Difference between revisions of "Tools Comparison 2022"

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Revision as of 15:28, 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
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 l3v1 l3v1 l3v1 l3v1, partially
SBML comp fully, all tests passed - partially - partially partially
SBGN + export - + - -
SedML + - - - + -
Combine archive + + + + + +
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