Whole yeast model: what and why
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Abstract
One of the most challenging fields in Life Science research is to deeply understand how complex cellular functions arise from the interactions of molecules in living cells. Mathematical and computational methods in Systems Biology are fundamental to study the complex molecular interactions within biological systems and to accelerate discoveries. Within this framework, a need exists to integrate different mathematical tools in order to develop quantitative models of entire organisms, i.e. whole-cell models. This note presents a first attempt to show the feasibility of such a task for the budding yeast Saccharomyces cerevisiae, a model organism for eukaryotic cells: the proposed model refers to the main cellular activities like metabolism, growth and cycle in a modular fashion, therefore allowing to treat them separately as single input/output modules, as well as to interconnect them in order to build the backbone of a coarse-grain whole cell model. The model modularity allows to substitute a low granularity module with one with a finer grain, whenever molecular details are required to correctly reproduce specific experiments. Furthermore, by properly setting the cellular division, simulations of cell populations are achieved, able to deal with protein distributions. Whole cell modeling will help understanding logic of cell resilience.
Cite this as
2018. Whole yeast model: what and why. PeerJ Preprints 6:e27327v1 https://doi.org/10.7287/peerj.preprints.27327v1Author comment
This is an abstract which has been accepted for the BBCC2018 Conference
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Pasquale Palumbo analyzed the data, prepared figures and/or tables, performed the computation work, authored or reviewed drafts of the paper, approved the final draft.
Marco Vanoni conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Federico Papa analyzed the data, prepared figures and/or tables, performed the computation work, authored or reviewed drafts of the paper, approved the final draft.
Stefano Busti performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, approved the final draft.
Lilia Alberghina conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
The research in this article did not generate any data or code.
Funding
This work was supported by the MIUR grant grant ISBE, ESFRI Research Infrastructures, SYSBIO Centre of Systems Biology. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
