Standardizing the exchange of model states between cellular models using MultiCellDS

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Peerdeman GY

University of Applied Sciences Leiden
"Standardizing the exchange of model states between cellular models using MultiCellDS"
Cell-based modeling has become a standard tool in biology for developing mechanistic hypotheses of tissue morphogenesis. A large number of model frameworks is available, each of which store represent and store cells as different types of mathematical objects, Storing and exchanging snapshots between different modeling frameworks is useful: it allows comparison of simulations, e.g., through measuring divergence of configurations, or usage of annotated experimental data as initial conditions. Recently, MultiCellDS was proposed as a standard for exchanging cellular data between modeling frameworks. Implementing MultiCellDS for modeling frameworks is challenging. Here we propose an extension to the MultiCellDS standard and introduced libCellShape, that acts as an interface to MultiCellDS for modeling frameworks. The library takes on much of the burden of storing and loading cellular snapshots to and from MultiCellDS files, and includes algorithms to convert lattice based snapshots to vertex based snapshots and vice versa. We demonstrate the use of libCellShape by exchanging snapshots between our Cellular Potts framework Tissue Simulation Toolkit and our vertex-based framework VirtualLeaf. We hope that libCellShape will allow different frameworks to exchange snapshots more easily and that more model types can be supported in the future.

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