Model reuse with CellML - across 3 continents and timezones

null Frank Sachse is a Research Assistant Professor in the Bioengineering Department and Faculty Investigator at the Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah. His research involvement with CellML is in the context of electrophysiological modelling of fibroblasts and their electrical interaction with myocytes (muscle cells). This was a team effort between Auckland curator Catherine Lloyd, Oxford modeller and tool developer Alan Garny, and Frank.

The multistep process of model creation

  1. The first step involved Catherine translating Frank’s fibroblast model into CellML. The model was originally implemented in C++ and included in a software framework for biophysical simulation.
  2. In the second step, Frank took the existing Pandit et al. 2001 myocyte model from the CellML Model Repository and further curated it ... with a little help from Alan.
  3. In the third step, Frank merged the Pandit et al. 2001 myocyte model with his fibroblast model to produce a coupled myocyte-fibroblast model.
  4. In the fourth and final step, Catherine used the simulation tools PCEnv (now known as OpenCell) and COR to curate the coupled model – removing duplicated connections, fixing unit definitions, etc.



Schematic of the coupled myocyte-fibroblast model.

The result of this multi-step process is a real example of how CellML can be applied to reuse existing models, and develop them further to produce a new, more complex models.