Project on Color Vision of Shrimp Helps Biology Students See Data Science in New Light

Patrick Green and Eleanor Caves

We are all data scientists these days, to one degree or another. The ability to explore and analyze data helps us make sense of our world.

Duke’s Data Expeditions program aims to introduce more undergraduates to data science early in their college education. The Information Initiative at Duke (iiD), in partnership with the Social Science Research Institute (SSRI), supports pairs of graduate students to prepare a dataset for use in an existing undergraduate course.

Patrick Green teaching Data ExpeditionsIn one Data Expedition project, Exploring Cleaner Shrimp Color Vision Capabilities Using R, Biology doctoral students Eleanor Caves and Patrick Green teamed up with Professor Sönke Johnsen to pilot their approach in an introductory summer course called Sensory Systems. Green and his advisor Sheila Patek then adapted it for use in an upper-level lab course, Principles of Animal Physiology.

“Especially if classes have a lab component, getting students some experience with importing, analyzing, and plotting data can be invaluable,” said Caves. “I remember struggling with Excel to write my own lab reports in college, and if someone had just given me the tools to code, and then inspired me to use those tools for a couple of reports, I would have been so much more comfortable with different aspects of data analysis.”

“This is a critical tool for students to learn,” Green added, “whether they use data in their future careers or whether they’re just trying to understand the world around them as they, for example, vote and raise families.”

Cleaner shrimp working on a fishCleaner shrimp are crustaceans that provide handy cleaning services to reef fish by removing ectoparasites. The project’s aim was to investigate how cleaner shrimp perceive the color patterns of other cleaner shrimp and fish. Caves collected the data as part of her doctoral dissertation.

In the class, she and Green introduced the ecology of cleaner shrimp, asked the students to make predictions about color vision capability and taught coding sessions in R.

Along the way, both the undergraduates and the instructors faced challenges.

“What makes coding frustrating on an individual level translates into the classroom,” said Caves. “Typos and minor errors that can send coding errors back at you occur on the students’ computers too, and you have to be ready to troubleshoot on your feet.”

Patrick Green working with Data Expeditions students

“Similar to Eleanor, I learned that these activities move more slowly than we might expect,” noted Green. “It was incredibly useful to have ‘teachable moments’ when students hit error messages. Even if these errors were caused by simple misspellings, it allowed us to show students that this is normal and fixable – not an impassible roadblock. Because we coded in real-time along with the students, we were also able to showcase our own mistakes and humanize the process, something I think is useful for students to see.”

The students soon learned how to subset, index, plot, change the color and shape of data points, add best fit lines, change line width and type, and create smooth spectral sensitivity curves (which show how sensitive photoreceptors are across the visible spectrum of light).

Figure from Data ExpeditionsAt the end, they created a figure of spectral sensitivity for several individuals of the same species. They compared their results to their predictions and discussed how they might use their new skills to analyze data they’ll collect in future lab-based courses.

And they seemed to enjoy the process. Caves noted, “I’ve been pleasantly surprised at how attentive the students remain and how engaged they seem the whole time.”

“It never occurred to me that I would need to learn how to code,” wrote one student in an end-of-class reflection, “but I am glad that I get to learn this.” Another student wrote, “It was actually easier than I expected, since coding seems so out of reach when you don’t know what is happening or what the terms mean. I could definitely use R in the future for projects where I am required to use data.”

At the end of the day, coding gives students a deeper understanding of data to solve real-world problems. “It gives students, even those who won’t go on to do research of their own, a respect for the scientific process, how we analyze our data, and where results come from, so that hopefully they can be more informed citizens and interpreters of the overwhelming number of facts they’re exposed to every day,” said Caves.

Eleanor Caves and Patrick Green with their advisors

Both Caves and Green received the Dean’s Award for Excellence in Mentoring from The Graduate School. They graduated this spring and are now postdoctoral researchers in Duke’s Biology Department with the Nowicki Lab.

“I have been surprised to learn during my Ph.D. that I can code, and that I am somewhat good at it,” Green reflected. “This has taken lots of trial and error, but I am motivated to continue learning and developing these skills in my research. Being able to use the same skills in my teaching is something that expands my teaching abilities and, I hope, will improve my ability to reach new generations of students.”

See other Data Expeditions projects and learn about a new program at Duke called Archival Expeditions. Photos at top and bottom courtesy of The Graduate School; other photos courtesy of Eleanor Caves and Patrick Green.

