Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations presents a fund
amental barrier to progress. Overcoming this requires modularity, enabling sub-systems to be specified independently and combined incrementally, and abstraction, enabling general properties to be specified independently of specific instances. These in turn require models to be represented as programs rather than as datatypes. Programmable modularity and abstraction enables libraries of modules to be created for generic biological processes, which can be instantiated and re-used repeatedly in different contexts with different components. We have developed a computational infrastructure to support this. We show here why these capabilities are needed, what is required to implement them and what can be accomplished with them that could not be done previously.
