Biocellion: accelerating computer simulation of multicellular biological system models. Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. Results: We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Availability and implementation: Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information.
Keywords for this software
References in zbMATH (referenced in 4 articles )
Showing results 1 to 4 of 4.
- Lötstedt, Per: Derivation of continuum models from discrete models of mechanical forces in cell populations (2021)
- Saxena, Gaurav; Ponce-de-Leon, Miguel; Montagud, Arnau; Vicente Dorca, David; Valencia, Alfonso: BioFVM-X: an MPI+OpenMP 3-D simulator for biological systems (2021)
- Cooper et al.: Chaste: Cancer, Heart and Soft Tissue Environment (2020) not zbMATH
- Mathias, Sonja; Coulier, Adrien; Bouchnita, Anass; Hellander, Andreas: Impact of force function formulations on the numerical simulation of centre-based models (2020)