Computing

In a structural bioinformatics course, students look at proteins in PyMOL and dock ligands with AutoDock Vina, but neither tool shows them the forces involved. PyMOL doesn’t display forces, and Vina’s scoring function is hard to inspect without reading its source code. The idea that molecular dynamics is Newton’s second law applied many times in a row is easy to state in a lecture and hard to see in practice.

Dataframe operations form the foundation of modern data science workflows, yet researchers often face vendor lock-in when choosing between different dataframe frameworks. My work addresses this by developing a unified operations library that abstracts away framework-specific implementations. The challenge lies in handling the fundamental differences between these systems—some pandas-like dataframes use row-by-row operations, others employ lazy evaluation with native expressions, some require distributed execution patterns, while others focus on parallelization.