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The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units

de Bono, B; Safaei, S; Grenon, P; Nickerson, DP; Alexander, S; Helvensteijn, M; Kok, JN; ... Baldock, RA; + view all (2015) The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units. Front Physiol , 6 (24) 10.3389/fphys.2015.00024. Green open access

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Abstract

A key challenge for the physiology modeling community is to enable the searching, objective comparison and, ultimately, re-use of models and associated data that are interoperable in terms of their physiological meaning. In this work, we outline the development of a workflow to modularize the simulation of tissue-level processes in physiology. In particular, we show how, via this approach, we can systematically extract, parcellate and annotate tissue histology data to represent component units of tissue function. These functional units are semantically interoperable, in terms of their physiological meaning. In particular, they are interoperable with respect to [i] each other and with respect to [ii] a circuitboard representation of long-range advective routes of fluid flow over which to model long-range molecular exchange between these units. We exemplify this approach through the combination of models for physiology-based pharmacokinetics and pharmacodynamics to quantitatively depict biological mechanisms across multiple scales. Links to the data, models and software components that constitute this workflow are found at http://open-physiology.org/.

Type: Article
Title: The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units
Location: Switzerland
Open access status: An open access version is available from UCL Discovery
DOI: 10.3389/fphys.2015.00024
Publisher version: http://dx.doi.org/10.3389/fphys.2015.00024
Language: English
Additional information: © 2015 de Bono, Safaei, Grenon, Nickerson, Alexander, Helvensteijn, Kok, Kokash, Wu, Yu, Hunter and Baldock. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. http://creativecommons.org/licenses/by/4.0/
Keywords: ApiNATOMY, fluid flow modeling, functional tissue units, histology, physiology circuit-boarding, physiology-based pharmacokinetics, visual knowledge management
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Pop Health Sciences > Institute of Health Informatics
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Pop Health Sciences > Institute of Health Informatics > CHIME
URI: http://discovery.ucl.ac.uk/id/eprint/1469964
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