Biologist Builds Skills in Coding to Study Deep-sea Marine Animals

Kate Thomas

Kate Thomas, a Ph.D. student in Biology, was among 18 Duke University students who received Graduate Student Training Enhancement Grants (GSTEG) in 2017-18 from the Office of the Vice Provost for Interdisciplinary Studies for training beyond their core disciplines. Her faculty mentor is Sönke Johnsen. She shared an update:

GSTEG funding allowed me to spend two months working on an interdisciplinary project that was outside the scope of my dissertation research. I wanted to improve my skills in coding and computational modeling, so I proposed to undertake a coding-intensive research project to work with a detailed record of over 30 years of deep-sea observations at the Monterey Bay Aquarium Research Institute (MBARI).

I was mentored by Steve Haddock (coauthor of the book Practical Computing for Biologists) and Anela Choy at the Monterey Bay Aquarium Research Institute in working with huge datasets using computational tools. I spent two months in residence at MBARI using physical oceanographic data collected at sea to model light levels in the deep ocean and test how these correlate to patterns of animal distributions.

Images courtesy of Kate Thomas

This project expanded the scope of my scientific training and how I think about my future research goals. In addition, it has turned into an ongoing collaboration across three institutions and a long-term effort to understand the variability of midwater light fields and their effects on deep-sea communities.

Thomas graduated this semester and will start a postdoc in August at the Natural History Museum in London.


This internal funding mechanism from the Office of the Vice Provost for Interdisciplinary Studies encourages doctoral and master’s students to step away from their core research and training to acquire skills, knowledge, or co-curricular experiences that will give them new perspectives on their research agendas. Graduate Student Training Enhancement Grants are intended to deepen preparation for academic positions and other career trajectories.

Biology Student Builds Computational Skills for Modeling and Data Analysis

Selcan Aydin

Eight months before defending her dissertation on the effects of genetic variation on signaling dynamics, Biology student Selcan Aydin spent two weeks in San Diego building skills needed for the modeling and data analysis challenges of her research.

She was among 19 Duke students who received Graduate Student Training Enhancement Grants (GSTEG) in 2016-17 for training beyond their core disciplines. Her faculty mentor was Nicolas Buchler. Recently Dr. Aydin reflected on her experience:

I attended the Computational Synthetic Biology Track of the Quantitative Biology (Qbio) Summer School, organized by the University of California, San Diego. This was a two-week professional workshop dedicated to the advancement of quantitative biology.

The workshop focused on different modeling approaches where experts in the field gave lectures in the morning, followed by hands-on training sessions in the afternoon. Attending the workshop allowed me to learn new modeling and data analysis methods that were useful for advancing my dissertation research.

In addition to learning new skills, I was exposed to cutting-edge research via seminars given by various experts in the Qbio field.

Finally, the group project I did with fellow trainees was very helpful in gaining hands-on mathematical modeling experience where I had the chance to interact with computational biologists. This allowed me to improve my collaboration and scientific communication skills in addition to the scientific knowledge I have gained in computational and mathematical modeling.

This internal funding mechanism from the Office of the Vice Provost for Interdisciplinary Studies encourages graduate students to step away from their core research and training to acquire skills, knowledge or co-curricular experiences that will give them new perspectives on their research agendas. Graduate Student Training Enhancement Grants are intended to deepen preparation for academic positions and other career trajectories.

See who received these grants for 2017-18, and read about other 2016-17 recipients’ experiences:

Image: Selcan Aydin (far right) and her fellow trainees on the last day of Quantitative Biology (Qbio) Summer School 2016

Doctoral Students Honored for Excellence in Mentoring

Duke graduate students Eleanor Caves (Biology), Joyell Arscott (Nursing) and Zachary Carico (Immunology) are this year’s student recipients of the Dean’s Award for Excellence in Mentoring.

Caves (pictured above) is part of a graduate student group that received a Duke Support for Interdisciplinary Graduate Networks (D-SIGN) grant for the 2016-2017 academic year. Her successful proposal, submitted with Rebecca Lauzon, Ph.D. student in Earth and Ocean Sciences, and Patrick Green, Ph.D. student in Biology, called for a new network of STEM graduate students and Master of Arts in Teaching students to create lesson plans based on current research and distribute them to local K-12 educators. The network utilizes the structure of a graduate student-run STEM outreach group called the Scientific Research and Education Network (SciREN), which develops relationships between researchers and educators to incorporate current research into K-12 classrooms. All lesson plans created for SciREN are freely available to educators through an online repository. The group’s faculty sponsors are Kate Allman and Brad Murray.

Doctoral Students Receive Grant for Science and Technology Policy


Two Duke University PhD candidates have been awarded a $25,000 grant to study the feasibility of establishing a North Carolina Science and Technology Policy Fellowship Program.

