Difference between revisions of "Tools Comparison 2022"
From BioUML platform
Ilya Kiselev (Talk | contribs) |
Ilya Kiselev (Talk | contribs) |
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|- | |- | ||
| − | |Model creation | + | |1. Model creation |
| visual\text-based | | visual\text-based | ||
| via tables | | via tables | ||
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| via tables | | via tables | ||
|- | |- | ||
| − | |Simulation | + | |2. Simulation |
| + | | + | ||
| + | | + | ||
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| + | | + | ||
|- | |- | ||
| − | |Parameter fitting | + | |3. Parameter fitting |
| + | | + | ||
| + | | + | ||
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| - | | - | ||
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| − | |Model analysis | + | |4. Model analysis |
| + | | + | ||
| + | | + | ||
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| + | | + | ||
|- | |- | ||
| − | |Database access | + | |5. Database access |
| + | | + | ||
| - | | - | ||
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|- | |- | ||
| − | |ODE | + | |1. ODE |
| + | | + | ||
| + | | + | ||
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| + | | + | ||
|- | |- | ||
| − | |Stochastic Gillespie-type | + | |2. Stochastic Gillespie-type |
| + | | + | ||
| + | | + | ||
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| + | | + | ||
|- | |- | ||
| − | |Algebraic | + | |3. Algebraic |
| + | | + | ||
| - | | - | ||
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| + | | + | ||
|- | |- | ||
| − | |Discrete | + | |4. Discrete |
| + | | + | ||
| + | | + | ||
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| + | | + | ||
|- | |- | ||
| − | |Modular modeling | + | |5. Modular modeling |
| + | | + | ||
| - | | - | ||
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| + | | + | ||
|- | |- | ||
| − | | | + | |6. Mixed formalisms |
| + | | + | ||
| - | | - | ||
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| + | | + | ||
|- | |- | ||
| − | |Agent-based | + | |7. Agent-based |
| + | | + | ||
| - | | - | ||
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| - | | - | ||
|- | |- | ||
| − | |Rule-based | + | |8. Rule-based |
| + | | + | ||
| - | | - | ||
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| - | | - | ||
|- | |- | ||
| − | |Population-based | + | |9. Population-based |
| + | | + | ||
| - | | - | ||
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|- | |- | ||
| − | |SBML | + | |1. SBML |
| l3v2, all tests passed | | l3v2, all tests passed | ||
| l3v1 except algebraic | | l3v1 except algebraic | ||
| Line 156: | Line 156: | ||
| l3v1, partially | | l3v1, partially | ||
|- | |- | ||
| − | |SBML comp | + | |2. SBML comp |
| fully, all tests passed | | fully, all tests passed | ||
| - | | - | ||
| Line 164: | Line 164: | ||
| partially | | partially | ||
|- | |- | ||
| − | |SBGN | + | |3. SBGN |
| + | | + | ||
| export | | export | ||
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| - | | - | ||
|- | |- | ||
| − | |SedML | + | |4. SedML |
| + | | + | ||
| - | | - | ||
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| - | | - | ||
|- | |- | ||
| − | |Combine archive | + | |5. Combine archive |
| + | | + | ||
| + | | + | ||
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| + | | + | ||
|- | |- | ||
| − | |SBOL | + | |6. SBOL |
| - | | - | ||
| - | | - | ||
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| - | | - | ||
|- | |- | ||
| − | |Antimony | + | |7. Antimony |
| + (in standalone) | | + (in standalone) | ||
| - | | - | ||
| Line 204: | Line 204: | ||
| - | | - | ||
|- | |- | ||
| − | |Bionetgen | + | |8. Bionetgen |
| + (in standalone) | | + (in standalone) | ||
| - | | - | ||
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| - | | - | ||
|- | |- | ||
| − | |BioPAX | + | |9. BioPAX |
| + | | + | ||
| - | | - | ||
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|- | |- | ||
| − | |Windows | + | |1. Windows |
| + | | + | ||
| + | | + | ||
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| + | | + | ||
|- | |- | ||
| − | |Linux | + | |2. Linux |
| + | | + | ||
| + | | + | ||
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| + | | + | ||
|- | |- | ||
| − | |MacOS | + | |3. MacOS |
| + | | + | ||
| + | | + | ||
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| + | | + | ||
|- | |- | ||
| − | |Web application | + | |4. Web application |
| + | | + | ||
| - | | - | ||
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|- | |- | ||
|'''Programming Language''' | |'''Programming Language''' | ||
| − | | Java | + | | 1. Java |
| − | | C++ | + | | 2. C++ |
| − | | Java | + | | 3. Java |
| − | | Java | + | | 4. Java |
| − | | Python | + | | 5. Python |
| − | | C++ | + | | 6. C++ |
|} | |} | ||
Revision as of 15:30, 7 February 2022
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 | |
| 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 | + | - | + | + | - | - |
| Formalism | ||||||
| 1. ODE | + | + | + | + | + | + |
| 2. Stochastic Gillespie-type | + | + | - | + | + | + |
| 3. Algebraic | + | - | + | - | + | + |
| 4. Discrete | + | + | + | + | + | + |
| 5. Modular modeling | + | - | + | - | + | + |
| 6. Mixed formalisms | + | - | - | - | - | + |
| 7. Agent-based | + | - | + | - | - | - |
| 8. Rule-based | + | - | - | - | - | - |
| 9. 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. SBGN | + | export | - | + | - | - |
| 4. SedML | + | - | - | - | + | - |
| 5. Combine archive | + | + | + | + | + | + |
| 6. SBOL | - | - | + | - | - | - |
| 7. Antimony | + (in standalone) | - | - | - | + | - |
| 8. Bionetgen | + (in standalone) | - | - | - | - | - |
| 9. BioPAX | + | - | - | + | - | - |
| Availability | ||||||
| 1. Windows | + | + | + | + | + | + |
| 2. Linux | + | + | + | + | + | + |
| 3. MacOS | + | + | + | + | + | + |
| 4. Web application | + | - | - | - | - | - |
| Programming Language | 1. Java | 2. C++ | 3. Java | 4. Java | 5. Python | 6. C++ |
