The main long-term goal of the UC Riverside Interdisciplinary Center for Data-driven Modeling in Biology (ICDMB) is to develop comprehensive predictive data-driven models of complex biological systems. All projects at this center combine quantitative experiments, novel image analysis, modeling and statistical approaches, and build upon the mutually complementary strength of the researchers at UC Riverside with support from collaborators at other institutions.
Center News & Events
Colloquium - Multi-Scale, Multicellular, Agent-Based Virtual-Tissue Simulations of Development,
Homeostasis and Disease
Tuesday | March 10th, 2026 | 2:00pm – 3:20pm | Skye 284
Dr. James A. Glazier
Professor
Department of Intelligent Systems Engineering
Director, Biocomplexity Institute
Indiana University, Bloomington
Abstract: Multi-scale, Multicellular Agent-Based Virtual-Tissue models are versatile tools for exploring how the complex interactions between cells and their local environment and between that environment of Development, Homeostasis and Diseaseand signaling and regulatory control lead to patterning during development, maintenance of tissues
during homeostasis and recovery after injury and failure of tissue organization and function due to damage or disease. This talk explores the evolution and application of multiscale, multicellular agent-based "Virtual Tissues" using the CompuCell3D (CC3D) modeling environment. The CC3D project originated more than 25 years ago in a collaboration between Dr. Glazier, Dr. Mark Alber and others at the University of Notre Dame under an NSF Biocomplexity grant. I will talk a bit about the history of the methodology and its strengths and limitations and then illustrate its use in a variety of contexts new and old, from the simulation of somite formation during development to epithelial homeostasis,
vascular invasion and kidney cystogenesis. I will highlight two recent applications of this approach. First, a computational model of neural tube closure defects, demonstrating how transcriptomics-driven perturbations can be mapped onto conserved pathways to enable probabilistic hazard assessment of developmental failure. Second, adult-tissue Virtual-Tissue toxicology models of the cornea (vCornea). I am particularly interested in suggestions for extensions and improvements around the core CPM formalism and for potential novel applications. You can download CompuCell3D from https://compucell3d.org/SrcBin
For a list of recent papers published using CompuCell3D see: https://compucell3d.org/Publications
Bio: James A. Glazier, PhD, is Professor of Intelligent Systems Engineering and a Director of the Biocomplexity Institute at Indiana University Bloomington. He develops physics-based, mechanistic multicellular “Virtual Tissue” simulations that link molecular and cellular perturbations to emergent tissue injury, repair, and disease phenotypes, with a growing emphasis on New Approach Methodologies (NAMs) and in vitro–to–in vivo extrapolation (IVIVE) for toxicology and drug discovery.
Glazier is a founder and long-term lead developer of CompuCell3D, an open-source, multiscale agent-based modeling environment that supports simulations of development, cancer, immune processes,and tissue repair. His work emphasizes enabling broad reuse of models through durable software infrastructure, documentation, and training, including an ongoing international workshop program on multiscale virtual-tissue modeling. Glazier also leads community efforts that connect mechanistic
modeling to translational needs, including the GLIMPRINT-NIH IMAG/MSM Working Group on Multiscale Modeling and Viral Pandemics partnership, which encourages multiscale immune modeling, standards, validation, and model reuse, and OpenVT, an NSF-funded initiative to create a FAIR, interoperable ecosystem for virtual tissue models and to reproducible modeling practices.
Glazier is a Fellow of the American Association for the Advancement of Science, the American Physical Society and the Institute of Physics (London), and has served as Chair of the APS Division of Biological Physics.
Sixth Biological Diffusion and Brownian Dynamics Brainstorm
Biological Diffusion and Brownian Dynamics Brainstorm 6 (BDBDB6) is an online workshop dedicated to exploring and informally discussing the latest experimental and theoretical advances in biological diffusion. This event will emphasize the Brownian Dynamics method and its applications in simulating biological macromolecules. Building on a tradition that began in 2007, the BDBDB series has been held periodically, with the most recent event taking place in 2021.
December 11th & 12th 2025
15th Annual Southern California Systems Biology Symposium
Colloquium - November 12th 2025
Mathematical modeling in cancer research:
How to build, validate, and apply models with biologists and clinicians
Prof. Russel Rockne, City of Hope
Colloquium - October 8th 2025
Reverse engineering morphogenesis through the integration of
quantitative experiments and multi-scale computational modeling
Dr. Jeremiah Zartman, Notre Dame
The 14th Annual Southern California Systems Biology Symposium (SoCal SysBio 2025)
Saturday, May 10th, 2025
Join us for the 14th Annual Southern California Systems Biology Symposium (SoCal SysBio 2025), a premier event bringing together researchers from across Southern California to share cutting-edge research, foster community, and stimulate collaborations. This event will provide an opportunity for research groups from academic campuses and hospitals across Southern California to present their latest findings and promote collaborations in all areas of Systems and Computational Biology involving data-driven computational and machine learning modeling. This symposium will feature:
- Invited Talks from leading experts in systems and computational biology
- Lightning Talks for concise, impactful presentations
- Poster Session showcasing the work of graduate students and postdoctoral researchers