.m. ET

harmful algal bloomsMost algae species are not harmful, but sometimes certain types can bloom in excessive amounts and cause severe damage to human health, aquatic ecosystems, and local economies. Harmful algal blooms (HABs), algae that produce unhealthy toxins, cause problems across the nation. EPA researchers are looking for ways to eliminate or reduce the negative effects of HABs.
Register to get up to speed.

iCSS Chemistry Dashboard
Thursday, May 26th 11:00 a.m. ET

screen shot of chemistry dashboardCurious about chemistry data for over 700,000 chemicals? Then you can’t miss this month’s Computational Toxicology Communities of Practice webinar. Tune in to learn more about our Interactive Chemical Safety for Sustainability Chemistry Dashboard. This online tool provides access to chemical structures, experimental and predicted data, and additional links to relevant websites and applications. Chemistry information on thousands of chemicals will now be more publicly accessible!
Contact Monica Linnenbrink ( to register.

Responding to Harmful Algal Blooms
Tuesday, May 31st, 2:00 p.m. ET

Lake ErieHarmful algal blooms pose particular challenges for small drinking water systems. In this month’s small systems webinar, EPA Environmental Engineer Nicholas Dugan will review the removal capacities of common processes used in drinking water treatment, present a strategy for evaluating an existing treatment facility, and discuss how to use this information to improve a facility’s performance. Heather Raymond of Ohio EPA’s Division of Drinking and Ground Waters will cover source and finished water monitoring options and their limitations and benefits. Bonus—Attendees have the option of receiving a certificate for one continuing education contact hour for each webinar. Register now!

For more events check out the EPA Research Events page.

About the Author: Michaela Burns is an Oak Ridge Associated Universities contractor and writer for the science communication team in EPA’s Office of Research and Development.

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

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Upcoming Events at EPA

By Michaela Burns

Interested in attending some of EPA’s public meetings or webinars? Here are a few that we are hosting at the end of April.

C-FERST bannerCommunity-Focused Exposure and Risk Screening Tool
Wednesday, April 20, 3:00 p.m. ET
Tune in for a webinar spotlighting the Community-Focused Exposure and Risk Tool (C-FERST), an online tool that when completed will help inform communities about their environmental and public health issues. C-FERST will include maps and tables with data on sources of pollution, environmental concentrations, estimated exposures and potential risks, demographics, and community characteristics. Register to attend the webinar and learn more.

Disinfection Byproduct Regulatory Issues and Solutions Webinar
Tuesday, April 26th at 2:00 p.m. ET
water coming out of faucetMark your calendar for this month’s small systems webinar—the topic is Disinfection Byproduct Regulatory Issues and Solutions. Gastrointestinal illnesses with symptoms like diarrhea, vomiting, cramps can be caused by pathogens and viruses that are often found in lakes, rivers, and reservoirs. This water must therefore be treated with disinfectant in order to be safe to drink. However some disinfectants react with naturally-occurring materials in the water to form byproducts that are associated with health risks.

EPA environmental engineer Michael Finn will review the Disinfectants and Disinfection Byproducts Rule, a series of regulations aimed at limiting public exposure to these disinfectant byproducts. Jolyn Leslie, a regional engineer for the Washington State Department of Health Office of Drinking Water, will discuss the challenges for small systems dealing with disinfectant byproducts in Washington State and the possible solutions.

Bonus—attendees may have the option of receiving a certificate for participating in this webinar. Register now!

EPA Research Tribal bannerTribal Science Webinar Series
Tuesday, April 26th at 3:00 p.m. ET
Checkout this month’s Tribal Science Webinar. Speakers will discuss the environmental work in the Strong Heart Study, the largest and longest study of cardiovascular disease and its risk factors in American Indian communities. Cynthia McOliver, an EPA environmental health scientist, will be joined by Ana Navas-Acien, a physician-epidemiologist with a specialty in preventive medicine and public health, and Joseph Yracheta of Missouri Breaks Industries Research, Inc. Register soon!.

Water Research Webinar
Wednesday, April 27th at 2:00 p.m. ET
Scientists doing water researchJoin EPA’s Dr. David Mount for this month’s Water Research Webinar. Dr. Mount will give a presentation on the effects of inorganic ions on aquatic organisms. Natural geochemical weathering introduces several inorganic ions to natural waters. These ions become part of the basic chemistry of surface waters. The problem begins when land uses, such as energy and mineral extraction, increase concentrations of these geochemical ions. The ecological effects of increased ion concentrations are being explored through several inter-related research efforts. This webinar provides an overview of EPA’s research in this area, and some of the implications for predicting ecological risks and informing management decisions. Register to learn more.

Computational Toxicology Communities of Practice Meeting
Thursday, April 28th at 11:00 a.m. ET
Shafer_Lab_02Interested in the latest research on neurotoxicity? Then you don’t want to miss this month’s Computational Toxicology Communities of Practice Meeting. Drs. William Mundy and Timothy Shafer will present EPA research focusing on new approaches to characterize neurotoxicity from exposure to chemicals. Contact Monica Linnenbrink ( to register.


About the Author: Michaela Burns is an Oak Ridge Associated Universities contractor and writer for the science communication team in EPA’s Office of Research and Development.

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

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Advancing Chemical Testing by the Thousands

Reposted from EPA Connect, the official blog of EPA leadership.

By Bob Kavlock

Bob Kavlock PortraitStudying thousands of chemicals at a time with the use of high-tech computer screening models and automated, often robot-assisted processes sounds like science fiction. But it’s not. EPA scientists are doing just that, leading the advancement of “high-throughput screening,” fast, efficient processes used to expose hundreds of living cells or isolated proteins to chemicals and then screen them for changes in biological activity—clues to potential adverse health effects related to chemical exposure.

