Difference between revisions of "Tools Comparison 2022"

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Here we collect information about similar software and their features in comparison with BioUML.<br.\>
 
Here we collect information about similar software and their features in comparison with BioUML.<br.\>
 
This comparison was made in February 2022. Previous was done in 2019 and is available at separate page [[Tools Comparison]].
 
This comparison was made in February 2022. Previous was done in 2019 and is available at separate page [[Tools Comparison]].
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Support of SBML standard can be measured by percentage of passed tests from test suite presented on SBML [http://raterule.caltech.edu/Facilities/Database/Simulator web site].<br> 
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Extensive comparison of different simulators according to their speed and % of passed SBML tests can be found in <ref>Maggioli, F., Mancini, T., Tronci, E. (2020). SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems. Bioinformatics, 36(7), 2165-2172. {{doi|https://doi.org/10.1093/bioinformatics/btz860}}</ref>
  
 
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==References==
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<References/>

Revision as of 16:45, 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.

Support of SBML standard can be measured by percentage of passed tests from test suite presented on SBML web site.
Extensive comparison of different simulators according to their speed and % of passed SBML tests can be found in [1]

BioUML COPASI iBioSim CellDesigner Tellurium Morpheus libRoadRunner
Link http://wiki.biouml.org/ http://copasi.org/ https://async.ece.utah.edu/tools/ibiosim/ https://www.celldesigner.org/ https://tellurium.analogmachine.org/ https://morpheus.gitlab.io/ http://libroadrunner.org/
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 + - + + - -
6. Jupyter notebooks + - + + - -
Model formalism
1. ODE + + + + + + +
2. Stochastic Gillespie-type + + - + + + +
3. Algebraic + - + - + +
4. Discrete + + + + + +
5. Flux balance
6. Modular modeling + - + - + +
7. Mixed formalisms + - - - - +
8. Agent-based + - + - - -
9. Rule-based + - - - - -
10. 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. SBML fbc fully, all tests passed
4. SBGN PD + export - + - -
5. SBGN-ML
6. SedML + + - - + -
7. Combine archive
8. SBOL - - + - - -
9. Antimony + (in standalone) - - - + -
10. Bionetgen + (in standalone) - - - - -
11. BioPAX + - - + - -
Availability
1. Windows + + + + + +
2. Linux + + + + + +
3. MacOS + + + + + +
4. Web application + - - - - -
Programming Language Java C++ Java Java Python C++

References

  1. ↑ Maggioli, F., Mancini, T., Tronci, E. (2020). SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems. Bioinformatics, 36(7), 2165-2172. doi:https://doi.org/10.1093/bioinformatics/btz860
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