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The principles of whole-cell modeling
Jonathan R Karr1, Koichi Takahashi2, Akira Funahashi3
1Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Current Opinion in Microbiology
|June 27, 2015
Summary
Whole-cell models predict cellular phenotypes from genotype, enabling bioengineering and medicine. Key principles include completeness, biophysical realism, and reproducibility, though challenges remain in experimental tools and theory.
Area of Science:
- Computational Biology
- Systems Biology
- Synthetic Biology
Background:
- Whole-cell models aim to predict emergent cellular phenotypes from genotype.
- Such models are crucial for advancing rational bioengineering and precision medicine.
Purpose of the Study:
- To outline the key principles of whole-cell modeling.
- To describe the process of constructing whole-cell models.
- To identify remaining challenges and necessary collaborations.
Main Methods:
- Development of bacterial whole-cell models.
- Focus on principles: single-cellularity, functional/genetic/molecular/temporal completeness, biophysical realism (dynamics, stochasticity), species-specificity, integration, and reproducibility.
- Outlining the model construction process and existing resources.
Main Results:
- Key principles for comprehensive whole-cell modeling have been identified.
- The construction process and available resources are outlined.
- Challenges in achieving complete models are highlighted, including experimental and theoretical gaps.
Conclusions:
- Achieving fully complete whole-cell models requires new experimental tools and a stronger theoretical understanding of hybrid mathematics.
- Interdisciplinary collaboration among diverse scientific and engineering fields is essential for progress.
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