{"database":"FAIRDOMHub","file_versions":[],"scores":null,"additional":{"omics_type":["Models"],"submitter":["Lutz Brusch"],"full_dataset_link":["https://fairdomhub.org/models/320?version=1"],"ModelFormat":["SBML"],"submitter_affiliation":["Technische Universität Dresden"],"repository":["FAIRDOMHub"],"pubmed_abstract":["Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale models in biological terms and mathematical expressions rather than programming code. Its graphical user interface supports the entire workflow from model construction and simulation to visualization, archiving and batch processing.","Bile, the central metabolic product of the liver, is transported by the bile canaliculi network. The impairment of bile flow in cholestatic liver diseases has urged a demand for insights into its regulation. Here, we developed a predictive 3D multi-scale model that simulates fluid dynamic properties successively from the subcellular to the tissue level. The model integrates the structure of the bile canalicular network in the mouse liver lobule, as determined by high-resolution confocal and serial block-face scanning electron microscopy, with measurements of bile transport by intravital microscopy. The combined experiment-theory approach revealed spatial heterogeneities of biliary geometry and hepatocyte transport activity. Based on this, our model predicts gradients of bile velocity and pressure in the liver lobule. Validation of the model predictions by pharmacological inhibition of Rho kinase demonstrated a requirement of canaliculi contractility for bile flow in vivo. Our model can be applied to functionally characterize liver diseases and quantitatively estimate biliary transport upon drug-induced liver injury."],"pubmed_title":["Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology.","A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule."],"pubmed_authors":["Starruß Jörn J, de Back Walter W, Brusch Lutz L, Deutsch Andreas A","Meyer Kirstin K, Ostrenko Oleksandr O, Bourantas Georgios G, Morales-Navarrete Hernan H, Porat-Shliom Natalie N, Segovia-Miranda Fabian F, Nonaka Hidenori H, Ghaemi Ali A, Verbavatz Jean-Marc JM, Brusch Lutz L, Sbalzarini Ivo I, Kalaidzidis Yannis Y, Weigert Roberto R, Zerial Marino M"],"description_synonyms":["Mathematical Models and Simulations, Simulation, simulation., Computer Modeling, NPIPA, morpheus, NPIP"],"pubmed_title_synonyms":["Environments, Impact, Environmental Impact, Environmental, Impacts, Environmental Impacts, NPIPA, Systems., Biology, morpheus, NPIP"],"pubmed_abstract_synonyms":["visualization, dTAF[[II]]230, TAF[[II]]250, d230, NPIPA, single-organism developmental process, postnatal development, TAF200, l(3)84Ab, dTAFII250, growth and development, BG:DS00004.13, TAFII-250, TAF250/230, EfW1, Cell, Impact, dTAF230, Environmental, dmTAF[[II]]230, development, TAFII250, Workflows, dmTAF1, Taf230, morpheus, p230, TAF[[II]]250/230, Impacts, TFIID, Environmental Impacts, Work Flow, TAF250, Taf[[II]]250, Taf200, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, cel, cell, NPIP, postnatal growth, Taf1p, TAF[II]250, CG17603, Diffusions, TAF[[II]], Environmental Impact, dTAF250, reaction, DmelCG17603, Taf250, SR3-5, Environments, TAF, growth, Work Flows, batch., TAF230, TAF1"],"name_synonyms":["Mathematical Models and Simulations, Simulation, simulation., Computer Modeling, NPIPA, morpheus, NPIP"],"additional_accession":[]},"is_claimable":false,"name":"Morpheus: open source modelling and simulation framework for multicellular systems","description":"Morpheus: open source modelling and simulation framework for multicellular systems","dates":{"created":"2018-06-08","publication":"2018-06-08","submission":"2018-06-08","last_modified":"2018-06-08"},"accession":"320","cross_references":{"pubmed":["24443380","28330614"]}}