Tools Comparison 2022

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Revision as of 16:07, 7 February 2022 by Ilya Kiselev (Talk | contribs)

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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 libRoadRunner
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++
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox