A Multiscale Infectious Disease Modeling Framework using CompuCell3D

Indiana University, Bloomington Host-pathogen interactions of viral infection involve biophysical mechanisms and complex dynamics from the subcellular to organismal scales. Understanding, let alone predicting and mediating, the many potential mechanisms responsible for adverse patient outcomes requires modeling and simulation capabilities at multiple scales and in the context of interacting mechanisms that produce emergent patient outcomes. Building reliable predictive capabilities of the time course and outcomes of viral infection requires a broad range of expertise, from virology, immunology and basic cell biology, to mathematics, computer science and engineering. A modeling and simulation environment that serves as the computing infrastructure of such predictive capabilities must then support flexible, concurrent and easy development and deployment of interconnected model modules developed by multiple research groups that collectively describe the host-pathogen response. In this talk such a simulation framework is presented. The simulation framework implements models of infection and immune response mechanisms, from viral internalization, replication and release, to immune response signaling and recruitment, in a local tissue patch with cellular resolution. The simulation framework is built using CompuCell3D, a widely used modeling and simulation environment for building multiscale, multicellular simulations using the Python programming language. The framework formulates a simulation as a modular set of model modules, each of which is loaded from a publicly available model library during simulation specification. The framework architecture treats the model library as a set of importable modules that can be easily added into a simulation, deployed in other model modules, or extended by additional model modules. The model library, which is maintained by the Biocomplexity Institute at Indiana University, is publicly available on GitHub to support collaborative, community development by multiple groups working simultaneously on specific modeling projects within the total simulation framework. This talk presents select examples of framework extensibility and modularity, including the addition and extension of models of tissue repair, as well as the particularization of the framework to hepatitis C virus by implementation of an existing subgenomic model of hepatitis C virus replication. For more information see: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008451 If you found this video useful, please check out our other videos on computational modeling, infection and immunology: https://youtube.com/playlist?list=PLiEtieOeWbMKh9VcQoinSwODcSZKMTGat Please consider joining our IMAG/MSM WG on Multiscale Modeling and Viral Pandemics: https://www.imagwiki.nibib.nih.gov/content/msm-viral-pandemics-meetings Please also consider joining the Global Alliance for Immune Prediction and Intervention: http://glimprint.org/