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  1. Building Simulations from the Ground Up: Modeling and Theory in Systems Biology.Miles MacLeod & Nancy J. Nersessian - 2013 - Philosophy of Science 80 (4):533-556.
    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, (...)
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  • What is a Simulation Model?Juan M. Durán - 2020 - Minds and Machines 30 (3):301-323.
    Many philosophical accounts of scientific models fail to distinguish between a simulation model and other forms of models. This failure is unfortunate because there are important differences pertaining to their methodology and epistemology that favor their philosophical understanding. The core claim presented here is that simulation models are rich and complex units of analysis in their own right, that they depart from known forms of scientific models in significant ways, and that a proper understanding of the type of model simulations (...)
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  • The Non-theory-driven Character of Computer Simulations and Their Role as Exploratory Strategies.Juan M. Durán - 2023 - Minds and Machines 33 (3):487-505.
    In this article, I focus on the role of computer simulations as exploratory strategies. I begin by establishing the non-theory-driven nature of simulations. This refers to their ability to characterize phenomena without relying on a predefined conceptual framework that is provided by an implemented mathematical model. Drawing on Steinle’s notion of exploratory experimentation and Gelfert’s work on exploratory models, I present three exploratory strategies for computer simulations: (1) starting points and continuation of scientific inquiry, (2) varying the parameters, and (3) (...)
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  • Individual Based Models in Ecology: An Evaluation, or How Not to Ruin a Good Thing.Joan Roughgarden - unknown
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