Tools Comparison

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Revision as of 22:55, 28 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.


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 + - + - + +
Combined formalisms + - - - - +
Agent-based + - + - - -
Rule-based + - - - - -
Population-based + - - - - -
Standards
SBML l3v2, all tests passed l3v1 except algebraic l3v2 l3v1 l3v1 l3v1, partially
SBML comp fully, all tests passed - partially - partially 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 C++
Personal tools
Namespaces

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