TY - JOUR
T1 - The Open Physiology workflow
T2 - modeling processes over physiology circuitboards of interoperable tissue units
AU - de Bono, Bernard
AU - Safaei, Soroush
AU - Grenon, Pierre
AU - Nickerson, David P
AU - Alexander, Samuel
AU - Helvensteijn, Michiel
AU - Kok, Joost N
AU - Kokash, Natallia
AU - Wu, Alan
AU - Yu, Tommy
AU - Hunter, Peter
AU - Baldock, Richard A
PY - 2015/2/24
Y1 - 2015/2/24
N2 - 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/.
AB - 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/.
U2 - 10.3389/fphys.2015.00024
DO - 10.3389/fphys.2015.00024
M3 - Article
C2 - 25759670
SN - 1664-042X
VL - 6
SP - 24
JO - Frontiers in physiology
JF - Frontiers in physiology
ER -