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

## TL;DR

The BIWT software uses single-cell and spatial data to create virtual cell models that simulate tissue dynamics, bridging static data with dynamic predictions.

## Contribution

BIWT introduces a new software tool for initializing spatial agent-based models directly from multiomic data, enabling data-driven virtual cell simulations.

## Key findings

- Initialization strategies in BIWT significantly influence tumor-immune dynamics and spatial clustering in virtual cells.
- BIWT provides a framework to generate virtual cells that reflect both experimental and clinical contexts using spatial multiomics data.

## 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.