Requirements for simulation of intracellular signalling pathways

Computational representation/abstractions and algorithms of the BTSSOC framework

Computational Abstraction

Tuple Spaces

Representation of intracellular compartments

Tuple centres

Representation of signalling components (i.e., membrane receptors, proteins, enzymes, and genes)

Chemical reaction sets

Representation of signalling molecules (i.e., first and secondary messengers), activation and deactivation signals

Reactants and concentrations recorded as tuples in the tuple centre

Type of chemical reaction allowed

  1. Collaborative activation
  2. Alternative activation
  3. Complex formation
  4. Decomposition reactions
  5. Standard equation for enzymatic reaction
  6. Interaction from and to extracellular space

Model of chemical reactions

Discrete system model

Action selection mechanism for chemical reactions

Gillespie algorithm [13] – an algorithm typically used to simulate systems of chemical/biochemical reactions efficiently and accurately – to execute chemical reactions with the proper rate.

User interaction and visualization of the simulation

Graphical user interfaces, viewer components, graphical components

Table 1: Mapping requirements for simulation of intracellular signaling pathways onto BTSSOC abstractions.