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Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices

Sarma, Gopal P. and Faundez, Victor (2017) Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices. Cellular Logistics, 7 (4).

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Abstract

Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems, a diverse array of biological systems have been the target of large-scale computational modeling efforts. Nonetheless, these research agendas have yet to prove decisively their value among the broader community of theoretical and experimental biologists. In this commentary, we examine a range of philosophical and practical issues relevant to understanding the potential of integrative simulations. We discuss the role of theory and modeling in different areas of physics and suggest that certain sub-disciplines of physics provide useful cultural analogies for imagining the future role of simulations in biological research. We examine philosophical issues related to modeling which consistently arise in discussions about integrative simulations and suggest a pragmatic viewpoint that balances a belief in philosophy with the recognition of the relative infancy of our state of philosophical understanding. Finally, we discuss community workflow and publication practices to allow research to be readily discoverable and amenable to incorporation into simulations. We argue that there are aligned incentives in widespread adoption of practices which will both advance the needs of integrative simulation efforts as well as other contemporary trends in the biological sciences, ranging from open science and data sharing to improving reproducibility.


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Item Type: Published Article or Volume
Creators:
CreatorsEmailORCID
Sarma, Gopal P.gopal.sarma@emory.edu0000-0002-9413-6202
Faundez, Victorvfaunde@emory.edu0000-0002-2114-5271
Keywords: biological simulation; integrative simulation; whole-cell models; phenomenological modeling; philosophy of physics
Subjects: Specific Sciences > Biology > Developmental Biology
Specific Sciences > Biology > Molecular Biology/Genetics
Specific Sciences > Biology > Systematics
Specific Sciences > Complex Systems
Specific Sciences > Computer Science > Artificial Intelligence
General Issues > Models and Idealization
Specific Sciences > Biology > Neuroscience
General Issues > Reductionism/Holism
Depositing User: Dr. Gopal Sarma
Date Deposited: 05 Dec 2017 18:17
Last Modified: 05 Dec 2017 18:17
Item ID: 14173
Journal or Publication Title: Cellular Logistics
Publisher: Taylor and Francis
Official URL: http://www.tandfonline.com/doi/full/10.1080/215927...
DOI or Unique Handle: 10.1080/21592799.2017.1392400
Subjects: Specific Sciences > Biology > Developmental Biology
Specific Sciences > Biology > Molecular Biology/Genetics
Specific Sciences > Biology > Systematics
Specific Sciences > Complex Systems
Specific Sciences > Computer Science > Artificial Intelligence
General Issues > Models and Idealization
Specific Sciences > Biology > Neuroscience
General Issues > Reductionism/Holism
Date: 2017
Volume: 7
Number: 4
URI: http://philsci-archive.pitt.edu/id/eprint/14173

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