Tools Comparison 2022
From BioUML platform
Revision as of 16:05, 7 February 2022 by Ilya Kiselev (Talk | contribs)
Here we collect information about similar software and their features in comparison with BioUML.
This comparison was made in February 2022. Previous was done in 2019 and is available at separate page Tools Comparison.
| BioUML | COPASI | iBioSim | CellDesigner | Tellurium | Morpheus | libRoadRunner | |||||||||
| Capabilities | |||||||||||||||
| 1. Model creation | visual\text-based | via tables | visual | visual | text-based | via tables | |||||||||
| 2. Simulation | + | + | + | via ext.tools | + | + | + | ||||||||
| 3. Parameter fitting | + | + | - | - | - | - | |||||||||
| 4. Model analysis | + | + | + | - | + | + | |||||||||
| 5. Database access | + | - | + | + | - | - | 6. Jupyter notebooks | + | - | + | + | - | - |
} | |
| Model formalism | |||||||||||||||
| 1. ODE | + | + | + | + | + | + | + | ||||||||
| 2. Stochastic Gillespie-type | + | + | - | + | + | + | + | ||||||||
| 3. Algebraic | + | - | + | - | + | + | |||||||||
| 4. Discrete | + | + | + | + | + | + | |||||||||
| 5. Flux balance | |||||||||||||||
| 6. Modular modeling | + | - | + | - | + | + | |||||||||
| 7. Mixed formalisms | + | - | - | - | - | + | |||||||||
| 8. Agent-based | + | - | + | - | - | - | |||||||||
| 9. Rule-based | + | - | - | - | - | - | |||||||||
| 10. Population-based | + | - | - | - | - | - | |||||||||
| Standards | |||||||||||||||
| 1. SBML | l3v2, all tests passed | l3v1 except algebraic | l3v1 | l3v1 | l3v1 | l3v1, partially | |||||||||
| 2. SBML comp | fully, all tests passed | - | partially | - | partially | partially | |||||||||
| 3. SBML fbc | fully, all tests passed | ||||||||||||||
| 4. SBGN PD | + | export | - | + | - | - | |||||||||
| 5. SBGN-ML PD | |||||||||||||||
| 6. SedML | + | + | - | - | + | - | |||||||||
| 7. Combine archive | |||||||||||||||
| 8. SBOL | - | - | + | - | - | - | |||||||||
| 9. Antimony | + (in standalone) | - | - | - | + | - | |||||||||
| 10. Bionetgen | + (in standalone) | - | - | - | - | - | |||||||||
| 11. BioPAX | + | - | - | + | - | - | |||||||||
| Availability | |||||||||||||||
| 1. Windows | + | + | + | + | + | + | |||||||||
| 2. Linux | + | + | + | + | + | + | |||||||||
| 3. MacOS | + | + | + | + | + | + | |||||||||
| 4. Web application | + | - | - | - | - | - | |||||||||
| Programming Language | Java | C++ | Java | Java | Python | C++ |
