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Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices
Gopal P Sarma1, Victor Faundez1,2
1School of Medicine, Emory University, Atlanta, GA, USA.
Cellular Logistics
|January 4, 2018
Summary
Integrative biological simulations face challenges in proving their value. This commentary explores philosophical and practical issues, suggesting physics analogies and improved community practices to advance biological modeling and open science.
Area of Science:
- Integrative biological simulations
- Computational modeling in life sciences
Background:
- Biological simulations have a diverse history, targeting systems from cells to ecosystems.
- The value of large-scale computational modeling remains debated within the biological community.
Purpose of the Study:
- To examine philosophical and practical issues surrounding integrative biological simulations.
- To explore the potential of simulations in biological research by drawing analogies from physics.
- To propose improvements in community workflow and publication practices for better simulation integration and discoverability.
Main Methods:
- Philosophical examination of modeling in biology and physics.
- Analysis of community workflow and publication practices.
- Discussion of analogies from physics sub-disciplines.
Main Results:
- Identified philosophical and practical challenges for integrative simulations.
- Suggested physics sub-disciplines as cultural analogies for biological modeling.
- Highlighted the need for pragmatic viewpoints balancing philosophical belief and current understanding.
Conclusions:
- Adoption of improved practices can advance integrative simulation efforts.
- Aligned incentives exist with open science, data sharing, and reproducibility trends.
- Enhanced discoverability and incorporation of research are crucial for simulation integration.
Keywords:
biological simulationintegrative simulationphenomenological modelingphilosophy of physicswhole-cell modelsMore Related Videos
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