This section explains basic architecture of Cellware and includes the layer architecture, structure of subsystems and class diagram of modelling and simulation environment.
7.5.1 Cellware Architecture
Figure 7-6 depicts the conceptual architecture of Cellware. The layer view of the architecture consisting of the Application Layer, Middle Layer and System Layer.
Figure 7-6: Cellware Architecture
7.5.2 Structure of Modeling and Simulation Environment
Cellware modelling and simulation environment consists of following four main subsystems:- Graphic editing subsystem
- 2D graph editor
- Model description template
- Model components/properties viewer
- Biological specification subsystem
- Gene specification editor
- Protein specification editor
- Modifier specification editor
- Metabolite specification editor
- MRNA specification editor
- Reaction specification editor
- I/O subsystem
- Cellware model input/output
- SBML model input/output
- Cellware model to printer
- Simulation subsystem
- Simulation setup editor
- Simulation submission and result acquirement from Grid
- Simulation real-time plotting on local
7.5.3 Class Diagram of Pathway Model
Genes, protein, modifiers, metabolites, mRNAs and reactions form a Cellware pathway model. Each of these constituent components of a pathway model possesses ample graphical and biological information. The graphical information is defined in parents' classes, and the biological information is store in the classes that aggregate to class CellWareModel. The class diagram is shown in Figure 7-7.
Figure 7-7: Class Diagram of Cellware Model
7.5.4 Object Structure of Algorithms Manager
Cellware Simulation Environment is implemented with consideration to future extension to the algorithms library. The Simulation Manager allows for plug-in algorithms to the library by inheriting methods from the public class TestTube. Figure 7.8 shows the class diagram of simulation environment.
Figure 7-8: Class Diagram of Simulation Environment