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BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells.

Daniel R Bergman·Jeanette A I Johnson·Marwa Naji·Max Booth·Heber Lima da Rocha·Atul Deshpande·Dimitrios N Sidiropoulos·Tamara Lopez-Vidal·Randy Heiland·Luciane T Kagohara·Robert A Anders·Lei Zheng·Elizabeth M Jaffee·Genevieve Stein-O'Brien·Paul Macklin·Elana J Fertig
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Abstract

SUMMARY: Whereas transcriptomic and spatial profiling offer static snapshots of tissue structure, mechanistic models use biological rules to predict how tissues evolve. We present the BioInformatics WalkThrough (BIWT) software to directly initialize spatial agent-based models from single-cell and spatial molecular data. We demonstrate how initialization strategies affect tumor-immune dynamics and spatial clustering, positioning BIWT as a software suite to generate data-driven virtual cells representing both experimental and clinical contexts. AVAILABILITY AND IMPLEMENTATION: The BIWT software is available at https://github.com/PhysiCell-Tools/PhysiCell-Studio. The sample dataset for running the BIWT is available at https://zenodo.org/records/16365625. The code and instructions for reproducing the use case example is available at https://github.com/drbergman/BIWT-Paper.

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SoftwareComputational BiologyHumansNeoplasmsModels, BiologicalSingle-Cell AnalysisMultiomicsJournal ArticleResearch Support, N.I.H., Extramural

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Daniel R Bergman, Jeanette A I Johnson, Marwa Naji, Max Booth, Heber Lima da Rocha, Atul Deshpande, Dimitrios N Sidiropoulos, Tamara Lopez-Vidal, Randy Heiland, Luciane T Kagohara, Robert A Anders, Lei Zheng, Elizabeth M Jaffee, Genevieve Stein-O'Brien, Paul Macklin, Elana J Fertig. 2025-11-01. BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells.. https://doi.org/10.1093/bioinformatics%2Fbtaf571

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