To say Northwestern Engineering’s Luís Amaral has diverse research interests is an understatement. He’s investigated how the so-called Golden Age of Hollywood was not so great for women when female representation in films plummeted, explored the potential impacts of climate change on Great Lakes travel, and discovered a previously unknown mechanism that drives aging.
Amaral values information and – just as importantly – making it widely accessible.
The Erastus Otis Haven Professor and a professor of engineering sciences and applied mathematics at the McCormick School of Engineering, Amaral and his lab and collaborators have developed a series of apps and software programs to assist in scientific research. Examples include Earthtunes, which allows users to listen to the motions of the Earth’s crust; Silhouette, which helps analyze images of gene expression in fruit fly eyes; and Find My Understudied Genes, which make it easier to study genes that have largely been avoided in science.
“When you think about doing research, you develop software that is only used in your lab or for the paper, and it never gets used again,” Amaral said. “But if you can actually make it a nice piece of professional software, then others will want to use it.”
The key member of Amaral’s team was Helio Tejedor, who brought his development expertise to the lab, joining in 2016. Tejedor was key in translating Amaral’s scientific knowledge into robust and user-friendly applications. Tejedor led the apps’s technical development from concept to completion until his departure in August.
“Helio is really an amazing developer. He was able to take these ideas that we have for research projects and transform them into applications that anyone can download, use, and interact with,” Amaral said. “Is there a research problem that you are trying to solve? Is there a computational approach that you are going to use? Can you benefit a lot of other people and make the world aware of Northwestern by creating an app? Those are the challenges we have tackled.”
When Amaral was co-directing the Northwestern Institute on Complex Systems (NICO), he brought Tejedor in as a developer to help other groups take advantage of his skills in app development. Their first project, Silhouette, was released in 2019 and is available on the macOS operating system. Downloaded more than 15,000 times, Silhouette turns raw microscopy data into cell-specific measurements that are suitable for quantitative analysis. To generate each measurement, Silhouette automatically identifies all cells within an image then quantifies the properties of each identified cell. In addition to morphological properties such as cell size and position, the intensities of fluorescent reporters are quantified by averaging all the pixels within each identified cell.
“Nicolás Peláez, a graduate student in Amaral and Richard Carthew’s lab was the real champion of this project. Close partnerships were really critical to our success,” Tejedor said.
Amaral has also enlisted the help of students to build other apps. Reese Richardson, a PhD student in interdisciplinary biological sciences, championed Find My Understudied Genes.
That app, available on macOS, iOS and Windows, is a data-driven tool to help biomedical researchers identify understudied genes and characterize their tractability for future research. Users submit a list of human genes and can filter these genes down based on a large list of factors, including the number of articles about a gene, the probability of differential expression, the homology in model organisms, the availability of reagents, and the number of articles about relationship between gene and disease, among others. Find My Understudied Genes was recently profiled in a Nature feature.
Richardson oversaw the development of the app’s database. To do this, he corralled data from more than three dozen different sources and matched it all to one another. From there, the team tested various features to determine what would be most useful to biologists.
“I learned how difficult it is to develop and maintain high-quality applications,” Richardson said. “We strive for high standards of usability and data quality, so I definitely picked up a few lessons along the way about rigor in data analysis and preparation of tools for other scientists.”
The apps also allow scientists to upload and store their data, inviting fellow researchers to check their methods and verify findings.
“That makes all the work across labs around the world more reproducible. We should be getting the same results and understand when we don't,” Amaral said. “It's also very important in enabling better science to be done across the world.”
Amaral used artificial intelligence to analyze data from a wide variety of tissues, collected from humans, mice, rats, and killifish, and discovered that the length of genes can explain most molecular-level changes that occur during aging.
Using machine learning technology, a research team in Amaral’s lab simulated the impact of losing 67 percent of direct air routes and found insufficient rail connections could lead to more driving and more pollution.
Research by a Northwestern-led team with Amaral said barriers to accessing US court documents prevent transparency needed to establish a fair and equal justice system.
A comprehensive data analysis from Amaral showed women's participation dropped across job roles in film from 1920 to 1950.
A common thread through Amaral’s work is a willingness and eagerness to collaborate with researchers in other disciplines. That carries through to the apps. Besides working with developers, Amaral has teamed with scientists from a wide spectrum.
Silhouette was developed in cooperation with Carthew, Owen L. Coon Professor of molecular biosciences in Northwestern’s Weinberg College of Arts and Sciences and director of the National Institute for Theory and Mathematics in Biology. Carthew studies the unique and complex biology of cells in the context of tissues and organs. He has done extensive research on organisms such as the fruit fly that provide an unprecedented opportunity to understand the cell biology of multicellularity.
Another collaboration led to RainFlow. Developed by Amaral, Tejedor, and Northwestern IT data scientist Ritika Giri, the macOS application is designed to help researchers with Reproducible Analysis and Integration of their Flow Cytometry data.
Then there’s Earthtunes. First released in 2020 and downloaded more than 2,500 times, Earthtunes helps the user listen to normally inaudible sounds within the solid Earth beneath us. These sounds are caused by seismic waves and are so low in frequency that our ears cannot hear them. Most of these seismic waves are weak and continuously generated by a range of environmental sources. Some of these seismic waves are strong and caused by earthquakes.
To create this app, Amaral helped assemble a 10-person team, led by Suzan van der Lee, Sarah Rebecca Roland Professor and director of computing in Weinberg’s Department of Earth and Planetary Sciences. Van der Lee uses seismograms, records of seismic waves, to generate understanding of the dynamics of Earth's interior and plate tectonics.
Van der Lee had been searching for a way to share content on seismic waves passing through the Midwest and other parts of the Earth, outside of the West Coast and New Madrid Zone in Missouri. A Northwestern colleague suggested she should sonify the data and received a grant for the work, eventually connecting with Amaral and Tejedor. Van der Lee provided the content and the science, and Amaral’s group provided the app-building knowhow, eventually assisted by research specialist Omkar Ranadive, who built a version of the App for Android phones.
Now, van der Lee uses the app for demonstrations with younger students and relishes how available the information is for anybody to explore. Instead of having to figure out how to read seismogram graphs, users can simply use the app and listen to what’s happening below the Earth’s surface.
“It helps enormously in trying to understand your environment in the moment,” Van der Lee said. “I don't think our students think much of having this data at their fingertips and ears, because that's what life is like for them. That's how things just are. But for me, who’s a little older, this is really changing the game of how you can engage scientifically with your environment.”
That’s Amaral’s goal.
“It's really, really an amazing feeling to know people are using these apps,” Amaral said.
