BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41093751.
- Also identified by DOI 10.1093/bioinformatics/btaf571 and PMC identifier 12597895.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. 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.
Medical subject headings
- Software
- Computational Biology
- Models, Biological