Difference between revisions of "Tools Comparison"
From BioUML platform
Ilya Kiselev (Talk | contribs) |
Ilya Kiselev (Talk | contribs) |
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| visual | | visual | ||
| visual | | visual | ||
| + | | text-based | ||
| via tables | | via tables | ||
| − | |||
|- | |- | ||
|Simulation | |Simulation | ||
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| + | | + | ||
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|- | |- | ||
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| + | | + | ||
| - | | - | ||
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|SBML | |SBML | ||
| − | | | + | | l3v2 import\export, all tests passed |
| − | | l3v1 import\export | + | | l3v1 import\export, except algebraic |
| l3v1 import\export | | l3v1 import\export | ||
| l3v1 import\export | | l3v1 import\export | ||
| − | | | + | | l3v1 import]export |
| | | | ||
|- | |- | ||
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| import\export, all tests passed | | import\export, all tests passed | ||
| - | | - | ||
| − | | import\export, | + | | import\export, partially |
| - | | - | ||
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| - | | - | ||
| - | | - | ||
| + | | + | ||
| - | | - | ||
| − | |||
|- | |- | ||
|SBOL | |SBOL | ||
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| - | | - | ||
| + | | + | ||
| − | | | + | | - |
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|Bionetgen | |Bionetgen | ||
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| - | | - | ||
| - | | - | ||
| − | | | + | | - |
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|BioPAX | |BioPAX | ||
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| + | | + | ||
| - | | - | ||
| − | | | + | | - |
|- | |- | ||
|'''Availability''' | |'''Availability''' | ||
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| + | | + | ||
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|- | |- | ||
|Linux | |Linux | ||
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| + | | + | ||
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|MacOS | |MacOS | ||
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| + | | + | ||
| + | | + | ||
| − | | | + | | + |
|- | |- | ||
|Web application | |Web application | ||
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| - | | - | ||
| - | | - | ||
| − | | | + | | - |
|- | |- | ||
|'''Programming Language''' | |'''Programming Language''' | ||
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| Java | | Java | ||
| Java | | Java | ||
| − | | | + | | Python |
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|} | |} | ||
Revision as of 23:09, 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 | 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 | + | - | + | - | + | |
| Agent-based | + | - | + | - | - | - |
| Rule-based | + | - | - | - | - | - |
| Population-based | + | - | - | - | - | - |
| Standards | ||||||
| SBML | l3v2 import\export, all tests passed | l3v1 import\export, except algebraic | l3v1 import\export | l3v1 import\export | l3v1 import]export | |
| SBML comp | import\export, all tests passed | - | import\export, 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 |
