My research explores philosophical issues in scientific modeling and experimentation: What is the empirical significance of mathematical abstractions? How do they represent a target of inquiry? How do we judge the reliability of our means of generating and processing data, especially when these are automated and result in massive amounts of information? To answer these questions, I focus on the fields of molecular biology, systems biology, and biophysics, which have recently experienced a rise of new modeling and data-gathering practices pertinent to these questions. I am developing a framework that can address these issues from an integrated philosophical and historical standpoint.