Difference between revisions of "Tools Comparison"
From BioUML platform
Ilya Kiselev (Talk | contribs) |
Ilya Kiselev (Talk | contribs) |
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|Model creation | |Model creation | ||
| visual\text-based | | visual\text-based | ||
| − | | | + | | via tables |
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| + | | + | ||
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|Parameter fitting | |Parameter fitting | ||
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| l3v1 import\export, all tests passed | | l3v1 import\export, all tests passed | ||
| l3v1 import\export partially | | l3v1 import\export partially | ||
| − | | l3v1 | + | | l3v1 import\export |
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| import\export, all tests passed | | import\export, all tests passed | ||
| − | | | + | | - |
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|SBGN | |SBGN | ||
| + | | + | ||
| − | | | + | | export |
| − | | | + | | - |
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|SedML | |SedML | ||
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|- | |- | ||
| + | |SBOL | ||
| + | | - | ||
| + | | - | ||
| + | | + | ||
| + | | _ | ||
| + | | _ | ||
| + | | _ | ||
|Antimony | |Antimony | ||
| + (in standalone) | | + (in standalone) | ||
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| - | | - | ||
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|Windows | |Windows | ||
| − | |+ | + | | + |
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| C | | C | ||
| Java | | Java | ||
| − | | | + | | Java |
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|} | |} | ||
Revision as of 22:29, 2 May 2019
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 | |||||||||||
| Simulation | + | + | + | + | + | ||||||||
| Parameter fitting | + | + | |||||||||||
| Model analysis | + | + | + | - | + | ||||||||
| Database access | + | - | + | - | |||||||||
| Formalism | |||||||||||||
| ODE | + | + | + | + | + | + | |||||||
| Stochastic | + | + | + | + | |||||||||
| Algebraic | + | - | + | ||||||||||
| Discrete | + | + | + | ||||||||||
| Modular modeling | + | - | + | - | + | ||||||||
| Agent-based | + | - | + | - | ? | - | |||||||
| Rule-based | + | - | - | - | - | - | |||||||
| Population-based | + | - | - | - | - | - | |||||||
| Standards | |||||||||||||
| SBML | l3v1 import\export, all tests passed | l3v1 import\export partially | l3v1 import\export | ||||||||||
| SBML comp | import\export, all tests passed | - | import\export, all tests passed | - | |||||||||
| SBGN | + | export | - | ||||||||||
| SedML | + | - | - | ||||||||||
| SBOL | - | - | + | _ | _ | _ | Antimony | + (in standalone) | - | - | - | + | |
| Bionetgen | + (in standalone) | - | - | - | |||||||||
| BioPAX | + | - | - | ? | |||||||||
| Availability | |||||||||||||
| Windows | + | + | + | + | |||||||||
| Linux | + | + | + | + | |||||||||
| MacOS | + | + | + | + | |||||||||
| Web application | + | - | - | - | |||||||||
| Programming Language | Java | C | Java | Java |
