Building Simulations from the Ground-Up: Modeling and Theory in Systems Biology

Miles MacLeod, Nancy J. Nersessian

Research output: Contribution to journalArticleAcademicpeer-review

33 Citations (Scopus)
221 Downloads (Pure)


In this article, we provide a case study examining how integrative systems biologists build simulation models in the absence of a theoretical base. Lacking theoretical starting points, integrative systems biology researchers rely cognitively on the model-building process to disentangle and understand complex biochemical systems. They build simulations from the ground up in a nest-like fashion, by pulling together information and techniques from a variety of possible sources and experimenting with different structures in order to discover a stable, robust result. Finally, we analyze the alternative role and meaning theory has in systems biology expressed as canonical template theories like Biochemical Systems Theory.
Original languageEnglish
Pages (from-to)533-556
JournalPhilosophy of science
Issue number4
Publication statusPublished - 2013
Externally publishedYes


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