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Tracking frog calls in the Jetstream

IU undergraduate Eliza Foran gains hands-on data science skills helping biologists process bioacoustic data

How can technology help solve an amphibian crisis? IU sophomore Eliza Foran was determined to find out during her Research Experience for Undergraduates (REU) with IU’s Center of Excellence for Women & Technology. 

Foran is double majoring in biotechnology and environmental studies. Her interest in programming got her on IU’s Center of Excellence for Women & Technology’s email list, where she landed a spot with their REU program for UITS Research Technologies.

During the 2018-2019 school year, as a part of her REU, Foran was recruited by the IU-led National Center for Genome Analysis Support(NCGAS) to help field biologists obtain bioacoustics data through cost-effective workflows. 

Data scientist in the making
Data scientist in the making

Foran's experience has piqued her interest in data science—and now her career plans include studying data science to stabilize agriculture through urban farming.

In response to an amphibian crisis—some species of frog are dying out from the infectious disease chytridiomycosis—Foran and NCGAS bioinformatician and biologist Sheri Sanders participated in a national frog survey. Their goal was to identify which species of frog are in the Bloomington ecosystem, and how atmospheric differences affect their call.

To capture the frogs’ calls, they built recording devices from a Raspberry Pi microcomputer, a USB microphone, an atmospheric sensor, a USB thumb drive, and a battery/solar panel. The units are placed in a waterproof electrical box with waterproof "sound" cones for the microphone. The entire workflow cost about $100, while some bioacoustics software alone can cost upwards of $500 per year.

The recording devices listened for nighttime frog calls and transferred them to the Jetstream cloud system, which outputted multiple bioacoustics analyses. Led by IU, Jetstream is the first production cloud system funded by the National Science Foundation for the national science and engineering research communities.

Everyone in UITS Research Technologies has been incredibly helpful in providing access and resources to help me learn about data science.

Eliza Foran, IU undergraduate

For her part, Foran focused on making sure the Raspberry Pis were working and that the whole operation was running according to plan. This work resulted in a poster, “Developing a workflow for bioacoustic recording devices and frog call analysis within Jetstream.” Foran submitted it to the Research Services Expo’s Inaugural Student Poster Expo, where she tied for Best Visualization. Additionally, she submitted that same poster in the Center of Excellence for Women & Technology Women’s Research Poster Competition back in April. And that’s just the beginning.

“We are currently making a machine learning application so frog calls can be identified automatically,” said Foran. “This helps not only field researchers, but people who have big databases of unidentified frog calls. We will be presenting a poster about the app at the Practice and Experience in Advanced Research Computing conference later this month in Chicago.”

Frog calls for the win
Frog calls for the win

Foran discusses her award-winning work at the Research Services Expo’s Inaugural Student Poster Expo.

This summer, Foran continues to hone her data science skills as a participant in the Pervasive Technology Institute at Indiana University REU, where she again will have the chance to work with Jetstream.

Her NCGAS experience has piqued her interest in data science—and now her career plans include studying data science to stabilize agriculture through urban farming.

"Everyone in UITS Research Technologies has been incredibly helpful in providing access and resources to help me learn about data science,” Foran said.