Publishing a model in CellML to overcome the potential errors of manuscript translation


Richard Faville recently completed his PhD at the Auckland Bioengineering Institute, The University of Auckland where he studied electrical activity and smooth muscle contraction in the gut. One of the main objectives of his research was to develop a realistic mathematical model to quantitatively describe pacemaker activity in the interstitial cells of Cajal (ICC). These cells reside in the gastrointestinal tract where they act as a pacemaker to trigger smooth muscle contraction in the walls of the gut.

Richard’s model was developed in two stages

  1. The first model describes a single ICC pacemaker unit:null
  2. The second model embeds this pacemaker unit within a whole cell:null

The advantage of using CellML 1.1

This latter model was implemented in CellML 1.1, and represents an elegant example of how the import feature of CellML 1.1 can be used to reduce the size and complexity of a single model.  In this particular case, the cell and the pacemaker unit were defined as two separate files, and the pacemaker was imported into the cell ten times. This allowed Richard to avoid the need to duplicate the pacemaker code and create a monolithic single file.