COPASI and CellDesigner: Comparison

COPASI and CellDesigner are software packages for modelling and simulation of biochemical networks.

1. Common features

Models in both packages are based on compartments, species and reactions. Both packages have an area where the model tree is displayed, the area for entering and editing model parameters

2. Differences

2.1 CellDesigner

Networks are drawn based on the process diagram and are stored using SBML. CellDesigner supports a rich set of graphical elements for various compartments, species and reactions. There are predefines shapes for certain species, such as ‘truncated protein’ or ‘simple molecule’, or reactions, such as ‘transport’ or ‘dissociation’. Elements are added to the module by selecting them from a toolbar. Visual representation of the model is the strong advantage of CellDesigner. Figure 1 represents a model of MAPK-42 opened with CellDesigner. CellDesigner allows entering kinetic reactions by hand, but does not have predefined rate laws so they also have to be entered by hand for each reaction.

Figure 1 - CellDesigner with MAPK-42 model

2.2 COPASI

COPASI is less rich visually, but has advanced functionality for model simulation and analysis. The species are added to the model automatically by typing the attributes into the line in the list. Reactions can also be added directly by typing the chemical equation into the cell in the table. Unlike CellDesigner, COPASI has a number of predefined kinetic laws, can switch between stochastic and deterministic simulation methods and supports a number of methodologies for model analysis – computation of steady states, stoichiometric matrix, parameter estimation and optimisation. An important feature is the mathematical view where the model is described as a set of differential equations. Figure 2 represents the same model of MAPK-42 opened with COPASI, where differential equations are shown.

Figure 2 - COPASI with MAPK-42 model

3. SBML support

Both packages can read and write SBML, which is a file format for exchanging systems biology models. CellDesigner stores visual layout information in SBML annotations, but also has an option of exporting into ‘pure’ SBML in case conversion is required to a different software package which does not support annotations. CellDesigner can read and write SBML, and store rich enhanced functions as SBML annotations. COPASI converts its native model structure to SBML on exporting. Notes and annotations are preserved while importing and re-exporting as long as the objects that contains them is not deleted from the model.

4. Conclusion

While the strongest advantage of CellDesigner is the support for model building and editing via rich graphical representation, COPASI appears to be more suitable for simulation and analysis.

by Evgeny. Also posted on my website