Enabling Student Projects in Computational Biology with the Morpheus Simulation Framework

Computational biology is an interdisciplinary field with contributors from a range ofbackgrounds. Reproducibility therefore hinges not only on technical factors but also on the usabilityof the tools involved. In this paper, we present a usability test of the MorpheusML ecosystem inwhich three teams of high school students, none with prior experience in computational modeling,were tasked with developing a model of a biological process in MorpheusML and submitting it tothe public MorpheusML model repository within a single workday. Success was judged against therepository’s own acceptance criteria: a submission must faithfully reproduce the target result and passa review process that checks both the model and its documentation. All three teams produced andsubmitted a working model within the day, two of them fully reproducing their target result. In thefirst case study, the students additionally uncovered a parameter swap in an influential, widely citedpaper, underlining the value of reproduction as a quality-control mechanism. We conclude that theMorpheusML ecosystem is usable in practice, and we discuss its potential as a low-barrier entry pointinto authentic scientific practice.