This scientific advance is positioned to transform how we understand the safety of chemicals going forward. Twenty years ago, using high-throughput screening to test chemicals for potential human health risks seemed like technology that belonged in a science fiction television series rather than in real life.

Back then there were several large data gaps that would not allow us to extrapolate from the isolated biological changes we observe on a cellular level to adverse human health effects. However, through our computational toxicology (CompTox) research, which integrates, biology,

Robotic arm moving samples for screening

Robotic arm moves samples for automated chemical screening.

biotechnology, chemistry, and computer science, that is changing. We are helping to transform the paradigm of chemical testing from one that relies almost solely on expensive and time-consuming animal testing methods to one that uses the full power of modern molecular biology and robotics.

A significant part of this effort is the Toxicity Forecaster (ToxCast), launched in 2007. ToxCast allows us to prioritize potentially toxic chemicals for more extensive testing as well as giving us the opportunity to test newer, possibly safer alternatives to existing chemicals. By 2013, we evaluated more than 2,000 chemicals from industrial and consumer products to food additives using more than 500 high-throughput screening assays.

Read the rest of the post. 

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

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EPA Scientists Presented Open Science at White House

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.

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

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Science Matters: Predicting the Future of Children’s Health

Children's Health MonthTo observe October as Children’s Health Month, we will periodically post Science Matters feature articles about EPA’s children’s health research here on the blog.  Learn more about EPA’s efforts to protect children’s health by going to

According to the Centers for Disease Control and Prevention, approximately one in every 33 babies born in the United States is born with a birth defect. Birth defects can heighten the risk of long-term disability as well as increase the risk of illness, potentially impacting a child for the rest of his or her life. Unfortunately, the causes of most birth defects are unknown.

EPA researchers are tapping powerful, high-tech computer systems and models to better determine how prenatal exposure to environmental factors might impact embryo and fetal development. Working on EPA’s Virtual Embryo (v-Embryo™) project, they create computer models of developing body systems and combine them with data from a number of EPA studies and toxicity databases to “virtually” examine the effects of a variety of prenatal exposures.

Virtual Embryo simulates how chemicals and pesticides, including those that disrupt the endocrine system, interact with important biological processes that could disrupt fetal development.  The chemicals used in simulations are identified by EPA’s Toxicity Forecaster as having the potential to affect development.

The predictions from the computer simulations need to be further tested against non-virtual observations. However, the models provide scientists with a powerful tool for screening and prioritizing the chemicals that need to be more closely examined, greatly reducing the cost and number of targeted studies needed.

“We’ve built small prototype systems, now what we want to do is move into complex systems models that will be more relevant to environmental predictions,” said Thomas B. Knudsen, Ph.D., an EPA systems biologist who is leading the project.

Virtual Embryo models have focused on blood vessel development and limb development, but are being expanded to include early development of the male reproductive system, which is known to be particularly sensitive to endocrine disrupting chemicals.

Knudsen says that having more models is important because different chemicals can affect biological systems in various ways. Luckily, the time it takes to develop new models decreases as researchers’ model-developing knowledge grows.

“The important challenge for us is to try to integrate some of this work with other issues of broad importance to children’s health,” said Knudsen. “We’re focused primarily on embryonic development, but a person doesn’t stop developing at birth. We have to take what we are learning from the embryo and extend that information into life stages beyond birth.”

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

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Scientist at Work: Interview with Thomas Knudsen

Dr. Tom Knudsen is a developmental systems biologist at EPA’s Center for Computational Toxicology. His research focuses on developing predictive models of developmental toxicity, building and testing sophisticated computer models such as the Virtual Embryo Project. This effort explores the potential for chemicals to disrupt prenatal development—one of the most important lifestages.

In addition to his research at EPA, Dr. Knudsen is an Adjunct Professor at the University of Louisville, Editor-in-Chief of the scientific journal Reproductive Toxicology, and Past-President of the Teratology Society.

Before joining EPA, he was Professor at the University of Louisville.

How does your science matter?

I am part of an exciting effort to develop new ways to explore development toxicology and prioritize the testing of chemicals using vast amounts of data and biological knowledge, powerful computers, sophisticated computer models and very large databases. Instead of the conventional approach to developmental toxicology, which over the past 50 years or so has relied on tests conducted on pregnant lab animals, we are developing virtual models that are both faster and less expensive.

For example, in the Virtual Embryo project we are using a suite of screening models that look at the interactions of various chemicals with the complex biology of a developing embryo. We think that these models and tools will be a new way of asking questions about how a pregnant woman’s exposure to chemicals in the environment might result in a risk to development.

Our work will help protect human health, greatly increase the number of chemicals we can screen quickly, and reduce costs all at the same time. So I guess it really does matter.

What do you like most about your research?

Most days I feel like I have the best job in the country!

The team that I work with consists of bright and exceptionally talented scientists, among them more than a half dozen outstanding young scientists and post-doctoral fellows. As a like-minded team, we strive to unravel complexity in a biological system such as the embryo.

I really enjoy the many opportunities for productive collaboration here at EPA. The opportunity to conceptualize the Virtual Embryo Project and see it grow and evolve has been most gratifying, not only because of the innovative science that it allows, but also because of the opportunities that it presents for professional development of young scientists.

Click here to keep reading Thomas’s interview.

To read more Scientists at Work interviews, click here.

Editor's Note: The opinions expressed here are those of the author. They do not reflect EPA policy, endorsement, or action.

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