Hi I am wondering if we can execute a genome on the sub-cellular level by running it on the computer. What I mean is using the genome as data to examine by having the cells reproduce and see what happens as they grow.

  • $\begingroup$ Given that Nicolai has adequately answered the question, I vote to close this question. $\endgroup$
    – S Pr
    Feb 18 '20 at 14:07
  • $\begingroup$ Welcome to Biology.SE! Please take the tour and then go through the help pages starting with How to Ask questions effectively on this site. In particular, note that "speculative" questions are off-topic. ——— You might also want to make sure you have a good grounding in the basics of biology — that will help you understand why the answer is "No". I have found that when learning about a new area starting with a relatively accessible and reliable source like Khan Academy is very helpful. Thanks! 😊 $\endgroup$
    – tyersome
    Feb 18 '20 at 20:14

A simple genome can be modeled, however imperfectly, on a computer, where some have taken experimental genomics data and built simulations from it.

For instance, from the paper A Whole-Cell Computational Model Predicts Phenotype from Genotype:

Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. Our whole-cell model accounts for all annotated gene functions and was validated against a broad range of data. The model provides insights into many previously unobserved cellular behaviors, including in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. In addition, experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery...

We have developed a comprehensive whole-cell model that accounts for all of the annotated gene functions identified in M. genitalium and explains a variety of emergent behaviors in terms of molecular interactions. Our model accurately recapitulates a broad set of experimental data, provides insight into several biological processes for which experimental assessment is not readily feasible, and enables the rapid identification of gene functions as well as specific cellular parameters.



Given the vast behavioral repertoire and biological complexity of even the simplest organisms, accurately predicting phenotypes in novel environments and unveiling their biological organization is a challenging endeavor. Here, we present an integrative modeling methodology that unifies under a common framework the various biological processes and their interactions across multiple layers. We trained this methodology on an extensive normalized compendium for the gram-negative bacterium Escherichia coli, which incorporates gene expression data for genetic and environmental perturbations, transcriptional regulation, signal transduction, and metabolic pathways, as well as growth measurements. Comparison with measured growth and high-throughput data demonstrates the enhanced ability of the integrative model to predict phenotypic outcomes in various environmental and genetic conditions, even in cases where their underlying functions are under-represented in the training set. This work paves the way toward integrative techniques that extract knowledge from a variety of biological data to achieve more than the sum of their parts in the context of prediction, analysis, and redesign of biological systems.


Gentle advice: Avoid answers from cartoonists, whose domain of knowledge does not include biology.

  • $\begingroup$ I think it's a bit of a stretch calling these sorts of models "executing a genome". They are using a whole lot more data than DNA. $\endgroup$
    – Bryan Krause
    Feb 19 '20 at 13:34
  • $\begingroup$ I can't speak to semantics but the question directly asks if it possible to model the genome on a computer. Researchers have done this using sequencing data, as the cited articles show. $\endgroup$ Feb 19 '20 at 19:30
  • $\begingroup$ Shrug Whatever. $\endgroup$ Feb 19 '20 at 20:37

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