Model reuse with CellML: The Sachse myocytefibroblast model

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Model reuse with CellMLThe Sachse
myocyte-fibroblast model (3 continents time
zones!) Frank B. Sachse Nora Eccles Harrison
Cardiovascular Research and Training
Institute, University of Utah, US Catherine
Lloyd, James Lawson The Auckland Bioengineering
Institute, University of Auckland, NZ Alan
Garny Department of Physiology, Anatomy
Genetics, University of Oxford, UK
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Cardiac modeling and simulation
Research is based on previously developed
models. Significant effort spent in
re-implementation of models.
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Step 1 Catherine Lloyd (Auckland) translated
the fibroblast model into CellML 3 hours
(Sachse et al., Ann Biomed Eng, 36(1)41-56, 2008)
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Step 2 Frank Sachse (Utah) took the existing
Pandit myocyte model from the CellML Model
Repository and further curated it with a little
help from Alan Garny (Oxford) 2-3 days
(Pandit et al., Biophys J, 81(6)3029-51, 2001)
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Step 3 Frank Sachse (Utah) merged the
Pandit myocyte model with the fibroblast model to
produce a coupled myocyte-fibroblast model 2
days
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Step 4 Model Curation Catherine Lloyd
(Auckland) used the simulation tools PCEnv and
COR to curate the coupled model removing
duplicated connections, fixing unit definitions,
etc 1 hour
With the help of Frank Sachse (Utah), James
Lawson (Auckland) fixed the units so the model
ran in all three simulation tools JSIM, PCEnv
and COR 2-3 days
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Step 5 James Lawson (Auckland) created a PCEnv
session file for the coupled model 4 hours
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Step 6 (Future) Decomposition of the coupled
myocyte-fibroblast model and its translation into
CellML 1.1

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which will facilitate the duplication of the
fibroblast model and the connection of multiple
cells
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Step 7 (Future) And even further decomposition
of the model into its constituents - channels,
pumps, and intracellular calcium fluxes - as we
build a library of reusable components.
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Acknowledgments
Frank Sachse(Utah) Catherine Lloyd (Auckland) J
ames Lawson (Auckland) Alan Garny(Oxford)