Chris Skalnik

Covert Lab

4 snapshots of a colony of cells with various cell and background coloration.

Image adapted from vivarium_lacy.png, which was added to the Vivarium Core repository by Eran Agmon. It shows a colony of cells undergoing a glucose-lactose shift simulated by Vivarium. From left to right, the snapshots show environmental glucose concentrations, glucose flux for each cell, environmental lactose concentrations, and LacY concentration in each cell.

Papers

  • I used Vivarium to create an agent-based model of a colony of Escherichia coli where each cell was modeled by a snapshot from the Covert Lab’s Whole-Cell Modeling Project. This produced the first “whole-colony” model. A manuscript presenting my work is currently in review and available on BioRxiv:

    Skalnik, C. J., Agmon, E., Spangler, R. K., Talman, L., Morrison, J. H., Peirce, S. M., & Covert, M. W. (2021). Whole-Colony Modeling of Escherichia coli. BioRxiv, 2021.04.27.441666. DOI: 10.1101/2021.04.27.441666

  • Vivarium is a tool for composing and simulating integrative, multiscale models that I help develop. Check out its documentation to learn more! A manuscript documenting this tool is currently in review and available on BioRxiv:

    Agmon, E., Spangler, R. K., Skalnik, C. J., Poole, W., Peirce, S. M., Morrison, J. H., & Covert, M. W. (2021). Vivarium: An interface and engine for integrative multiscale modeling in computational biology. BioRxiv, 2021.04.27.441657. DOI: 10.1101/2021.04.27.441657

Software