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


Aneil Mallavarapu, Matthew Thomson, Benjamin Ullian, Jeremy Gunawardena

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 accomplishes this. We show here why such capabilities are needed, what is required to implement them and what can be accomplished with them that could not be done previously.

(keywords) bioinformatics, biology, lisp, programming, systems

Journal of the Royal Society Interface,  2008.

@misc{MallavarapuInterface2008,
   citeulike-article-id = {6520744},
   citeulike-linkout-0 = {http://dx.doi.org/10.1098/rsif.2008.0205},
   doi = {10.1098/rsif.2008.0205},
   keywords = {bioinformatics, biology, file-import-10-01-11, lisp, programming, systems},
   posted-at = {2010-01-11 18:00:48},
   priority = {2},
   title = {Programming with models: modularity and abstraction provide powerful capabilities for systems biology},
   url = {http://dx.doi.org/10.1098/rsif.2008.0205}
}
Tags:

Publication

— authors

Aneil Mallavarapu, Matthew Thomson, Benjamin Ullian, Jeremy Gunawardena

— status

published

— sort

article in journal

Venue

— journal

Journal of the Royal Society Interface

— publication date

2008

URLs

original page

Identifiers

— DOI

10.1098/rsif.2008.0205

BibTeX

— BibTeX ID
MallavarapuInterface2008
— BibTeX category
misc

Partita IVA: 01131710376 - Copyright © 2008-2021 APICe@DISI Research Group - PRIVACY