Tools Comparison
From BioUML platform
Revision as of 22:59, 28 February 2022 by Ilya Kiselev (Talk | contribs)
Here we collect information about similar software and their features in comparison with BioUML.
| BioUML | COPASI | iBioSim | CellDesigner | Tellurium | Morpheus | |
| Capabilities | ||||||
| Model creation | visual\text-based | via tables | visual | visual | text-based | via tables |
| Simulation | + | + | + | via ext.tools | + | + |
| Parameter fitting | + | + | - | - | - | - |
| Model analysis | + | + | + | - | + | + |
| Database access | + | - | + | + | - | - |
| Formalism | ||||||
| ODE | + | + | + | + | + | + |
| Stochastic Gillespie-type | + | + | + | + | + | + |
| Algebraic | + | - | + | - | + | + |
| Discrete | + | + | + | + | + | + |
| Modular modeling | + | - | + | - | + | + |
| Combined formalisms | + | - | + | - | - | + |
| Agent-based | + | - | + | - | - | - |
| Rule-based | + | - | - | - | - | - |
| Population-based | + | - | + | - | - | - |
| Standards | ||||||
| SBML | l3v2, all tests passed | l3v1 except algebraic | l3v2 | l3v1 | l3v1 | l3v1, partially |
| SBML comp | fully, all tests passed | - | + | - | partially | partially |
| SBGN | + | export | - | + | - | - |
| SedML | + | - | + | - | + | - |
| SBOL | - | - | + | - | - | - |
| Antimony | + (in standalone) | - | - | - | + | - |
| Bionetgen | + (in standalone) | - | - | - | - | - |
| BioPAX | + | - | - | + | - | - |
| Availability | ||||||
| Windows | + | + | + | + | + | + |
| Linux | + | + | + | + | + | + |
| MacOS | + | + | + | + | + | + |
| Web application | + | - | - | - | - | - |
| Programming Language | Java | C++ | Java | Java | Python | C++ |
