CellSys

[…] running multiple non-interacting single-cell instances concurrently on massively parallel computers. More examples include HPC ABM frameworks for multi-core CPUs such as CompuCell3D (Swat et al., ,), CellSys (Hoehme and Drasdo, ), and Morpheus (Starruß et al., ). These frameworks target multi-core CPU acceleration on a single compute node using OpenMP. In addition, other techniques have been propo […]

[…] s with graphical model editors, integrated ODE and PDE solvers, and support for molecular-scale sub-models, but they currently cannot scale to large numbers (105 or more) of cells. TiSim (part of the CellSys package []) can simulate many more cells by using a cell-centered, off-lattice approach. However, it is currently closed source, and its executables are restricted to a limited set of simulati […]

[…] of cell-based model. A longer-term challenge is to extend such comparison studies across simulation tools, of which there is an increasing ecosystem, including CompuCell3d [], Morpheus [], EPISIM [], CellSys [], VirtualLeaf [], Biocellion [], BioFVM [], LBIBCell [] and EmbryoMaker []. We emphasize here the lack of ‘benchmarks’ on which to make such comparisons. We propose that the present study of […]

[…] In the upcoming open-source software framework CellSys, the quantifications obtained from TiQuant can directly be used as an input for the CellSys modelling engine. As an illustration of this application of the processing pipeline, we refer to a m […]