Community Highlight: Steven Biller
Steven Biller, Wellesley College
Introduce yourself and your work.
(Steven Biller) I am a faculty member in the Biological Sciences department at Wellesley College in Wellesley, MA. I’ve been involved in both the KBase Educators Program and am on the Steering Committee for MICROnet. My first job out of college involved running an ABI 3700 sequencer, and genomics has been an important component of my work ever since. My research centers on the marine microbiome, with a particular focus on my favorite bacterium Prochlorococcus – the smallest and most abundant photosynthetic cell on Earth. Our work is broadly interested in the mechanisms that shape Prochlorococcus diversity, including horizontal gene transfer, mobile elements, and interactions with other cells.
How has using KBase supported your role as an instructor?
(SB) The KBase platform has enabled me to completely change the way I approach teaching foundational data science and genomics concepts to undergraduates. I teach an upper-level bioinformatics course in a Biological Sciences department. Students come to the course with diverse backgrounds: some have little to no computing experience, while other students have extensive programming knowledge but only the minimum Biology prerequisites. In early iterations of the class, we went through exercises working in traditional UNIX command-line environments. While this was valuable exposure, I found that we often spent most of our time just getting something to work, leaving little time for the data analysis tasks that represent the most important learning outcomes. KBase has allowed me to remove this operational barrier, making it much easier to run the initial computational tools and letting them spend their time interpreting the output to address their biological questions.
Inspired and supported by my experience working with the KBase Educators group, I have transitioned this course away from analyzing existing datasets toward student-designed research projects. Here, students design a set of questions they want to address about microbes from the local campus environment, collect samples and metadata, isolate their own microbes, sequence them, then carry out KBase-enabled analyses of those genomes to address their research questions. This type of open-ended, student-driven project has led to great student learning outcomes. Analyzing data that they have collected makes students more invested in the outcomes than when I had simply provided pre-existing data to explore. In the end, we’ve generated genomes of sufficient quality to submit the assemblies to NCBI and release the final KBase Narratives depicting the analysis. I think it gives the students a lot of satisfaction to know that they were not just doing a canned exercise but instead making an actual contribution to world knowledge.
Do you have a favorite part about KBase?
(SB) I love how easy KBase makes it to run all the standard genome / metagenome assembly and annotation tools. As someone who has spent many hours over the years fighting with algorithm installation / compilation issues and debugging cluster submission scripts, it’s hard for me to convey to my students just how easy KBase makes this all seem.
What role do you see KBase having in open science principles?
(SB) The results of large-scale computational biology studies can be highly dependent on specific details of the algorithms chosen and the scripts used to transform raw data to biological interpretation. KBase’s ability to generate and openly share complete and reproducible pipelines, including annotations, is a great model. I also think the web-based interface makes it much easier to follow along with the logic than trying to interpret someone else’s scripts.
Can you share a tip on using KBase?
(SB) Don’t be afraid to press the “R” button in the “Apps” pane and explore the beta apps! There is a constantly changing set of tools available in the beta releases that can be incredibly useful for solving a bioinformatics problem you may have encountered.
References & Links
Behar, A. Zadvornaya, E. Wren, M. Andreadis, A. Tariq, M.E. Tian, S. Krishna, K. Keita, H. Eich, J. Enriquez, B.J. Hansten Monterrozo, C. Hyun, K.L. Jenkins, K. Parameswar, M.M. Top, S. Waag, M.G. Ryan, A.M. Stein, S.J. Biller. “Genomes of nine cultured microbes from two hydrologically connected freshwater sites in Wellesley, MA.” Microbiology Resource Announcements 14:e00861-24 (2025) [doi: 10.1128/mra.00861-24]
Chao, E. Chou, V. Tang, A. Hofer, O. Dakhama, S. Gardner, V. James, P. Patel, S. Song, C. Tessier, A. Wolberg, S.J. Biller. “Genomes of eight cultured microbes from soil sites in Wellesley, MA.” Microbiology Resource Announcements 15:e01174-25 (2026) [doi: 10.1128/mra.01174-25]
- ASM MRA KBase Collection: https://journals.asm.org/journal/mra/kbase
- 2025 Outstanding Instructor Award: https://journals.asm.org/journal/mra/2025-instructor-award
