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

TL;DR

This paper discusses the philosophical, practical, and community aspects of integrative biological simulations, emphasizing their potential, challenges, and the need for improved practices to enhance their scientific value.

Contribution

It provides a comprehensive analysis of philosophical considerations, community workflows, and publication practices to advance integrative biological simulation efforts.

Findings

Physics sub-disciplines offer useful analogies for biological simulations

Pragmatic philosophical approach balances idealism and infancy of understanding

Open science practices can improve simulation reproducibility and integration

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.