Table 1 Feature and requirement summary of Narrator. Summary of Narrator features and requirements according to criteria used in [42], addressing systems requirements, cross-compatibility, diagrammatic user interfaces or analytical capabilities of the simulators.
From: Modeling biochemical transformation processes and information processing with Narrator
Type/Name of Criterion | Value of Criterion |
|---|---|
Website | |
Hardware requirements | ~10 MB disk space |
Input (model definition) | Diagrammatic |
Software requirements | JRE version 1.5 |
Operating System | OS independent |
Import | SBML |
Export | SBML |
Open source | Yes (Sourceforge) |
Systems Biology Workbench | No |
Graphical representation of multiple compartments | Yes |
Representation of interface reactions | Yes |
Representation of multiple reactant types | No |
Representation of regulatory interactions | Yes |
Automated network layout | No |
Library of predefined rate expressions | No |
Editable list of all parameters/initial conditions | No |
Implementation of non-integer stoichiometries | Yes |
Ordinary differential equations | Yes |
Partial differential equations | No |
Stochastic | Yes |
Automated set-up of compartmentalization | No |
Direct calculations of steady states | No |
Steady-state stability analysis | No |
Steady-state sensitivity analysis | No |
Time-dependent sensitivity analysis | No |
Automated parameter scanning | No |
Time-dependent perturbations | Yes |
Parameter estimation/optimization | No |