Kiphynet: an online network simulation tool connecting cellular kinetics and physiological transport

Deepa Maheshvare, M and Charaborty, R and Haldar, S and Raha, S and Pal, D (2024) Kiphynet: an online network simulation tool connecting cellular kinetics and physiological transport. In: Metabolomics, 20 (5).

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Abstract

Introduction: Human 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. Objectives: To 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. Methods: To 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. Results: With 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. Conclusion: KiPhyNet 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/kiphynetdocs/. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2024.

Item Type:	Journal Article
Publication:	Metabolomics
Publisher:	Springer
Additional Information:	The copyright for this article belongs to Publisher
Keywords:	angiogenesis; Article; biochemistry; blood vessel; capillary density; capillary pressure; data visualization; diffusivity; discrete element analysis; dispersion; geometry; glioblastoma; human; kinetics; mathematical analysis; metabolism; microvasculature; morphology; online network simulation; physiology; simulation; skeletonization (surgical); spatiotemporal analysis; tumor microenvironment; biological model; computer simulation; Internet; kinetics; software; transport at the cellular level, Biological Transport; Computer Simulation; Humans; Internet; Kinetics; Models, Biological; Software
Department/Centre:	Division of Interdisciplinary Sciences > Computational and Data Sciences
Date Deposited:	09 Sep 2024 09:27
Last Modified:	09 Sep 2024 09:27
URI:	http://eprints.iisc.ac.in/id/eprint/86001

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