{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T20:41:54Z","timestamp":1775940114487,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T00:00:00Z","timestamp":1760572800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Cancer Institute \u2013 Cancer Center Support"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>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\u2013immune dynamics and spatial clustering, positioning BIWT as a software suite to generate data-driven virtual cells representing both experimental and clinical contexts.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf571","type":"journal-article","created":{"date-parts":[[2025,10,14]],"date-time":"2025-10-14T13:46:00Z","timestamp":1760449560000},"source":"Crossref","is-referenced-by-count":1,"title":["BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2166-6616","authenticated-orcid":false,"given":"Daniel R","family":"Bergman","sequence":"first","affiliation":[{"name":"Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University , Baltimore, MD, 21218,","place":["United States"]},{"name":"Convergence Institute, Johns Hopkins University , Baltimore, MD, 21218,","place":["United States"]},{"name":"Institute for Genome Sciences, 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21218,","place":["United States"]},{"name":"Convergence Institute, Johns Hopkins University , Baltimore, MD, 21218,","place":["United States"]},{"name":"Department of Pathology, Johns Hopkins University , Baltimore, MD, 21231,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University , Baltimore, MD, 21218,","place":["United States"]},{"name":"Convergence Institute, Johns Hopkins University , Baltimore, MD, 21218,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elizabeth M","family":"Jaffee","sequence":"additional","affiliation":[{"name":"Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University , Baltimore, MD, 21218,","place":["United States"]},{"name":"Convergence Institute, Johns Hopkins University , Baltimore, MD, 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