The California Council on Science and Technology, in partnership with the Gordon and Betty Moore Foundation and Simons Foundation, is funding multiple grants to support planning processes for creating immersive science and technology policy fellowship programs in state legislature.

Few state legislators have backgrounds in science, engineering or technology, yet they are routinely called on to make decisions on issues with complicated scientific and technological components. The Fellowship Program would provide the state legislature with non-partisan science PhDs to assist them in grappling with the complex issues of science underlying many legislative initiatives.

Andrew George and Dan Keeley, students in the Duke PhD program in Biology, won their bid for North Carolina with support from Science & Society, the Sanford School for Public Policy, the Duke Government Affairs Office and the North Carolina Sea Grant Program.

“We are going to have to work hard to engage public and private universities, business, and non-profits as well as legislators and members of the executive branch throughout the entire process to ensure that we are creating a fellowship that best serves the needs of the fellows and state policy,” says George. “A primary challenge of implementation is the difference in structure of the legislatures.”

To learn more, read the full article on the Duke Science & Society website.

Faculty Receive Bass Connections Awards to Develop Courses


Bass Connections has awarded four course development funds to groups of Duke faculty members whose pedagogical ideas will expand interdisciplinary curricular options for undergraduates as well as graduate and professional students.

This Spring an RFP invited Duke faculty, departments or schools to organize new courses or modify existing ones that align with one or more of the Bass Connections themes and are multidisciplinary, open to students at different levels and/or ask questions of societal importance. Such courses will augment theme leaders’ efforts to enrich the curricular pathways available to undergraduate and graduate students.

Managing Networks     

Submitted by Lisa Keister with Susan Alberts, Christopher Bail, Jonathon Cummings, James Moody, Martin Ruef

  • Faculty affiliations: Trinity College of Arts & Sciences (Biology, Evolutionary Anthropology, Sociology, Markets and Management Certificate Program); Fuqua School of Business; Nicholas School of the Environment (Marine Science and Conservation); Center for Population Health & Aging; Duke Institute for Brain Sciences; Duke Network Analysis Center; Duke Population Research Institute
  • Bass Connections theme: Information, Society & Culture

Networks are pervasive in the social, economic, political and natural worlds. Network data and methods – and concurrently our ability to conceptualize and analyze networks – have expanded dramatically in recent years, and Duke is a central location in which this research is being conducted. This course is about the role that networks play in organizations. It will involve multiple faculty from across schools, invite outside experts to provide guest lectures and include project-based assignments. Graduate students and post-docs from various disciplines will participate as assistants and project leaders.

Engineering and Anthropology of Biomedical Engineering (BME) Design in Uganda

Submitted by William Reichert and Kearsley Stewart

Dr. Reichert established the Duke-Makerere University in Kampala (MUK) BME Partnership in coordination with Duke BME, Duke Global Health Institute, Pratt School of Engineering, the Provost’s Office and the Duke Africa Initiative. The goal of this course is to integrate the design and anthropological elements of the Duke-MUK experience into a single course offered to both BME and global health undergraduate and graduate students. It will proceed pedagogically as a design class superimposed with the relevant anthropology of working directly with students in Uganda.

History of Global Health

Submitted by Nicole Barnes and Margaret Humphreys

  • Faculty affiliations: Trinity College of Arts & Sciences (History); School of Medicine; Duke Global Health Institute
  • Bass Connections theme: Global Health

The history of global health contains valuable perspectives for thinking through current health challenges. The course begins with the development of ancient medicine in Europe and China, and continues into the rise of biomedicine in the 19th and 20th centuries. It addresses particular diseases as case studies through which to explore important themes in global health history, and traces global circulations of people and commodities to show how international agencies, charities and governing bodies have spread both disease and the means to fight it.

Integrating Environmental Science and Policy

Submitted by Lori Bennear and Patrick Halpin

  • Faculty affiliations: Nicholas School of the Environment (Environmental Economics and Policy, Marine Science and Conservation); Trinity College of Arts & Sciences (Economics); Sanford School of Public Policy; Energy Initiative; Science & Society
  • Bass Connections theme: Energy

Environmental challenges are inherently multidisciplinary, drawing upon principles from ecology, earth sciences, biochemistry, economics, political science and ethics. Employing in-depth case studies, this course will explore the complex interactions that characterize current environmental problems. Course objectives include: exposing students to interdisciplinary approaches to environmental science and policy; allowing students to develop analytic tools to address environmental issues; and fostering collaborative group-based analytic experiences consistent with real-world environmental problem solving.

Faculty recipients of these course development funds will be invited to share their experiences at a luncheon or dinner at the end of year.

Learn how to get involved with Bass Connections.