ArticleBioinformatics (Oxford, England)2014
Biocellion: accelerating computer simulation of multicellular biological system models.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Article
- Skin in the game: a review of computational models of the skin.BioData mining · 2025Review
- TOPAS-Tissue: A Framework for the Simulation of the Biological Response to Ionizing Radiation at the Multi-Cellular Level.International journal of molecular sciences · 2024Article
- Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0.PLoS computational biology · 2024Article
- BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering.Bioinformatics advances · 2024Article
- Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.bioRxiv : the preprint server for biology · 2023Article
- Ontogeny of collective behaviour.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Review
- Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model.Entropy (Basel, Switzerland) · 2023Article
- Article
- Article
- Article
- CBMOS: a GPU-enabled Python framework for the numerical study of center-based models.BMC bioinformatics · 2022Article
- McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems.PLoS computational biology · 2022Article
- Rules of Engagement: A Guide to Developing Agent-Based Models.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Role ofFrontiers in digital health · 2022Review
- Seven challenges in the multiscale modeling of multicellular tissues.WIREs mechanisms of disease · 2022Review
- Derivation of continuum models from discrete models of mechanical forces in cell populations.Journal of mathematical biology · 2021Article
- Impact of Force Function Formulations on the Numerical Simulation of Centre-Based Models.Bulletin of mathematical biology · 2020Article
- A Multi-Scale Approach to ModelingEntropy (Basel, Switzerland) · 2020Article
- Mathematical modelling reveals cellular dynamics within tumour spheroids.PLoS computational biology · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationBiological 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.
resultsWe 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.