Modeling Multiscale Control of Liver Regeneration Jan B. Hoek and Rajanikanth Vadigepalli Daniel Baugh Institute for Functional Genomics and Computational Biology Department of Pathology, Anatomy, and Cell Biology Thomas Jefferson University, Philadelphia, Pennsylvania
Laser Capture Cell Type Microdissection Resolution Hepatic stellate cell Hepatocyte Single Cell Transcriptomics Single Cell Transcriptomics Cell-level Network Modeling Spatial modeling of Lobular of Cell Activation Scale Function Modeling Multiscale Control of Liver Regeneration
Credibility Plan – organized along Ten Simple Rules* Modeling molecular and cellular interaction network controlling liver regeneration response to injury. Define Context 1 Specific details in the manuscripts. Single cell gene expression from multiple liver cell types; Spatial data from intravital Appropriate data 2 imaging; Noninvasive measures of liver growth and function Evaluate computational model for match to Evaluate within context physiological data from liver resection in 3 normal and alcoholic liver disease models Assumptions and expected applicability are List Limitations 4 detailed in the manuscripts * Committee on Credible Practice of Modeling and Simulation in Healthcare
Credibility Plan – organized along Ten Simple Rules* Version Control Manual and Limited; Need to systematize 5 Manual and developer-dependent; Need to Documentation 6 systematize Model code and documentation available via Dissemination manuscript supplement; Need to share 7 through a generalized resource (BioModels?) Members of lab not involved with project conduct independent review; Need to Independent Review 8 establish a systematic workflow for independent external review Test Implementations So far: Matlab, CompuCell3D, and SBML 9 Conform to the best practice standards of Conform to Standards 10 SBML and BioModels * Committee on Credible Practice of Modeling and Simulation in Healthcare
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