Table 2:
Functionalities provided by different web applications
| Web-based applications | JWS online | Virtual cell | PyBios | WebCell | SYCAMORE | BASIS |
|---|---|---|---|---|---|---|
| Network visualization | Static | Dynamic/Interactive | Dynamic | Dynamic | Dynamic | Dynamic |
| Reaction network validation | ✓ | ✓ | ||||
| Moiety conservation analysis | ✓ | ✓ | ||||
| Time-course analysis | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
| Metabolic control analysis (MCA) | ✓ | ✓ | ✓ | |||
| Pathway analysis | ✓ | |||||
| Parameter scanning | ✓ | ✓ | ||||
| Parameter estimation | ✓ | ✓ | ||||
| Mathematic framework | ODE | ODE/PDE | ODE | ODE/DAE | ODE | SDE |
| Link to public databases | KEGG/Swissprot | BRENDA/SABIO-RK | ||||
| Data exchange formats | ||||||
| Import | SBML | SBML | SBML | SBML | SBML | |
| Export | SBML | SBML/CellML/MATLAB | SBML | SBML/MATLAB | SBML |
SDE, stochastic differential equations.