Community Highlight: Aaron Schirmer
My name is Aaron Schirmer (AS), and I am a Bernard J. Brommel Distinguished Professor and Fulbright Specialist in Biology Education at Northeastern Illinois University (NEIU). I have been an active member of the KBase Educators community since 2020. At NEIU, I teach a range of courses for non-majors, majors, and graduate students. In my classes and corresponding laboratory sections, I focus on creating relevant and engaging course materials that empower students to become productive and successful scientists. A particular emphasis in my teaching is developing exercises focused on data analysis, statistics, and critical thinking. I have found KBase to be an incredibly powerful tool for these activities.
For example, in General Biology II (BIO 202), my colleague Joel Olfelt and I developed a laboratory where students analyze changes in plant growth and the soil microbiome composition with and without fertilizer. This assignment uses the KBase platform to engage our undergraduates in authentic research early in their biology education. The project aligns with course goals by allowing students to apply the scientific method, conduct experiments, and interpret data on how organisms interact with their environment, thereby fostering scientific competence and confidence. Students value using “actual” research tools and gaining exposure to authentic research experiences. The plant growth experiment demonstrates how agricultural practices impact development firsthand, while the metagenomics work illustrates that other environmental impacts may be hidden yet still have a profound and lasting effect.
Aaron Schirmer giving a seminar on teaching students with KBase in Warsaw, Poland.
Interest in KBase for classroom use has been growing rapidly. This past spring, I participated in two regional data science workshops where KBase and some of my work were highlighted. This platform is also gaining international attention. This past summer, as part of my Fulbright activities, I traveled to Poland and introduced the platform and the KBase Educators’ group to colleagues at the University of Warsaw. My presentation shared examples of my teaching methodology and underscored KBase’s strengths as both a computational biology and data science tool. We then explored specific ways courses and academic programs at the University of Warsaw could integrate KBase into their curriculum. The presentation was extremely well received, and faculty showed a genuine interest in adopting the platform to their curriculum. Ultimately, my work with KBase and its educators’ community continues to prove that integrating authentic, high-powered data science tools into the undergraduate curriculum is the most effective way to equip students for modern biological research.
How has using KBase supported your work?
(AS) Northeastern Illinois University is a primarily undergraduate Minority Serving Institution (MSI). We are highly focused on the equitable advancement of science and committed to preparing the next generation of scientists to meet the many challenges that face our world. This critical work requires teaching students to be confident using cutting-edge technology, and in my opinion, KBase is perfect for this task! KBase provides free access to powerful computational resources, allowing students to run sophisticated, large-scale systems biology and bioinformatic analyses that would be impossible on a standard personal computer or a typical lab setup. Crucially, it provides these tools in a user-friendly interface, which lowers the barrier to entry. This means students can perform complex bioinformatics without needing extensive command-line programming expertise. This type of hands-on, active learning allows all students to engage directly with real-world biological data and current, open-source bioinformatics tools, strongly supporting “learning by doing” for key concepts in data science and bioinformatics.
Do you have a favorite part about KBase?
(AS) To me, the most exciting part of KBase is its scalability and adaptability for the classroom. Because it is free and provides an interface that does not require coding knowledge, KBase is highly scalable across a wide range of student skills and abilities. I currently use KBase in courses that range from General Biology II to advanced classes in Genomics and Proteomics. This flexibility allows me to tailor my assignments and curriculum to meet the students exactly where they are, providing them with essential access to and awareness of powerful tools that will benefit their future careers.
What role do you see KBase having in open science principles?
(AS) KBase is also an incredibly powerful tool for modeling and teaching open science principles. My colleagues and I constantly strive to teach best practices, whether that means demonstrating the ideal way to keep a lab notebook, present a poster, or run a PCR reaction. By using KBase as a model of open science, we are able to promote research integrity through increased transparency and reproducibility, fostering a more collaborative, innovative, and inclusive scientific community. These valuable experiences enhance students’ academic and career prospects, especially as more federal agencies and employers prioritize these skills. Ultimately, a strong understanding of open science principles equips students with the critical skills needed to succeed in an ever-evolving research landscape.
Can you share one “behind the scenes” thing about your work?
(AS) KBase features a wonderful user interface that visually represents complex analyses in an approachable, student-friendly way. However, one key tip I give faculty, especially those interested in data science, is to remember the significant amounts of data housed behind these visualizations that can be mined for further analysis. For example, in the General Biology II project I described, I export the relative abundance data from the genomic classifier application and use it for additional downstream statistical analyses. There is a tremendous amount of data available within KBase if you know where to look. Having students interact directly with this underlying data can make their educational experience with the platform significantly richer.
References & Links
Dow EG, Wood-Charlson EM, Biller SJ, Paustian T, Schirmer A, Sheik CS, Whitham JM, Krebs R, Goller CC, Allen B, Crockett Z and Arkin AP. (2021). Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform. Front. Educ. 6:711535. doi: 10.3389/feduc.2021.711535; Static Narrative: https://kbase.us/n/90997/63/
Schirmer, A and Parikh, K. (2025). Data from: General Biology 2 Sugar Beet Lab. KBase. doi: 10.25982/219850.28/2997179
