Programming with models: modularity and abstraction provide powerful capabilities for systems biology.

ABSTRACT: Mathematical models are increasingly used to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations presents a fundamental barrier to progress. Overcoming this requires modularity, enabling sub-systems to be specified independently and combined incrementally, and abstraction, enabling generic properties of biological processes 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, which can be instantiated and reused repeatedly in different contexts with different components. We have developed a computational infrastructure that accomplish

SUBMITTER: Mallavarapu A 

PROVIDER: S-EPMC2659579 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature