SBME Seminar: Simulation of Kidney Cystogenesis – Dr. James Glazier

SBME Seminar: Simulation of Kidney Cystogenesis – Dr. James Glazier

 
 
 
 
 
Seminar Abstract:
Bioengineering design requires the prediction of tissue dynamics. However, the difficulty of predicting the emergent development, homeostasis and disfunction of tissues from cells’ molecular signatures limits our ability to integrate molecular and genetic information to make meaningful predictions at the organ or organism level. Virtual Tissues are an approach to constructing quantitative, predictive mechanistic models starting from cell behaviors and combining subcellular molecular kinetics models, the physical and mechanical behaviors of cells and the longer-range effects of the extracellular environment. 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 and 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. For the past 20 years we have developed the open-source CompuCell3D modeling environment as a framework for the rapid development of complex multiscale Virtual Tissue Simulations. Virtual Tissue models help bridge the gap between molecule and physiological outcome. I will illustrate their use in a variety of contexts new and old focusing on epithelial organization, from the simulation of somite formation during development to epithelial homeostasis in the skin and the eye, kidney cystogenesis and developmental toxicology. I will also discuss the kinds of questions we can answer with Virtual Tissue models to gain scientific insight and for biomedical engineering applications. You can download CompuCell3D from https://compucell3d.org/SrcBin

For a list of recent papers published using CompuCell3D (ranging from toxicological perturbations of chicken embryonic development to the role of estrogen in muscle recovery after injury) see: https://compucell3d.org/Publications
 

Dr. Glazier Biography:
Dr. Glazier is Professor of Intelligent Systems Engineering and Director of the Biocomplexity Institute at Indiana University, Bloomington. He received his B.A. in Physics and Mathematics from Harvard University in 1983 and his Ph.D. in Physics from the University of Chicago in 1989. His research focuses on applying mechanistic, multiscale virtual-tissue computer simulations to understand embryonic development, homeostasis, toxicity and disease and to develop and optimize disease treatments. He leads the collaborative development of the open-source CompuCell3D (www.compucell3d.org) framework for the construction of mechanistic biomedical digital twins and actively disseminates these methods. He has worked extensively on community-building and model standards for multicellular modeling. He 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 Division of Biological Physics of the American Physical Society. He co-leads the IMAG/MSM Working Group on Multiscale Modeling and Viral Pandemics and is active in the development of infrastructure and community for the creation of biomedical digital twins. He recently co-founded GLIMPRINT (the Global Alliance for Immune Prediction and Intervention) which aims to support the development of immune digital twins.
 
Location:
LSC 1013