Specification of Cell Types Individual cells are the elementary
unit of our models. Nevertheless, they are not represented as
homogeneous bags in our framework. Instead we use Stochastic
P-systems (SP-systems) [Romero-Campero2009] as the computational
abstraction for an individual cell. The specification of an
individual cell consists of the following three main components:
- The molecular species (genes, RNAs, proteins, signals etc.)
present in the specific cell type are represented using string-
objects like proteinGFP, signal3OC6, etc. - The compartments
(cytoplasm, nucleus, mitochondria, etc) of individual cells as
well as some relevant regions related to individual cells (cell
surface, media surronding a cell, etc.) are defined using
membranes. The inclusion of compartments inside other
compartements as in the case of the nucleus being inside the
cytoplasm can also be specified. - The characteristic molecular
interactions taking place inside or between specific
compartments are described using rules where