Difference between revisions of "Tools Comparison"
From BioUML platform
Ilya Kiselev (Talk | contribs) |
Ilya Kiselev (Talk | contribs) |
||
| Line 23: | Line 23: | ||
| visual\text-based | | visual\text-based | ||
| via tables | | via tables | ||
| − | | | + | | visual |
| − | | | + | | visual |
| − | | | + | | via tables |
| − | | | + | | visual |
|- | |- | ||
|Simulation | |Simulation | ||
| Line 32: | Line 32: | ||
| + | | + | ||
| + | | + | ||
| − | | | + | | via ext.tools |
| + | | + | ||
| + | | + | ||
| Line 39: | Line 39: | ||
| + | | + | ||
| + | | + | ||
| − | | | + | | - |
| − | | | + | | - |
| − | | | + | | - |
| | | | ||
|- | |- | ||
| Line 56: | Line 56: | ||
| - | | - | ||
| + | | + | ||
| − | | | + | | + |
| | | | ||
| | | | ||
| Line 76: | Line 76: | ||
| + | | + | ||
|- | |- | ||
| − | |Stochastic | + | |Stochastic Gillespie-type |
| + | | + | ||
| + | | + | ||
| + | | - | ||
| + | | + | ||
| − | |||
| + | | + | ||
| | | | ||
| Line 144: | Line 144: | ||
| l3v1 import\export partially | | l3v1 import\export partially | ||
| l3v1 import\export | | l3v1 import\export | ||
| − | | | + | | l3v1 import\export |
| | | | ||
| | | | ||
| Line 160: | Line 160: | ||
| export | | export | ||
| - | | - | ||
| + | | + | ||
| | | | ||
| − | | | + | | - |
| − | + | ||
|- | |- | ||
|SedML | |SedML | ||
| Line 168: | Line 168: | ||
| - | | - | ||
| - | | - | ||
| − | | | + | | - |
| − | | | + | | - |
| | | | ||
|- | |- | ||
| Line 193: | Line 193: | ||
| - | | - | ||
| - | | - | ||
| − | | | + | | - |
| − | | | + | | |
|- | |- | ||
|BioPAX | |BioPAX | ||
| Line 200: | Line 200: | ||
| - | | - | ||
| - | | - | ||
| − | | | + | | + |
| − | | | + | | - |
| | | | ||
|- | |- | ||
| Line 217: | Line 217: | ||
| + | | + | ||
| + | | + | ||
| − | | | + | | + |
| | | | ||
|- | |- | ||
| Line 225: | Line 225: | ||
| + | | + | ||
| + | | + | ||
| − | | | + | | + |
| | | | ||
|- | |- | ||
| Line 233: | Line 233: | ||
| + | | + | ||
| + | | + | ||
| − | | | + | | + |
| | | | ||
|- | |- | ||
| Line 241: | Line 241: | ||
| - | | - | ||
| - | | - | ||
| − | | | + | |- |
| | | | ||
|- | |- | ||
Revision as of 22:53, 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 | via tables | visual |
| 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 | l3v1 import\export, all tests passed | l3v1 import\export partially | l3v1 import\export | 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 |
