ZIH Colloquium: Virtual Biological Tissue Simulations and Standards - Opportunities and Challenges

Virtual Biological Tissue Simulations and Standards - Opportunities and Challenges

Current cell atlas projects are generating exceptionally detailed series of snapshots of the molecular states of individual biological cells, and the spatial context of those cells in a variety of normal and abnormal tissues. However, using those atlases to generate biological understanding or to develop therapeutic interventions requires a practical way to generate dynamic virtual-tissue simulations (VTs) from these big data. VTs depend on the ability to take experimental spatial images, populate them with computational model components from repositories and to customize the states and parameters of those components from experimental data.
Unfortunately, we are far from being able to do most of these steps, largely because current computational models do not correspond to what we know about biological modularity or separate the underlying biological concepts and hypotheses from methodological details of implementation. Moreover, current software tools are not designed as interoperable components. As a result, a researcher trying to reuse a computational biology result often needs to try to extract the underlying biological model from incomplete specifications in publications and then translate it into a new mathematical and/or computational instantiation. Based on more than a century of experiences with our popular software CompuCell3D, we outline the success stories as well as difficulties in building and applying VTs and discuss possible areas of progress.

Prof. Dr. Glazier received his B.A. in Physics and Mathematics from Harvard University and his M.S. and Ph.D. in Physics from the University of Chicago. Dr. Glazier’s research focuses on embryonic development, developmental and chronic toxicity and developmental diseases. He leads the collaborative development of the open-source CompuCell3D multi-scale modeling and model-sharing environment. In 2016, he became one of the founding members of Indiana University’s Department of Intelligent Systems Engineering, which aims to apply advanced computing techniques to understand and control complex natural and engineered emergent systems.