Tools Comparison

From BioUML platform
Revision as of 22:57, 2 May 2019 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 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
Personal tools
Namespaces

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