Randy W. Heiland

PhysiCelldFBA: Linking single-cell genome-scale metabolism to spatially explicit multicellular dynamics

PhysiCelldFBA links single-cell metabolism to multicellular spatial dynamics by integrating genome-scale metabolic models with agent-based simulations.

UQ-PhysiCell: An extensible Python framework for uncertainty quantification and model analysis in PhysiCell

UQ-PhysiCell provides a Python framework for uncertainty quantification, calibration, and model analysis in PhysiCell simulations, enabling scalable and reproducible uncertainty-aware analysis of agent-based models.

Tumor-immune trajectory context connects static tissue architecture to clinical outcomes

This paper introduces a trajectory-centric framework to model dynamic tumor-immune interactions, showing that treatment-phase TME states predict immunotherapy response better than pre-treatment states.

Drug-loaded nanoparticles for cancer therapy: a high-throughput multicellular agent-based modeling study

This study develops a multicellular agent-based model to simulate nanoparticle interactions in cancer therapy and evaluates how pharmacokinetic parameters and therapeutic strategies affect tumor dynamics.

PhysiGym: bridging the gap between the Gymnasium reinforcement learning application interface and the PhysiCell agent-based model software

PhysiGym integrates PhysiCell with Gymnasium to enable reinforcement learning control of in silico biological processes, demonstrating tumor elimination in a case study.

Digitize your Biology! Modeling multicellular systems through interpretable cell behavior

The paper introduces a framework for mathematical modeling of multicellular systems using interpretable cell behavior rules derived from biological knowledge and multi-omics data.

Open Benchmarking for Cell-Based Multiscale Models: Lessons from a Community Initiative

This paper presents a community-driven benchmarking initiative for cell-based multiscale models, highlighting variations in tool implementations and advocating for standardized benchmarks and interoperability.

A simple framework for agent-based modeling with extracellular matrix

The paper introduces a simplified agent-based framework for modeling cell-ECM interactions using PhysiCell, demonstrating its utility in various biological processes.

PhysiCell Studio: a graphical tool to make agent-based modeling more accessible

PhysiCell Studio is a graphical tool that simplifies the creation and editing of multicellular models by providing a user-friendly interface for XML-based model definition.

PhysiCell training apps: Cloud hosted open-source apps to learn cell-based simulation software

The paper introduces cloud-hosted open-source tools to help researchers learn cell-based simulation software through modular exploration of key components.

Iterative community-driven development of a SARS-CoV-2 tissue simulator

Open-source agent-based PhysiCell model of SARS-CoV-2 infection in lung epithelium; version 5 clears virus in about 6 days in simulation, and delayed T cell arrival increases epithelial loss.

xml2jupyter: Mapping parameters between XML and Jupyter widgets

xml2jupyter maps XML configuration files to Jupyter widgets, enabling interactive simulation parameter tuning.

Learning-accelerated Discovery of Immune-Tumour Interactions

The paper presents a framework combining agent-based simulation and active learning to discover optimal cancer regression regions in immunotherapy models.

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow

This paper introduces a high-throughput framework integrating PhysiCell and EMEWS to test cancer hypotheses through mechanistic simulations and optimize therapeutic strategies.

PhysiBoSS: a multi-scale agent based modelling framework integrating physical dimension and cell signalling

PhysiBoSS integrates multi-scale agent-based modelling with Boolean networks to study cell population dynamics and treatment responses in 2D and 3D environments.

PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems

Open source off-lattice agent-based C++ simulator PhysiCell, coupled to the BioFVM diffusion solver, simulates 3-D multicellular tissues with cost linear in cell number, reaching roughly 10^6 cells.