BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells
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.
Authors
- Robert A. Anders (ORCID: https://orcid.org/0000-0002-2363-9072)
- Elana J. Fertig (ORCID: https://orcid.org/0000-0003-3204-342X)
- Elizabeth M. Jaffee (ORCID: https://orcid.org/0000-0003-3841-6549)
- Heber L. Rocha (ORCID: https://orcid.org/0000-0002-5876-2644)
- Paul Macklin (ORCID: https://orcid.org/0000-0002-9925-0151)
- Dimitrios N. Sidiropoulos (ORCID: https://orcid.org/0000-0001-5716-3917)
- Randy Heiland (ORCID: https://orcid.org/0000-0002-7440-2905)
- Genevieve Stein-O’Brien (ORCID: https://orcid.org/0000-0001-8681-9110)
- Martin J. Booth (ORCID: https://orcid.org/0000-0002-9525-8981)
- Atul Deshpande (ORCID: https://orcid.org/0000-0001-5144-6924)
- Luciane T. Kagohara (ORCID: https://orcid.org/0000-0003-1706-0950)
- Tamara Y. Lopez-Vidal (ORCID: https://orcid.org/0000-0003-0618-7008)
- Marwa Naji
- Daniel Bergman (ORCID: https://orcid.org/0000-0002-2166-6616)
- Lei Zheng (ORCID: https://orcid.org/0000-0003-4163-2541)
- Jeanette Johnson
Institutions
- Human Genome Sciences (United States) (US)
- University of Maryland, Baltimore (US)
- Johns Hopkins University (US)
- Johns Hopkins Medicine (US)
- Johns Hopkins University Applied Physics Laboratory (US)
- Intelligent Systems Research (United States) (US)
- Indiana University Bloomington (US)
- National Institute of Mental Health (US)
- Sidney Kimmel Comprehensive Cancer Center (US)
Publication Details
- Journal
- Bioinformatics
- Published
- 2025-10-14
- DOI
- https://doi.org/10.1093/bioinformatics/btaf571
- Primary Topic
- Mathematical Biology Tumor Growth
- Type
- article
- Field-Weighted Citation Impact
- 0.00