ArticleMetabolomics : Official journal of the Metabolomic Society2024
Kiphynet: an online network simulation tool connecting cellular kinetics and physiological transport.
Article in Metabolomics : Official journal of the Metabolomic Society, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
introductionHuman metabolism is sustained by functional networks that operate at diverse scales. Capturing local and global dynamics in the human body by hierarchically bridging multi-scale functional networks is a major challenge in physiological modeling.
objectivesTo develop an interactive, user-friendly web application that facilitates the simulation and visualization of advection-dispersion transport in three-dimensional (3D) microvascular networks, biochemical exchange, and metabolic reactions in the tissue layer surrounding the vasculature.
methodsTo help modelers combine and simulate biochemical processes occurring at multiple scales, KiPhyNet deploys our discrete graph-based modeling framework that bridges functional networks existing at diverse scales. KiPhyNet is implemented in Python based on Apache web server using MATLAB as the simulator engine. KiPhyNet provides the functionality to assimilate multi-omics data from clinical and experimental studies as well as vascular data from imaging studies to investigate the role of structural changes in vascular topology on the functional response of the tissue.
resultsWith the network topology, its biophysical attributes, values of initial and boundary conditions, parameterized kinetic constants, biochemical species-specific transport properties such as diffusivity as inputs, a user can use our application to simulate and view the simulation results. The results of steady-state velocity and pressure fields and dynamic concentration fields can be interactively examined.
conclusionKiPhyNet provides barrier-free access to perform time-course simulation experiments by building multi-scale models of microvascular networks in physiology, using a discrete modeling framework. KiPhyNet is freely accessible at http://pallab.cds.iisc.ac.in/kiphynet/ and the documentation is available at https://deepamahm.github.io/kiphynet_docs/ .
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