{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T15:29:52Z","timestamp":1781105392149,"version":"3.54.1"},"reference-count":14,"publisher":"IGI Global Scientific Publishing","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,7,1]]},"abstract":"<p>Multi-scale modeling of complex biological systems remains a central challenge in the systems biology community. A method of dynamic knowledge representation known as agent-based modeling enables the study of higher level behavior emerging from discrete events performed by individual components. With the advancement of computer technology, agent-based modeling has emerged as an innovative technique to model the complexities of systems biology. In this work, the authors describe SPARK (Simple Platform for Agent-based Representation of Knowledge), a framework for agent-based modeling specifically designed for systems-level biomedical model development. SPARK is a stand-alone application written in Java. It provides a user-friendly interface, and a simple programming language for developing Agent-Based Models (ABMs). SPARK has the following features specialized for modeling biomedical systems: 1) continuous space that can simulate real physical space; 2) flexible agent size and shape that can represent the relative proportions of various cell types; 3) multiple spaces that can concurrently simulate and visualize multiple scales in biomedical models; 4) a convenient graphical user interface. Existing ABMs of diabetic foot ulcers and acute inflammation were implemented in SPARK. Models of identical complexity were run in both NetLogo and SPARK; the SPARK-based models ran two to three times faster.<\/p>","DOI":"10.4018\/jats.2010070102","type":"journal-article","created":{"date-parts":[[2010,9,7]],"date-time":"2010-09-07T20:03:51Z","timestamp":1283889831000},"page":"18-30","source":"Crossref","is-referenced-by-count":19,"title":["SPARK"],"prefix":"10.4018","volume":"2","author":[{"given":"Alexey","family":"Solovyev","sequence":"first","affiliation":[{"name":"University of Pittsburgh, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxim","family":"Mikheev","sequence":"additional","affiliation":[{"name":"University of Pittsburgh, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leming","family":"Zhou","sequence":"additional","affiliation":[{"name":"University of Pittsburgh, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joyeeta","family":"Dutta-Moscato","sequence":"additional","affiliation":[{"name":"University of Pittsburgh, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cordelia","family":"Ziraldo","sequence":"additional","affiliation":[{"name":"University of Pittsburgh, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary","family":"An","sequence":"additional","affiliation":[{"name":"University of Chicago and University of Pittsburgh, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoram","family":"Vodovotz","sequence":"additional","affiliation":[{"name":"University of Pittsburgh, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Mi","sequence":"additional","affiliation":[{"name":"University of Pittsburgh, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2432","reference":[{"key":"jats.2010070102-0","doi-asserted-by":"publisher","DOI":"10.1097\/00024382-200116040-00006"},{"key":"jats.2010070102-1","author":"G.An","year":"2004","journal-title":"Innate Immune Response"},{"key":"jats.2010070102-2","doi-asserted-by":"publisher","DOI":"10.1097\/01.CCM.0000139707.13729.7D"},{"key":"jats.2010070102-3","doi-asserted-by":"publisher","DOI":"10.1097\/BCR.0b013e31816677c8"},{"key":"jats.2010070102-4","doi-asserted-by":"publisher","DOI":"10.1002\/wsbm.45"},{"key":"jats.2010070102-5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000294"},{"key":"jats.2010070102-6","doi-asserted-by":"crossref","unstructured":"Bankes, S. C. (2002) Agent-based modeling: a revolution? In Proceedings of the Natl Acad Sci USA (pp. 7199-7200).","DOI":"10.1073\/pnas.072081299"},{"key":"jats.2010070102-7","doi-asserted-by":"crossref","unstructured":"Bonabeau, E. (2002). Agent-based modeling: methods and techniques for simulating human systems. In Proceedings of the Natl Acad Sci (pp. 7280-7287).","DOI":"10.1073\/pnas.082080899"},{"key":"jats.2010070102-8","doi-asserted-by":"publisher","DOI":"10.1126\/science.1116681"},{"key":"jats.2010070102-9","doi-asserted-by":"crossref","unstructured":"Inchiosa, M. E., & Parker, M. T. (2002). Overcoming design and development challenges in agent-based modeling using ASCAPE. In Proceeding of the Natl Acad Sci (pp. 7304-7308).","DOI":"10.1073\/pnas.082081199"},{"key":"jats.2010070102-10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0002789"},{"key":"jats.2010070102-11","unstructured":"Luke, S., Balan, G. C., Panait, L., Claudio, C. R., & Paus, S. (2003). 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