Difference between revisions of "Tools Comparison"
From BioUML platform
Ilya Kiselev (Talk | contribs) |
Ilya Kiselev (Talk | contribs) |
||
| (3 intermediate revisions by one user not shown) | |||
| Line 79: | Line 79: | ||
| + | | + | ||
| + | | + | ||
| − | | | + | | + |
| + | | + | ||
| + | | + | ||
| Line 111: | Line 111: | ||
| + | | + | ||
| - | | - | ||
| − | | | + | | + |
| - | | - | ||
| - | | - | ||
| Line 135: | Line 135: | ||
| + | | + | ||
| - | | - | ||
| − | | | + | | + |
| - | | - | ||
| - | | - | ||
| Line 159: | Line 159: | ||
| fully, all tests passed | | fully, all tests passed | ||
| - | | - | ||
| − | | | + | | + |
| - | | - | ||
| partially | | partially | ||
| Line 255: | Line 255: | ||
| Java | | Java | ||
| C++ | | C++ | ||
| − | | Java | + | | Java/C |
| Java | | Java | ||
| Python | | Python | ||
| C++ | | C++ | ||
|} | |} | ||
Latest revision as of 23:07, 28 February 2022
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/C | Java | Python | C++ |
