Open Science

Jun 23, 2014

Open Science and Cyanobacterial Research at EPA

Application Programming Interfaces, Around the Water Cooler, cyanobacteria, EPA National Lakes Assessment, EPA Water Research, EPA's Environmental Dataset Gateway, harmful algal blooms, microcystin, Open Science, PLOS One, SPARROW model 0 Comments

By: Jeff Hollister, Betty Kreakie, and Bryan Milstead

Algal bloom containing cyanobacteria.

It wasn’t long ago that science always occurred along a well-worn path. Observations led to hypotheses; hypotheses led to data collection; data led to analyses; and analyses led to publications. And along this path, data, hypotheses, and analyses were held close and, more often than not, the only public-facing view of the research was the final publication.

Science has come a long way with this model. However, it was conceived when print was the main media and most scientific questions could be investigated by few scientists over a short period of time.

Then came computers. Then came the internet.

Just like in every other aspect of modern life, these advances are greatly impacting science. It has changed who conducts our science, how we share it, and how others interact with scientific information. All of these changes are playing out through the increasing openness of all parts of the scientific process.

This broad area has been defined as having several components. These components suggest that “open science”:

is transparent (and, of course, open)
includes all parts of research (data, code, etc.)
allows others to repeat the work
should be posted on an open and accessible website (while protecting Personally Identifiable Information, etc.)
occurs along a gradient (i.e. not just a binary open vs. not open)

At EPA, we are learning how to make our research on cyanobacteria and human health (for more info join our webinar) meet those criteria. We are implementing open science in three ways: (1) making our work available via open access publishing; (2) providing access to the code used in our analysis; and (3) making our data openly available.

Several members of our research group have embraced open access options for publishing their research. For instance, our colleague Elizabeth Hilborn and her co-authors published results of their study—examining a group of dialysis patients following exposure to the cyanobacteria toxin microcystin—in one of the pioneering open access journals, PLoS ONE. Also in PLoS ONE, EPA scientist Bryan Milstead and his collaborators published a modeling method to combine the U.S. Geological Survey’s SPARROW model (a modeling tool for interpreting regional water-quality monitoring data), lake depth, lake volume, and EPA National Lakes Assessment data to estimate nutrient concentrations.

As our work progresses, we will continue to choose open access journals. In our experience, this has allowed our research to reach a larger audience and we can more easily track the impact through readership levels using available tools such as PLoS Article Level Metrics.

We are also sharing our data. Currently, this is accomplished through supplements added to publications and through sites such as the EPA’s Environmental Dataset Gateway. We plan to expand these efforts via data publications, version-controlled repositories, and through the development of Application Programming Interfaces (APIs) that provide access to data for developers and other scientists.

The goal of these efforts, and more (stay tuned for a future post on how coding fits in to open science), is to increase the reproducibility of our work (but challenges remain), reach broader audiences, and eventually have a greater impact on our understanding and management of harmful algal blooms.

About the Authors: EPA ecologists Jeff Hollister, Betty Kreakie and Bryan Milstead study greenwater for a living. If you have questions for them, join the webinar on June 25^th or follow the twitter chat on June 26^th using #greenwater.

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Jun 9, 2014

When Green Goes Bad

Around the Water Cooler, cyanobacteria, green water, harmful algal bloom, Nutrient pollution, Open Science, Safe and Sustainable Water Research 2 Comments

By Lahne Mattas-Curry

When you think about the environment, what color comes to mind? Green, right? Because in everything we know in the environment “Green is Good.”

And while that is very often true, in the case of lakes and ponds that suddenly go green, it is most likely the result of an algae bloom, which, increasingly, contain many harmful cyanobacteria. Also known as “blue-green algae,” some species of these tiny, photosynthetic aquatic organisms produce toxins. The impacts of these harmful algal blooms are widespread and often not good. Not good at all.

From acute adverse human health impacts such as respiratory and gastrointestinal problems (yuck) to known deaths of animals (keep the family dog out of green water, please!!), blooms like these are becoming a more frequent occurrence and are having greater impacts.

To better understand how algal blooms impact human health, identify the toxicity of cyanobacteria, predict the probability of bloom occurrences, and share this information broadly, our researchers have been working on a research project focused this topic since 2012.

The researchers involved in the project will be sharing what they have learned during a webinar on Wednesday, June 25 from 12:00 to 1:00pm as part of EPA’s Water Research Webinar Series.

We hope you will join them to hear an overview of the breadth of their algae bloom research, and learn details about ecological modeling they conducted on cyanobacterial blooms in U.S. lakes. They will explain how they embraced the concept of “Open Science”—the movement to make scientific research and data accessible to the public.

And if that’s not enough, they will also be available for a twitter chat on June 26 from 2:00pm to 3:00pm. You can submit questions now by using #greenwater or you can wait until the day of the chat. Please follow us @EPAresearch.

To register for the webinar, please send an email to sswr@epa.org with your name, title, organization and contact information.

Meet our Scientists

Jeff Hollister, Ph.D.
EPA research ecologist Jeff Hollister received his Ph.D. in Environmental Science from the University of Rhode Island. His past experience is in applications of geospatial technologies to environmental research and broad-scale environmental monitoring, modeling, and assessment. His current research focuses on how nutrients drive the risk of cyanobacterial blooms in lakes and ponds.

Betty Kreakie, Ph.D.
EPA research ecologist Betty Kreakie earned her Ph.D. in integrative biology from the University of Texas. Her work focuses on the development of spatially-explicit landscape level models that predict how biological populations and communities will respond to human-caused influences, such as nutrient and contaminant pollution, climate change, and habitat conversion.

Bryan Milstead, Ph.D.
EPA post-doctoral research ecologist Bryan Milstead received his Ph.D. from Northern Illinois University for work on small mammal population dynamics in Chile. Before coming to EPA, he worked for the U.S. National Park Service and for the Charles Darwin Foundation for the Galapagos Islands. His current work focuses on understanding how nutrient over-enrichment affects the aesthetic quality and risk of cyanobacteria blooms in lakes.

About the Author: Lahne Mattas-Curry communicates the many cool things happening in water science for EPA and hates #greenwater. She urges everyone to think twice about what fertilizers they use on their lawn and encourages pet owners to “pick up the poop” to reduce nutrient pollution.

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.