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

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  • Bernard de Bono
  • Soroush Safaei
  • Pierre Grenon
  • David P Nickerson
  • Samuel Alexander
  • Michiel Helvensteijn
  • Joost N Kok
  • Natallia Kokash
  • Alan Wu
  • Tommy Yu
  • Peter Hunter
  • Richard A Baldock

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    Rights statement: Copyright © 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.

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http://journal.frontiersin.org/article/10.3389/fphys.2015.00024/full
Original languageEnglish
Pages (from-to)24
JournalFrontiers in physiology
Volume6
DOIs
Publication statusPublished - 24 Feb 2015

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/.

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