Difference between revisions of "Tools Comparison"

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|Model analysis
 
|Model analysis
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|Database access
 
|Database access
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|'''Formalism'''
 
|'''Formalism'''
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|Algebraic
 
|Algebraic
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|Discrete
 
|Discrete
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|Modular modeling
 
|Modular modeling
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|Combined formalisms
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|Agent-based
 
|Agent-based
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|SBML
 
|SBML
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| l3v2 import\export, all tests passed
+
| l3v2, all tests passed
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| l3v1 import\export, except algebraic
+
| l3v1 except algebraic
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| l3v1 import\export
+
| l3v2
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| l3v1 import\export
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| l3v1
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| l3v1 import]export
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| l3v1
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|
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| l3v1, partially
 
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|SBML comp
 
|SBML comp
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| import\export, all tests passed
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| fully, all tests passed
 
| -
 
| -
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| import\export, partially
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| +
 
| -
 
| -
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| partially
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| partially
 
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|SBGN
 
|SBGN
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|'''Programming Language'''
 
|'''Programming Language'''
 
| Java
 
| Java
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| C
+
| C++
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| Java
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| Java/C
 
| Java
 
| Java
 
| Python
 
| Python
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|
+
| C++
 
|}
 
|}

Latest revision as of 23:07, 28 February 2022

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
SBGN + export - + - -
SedML + - + - + -
SBOL - - + - - -
Antimony + (in standalone) - - - + -
Bionetgen + (in standalone) - - - - -
BioPAX + - - + - -
Availability
Windows + + + + + +
Linux + + + + + +
MacOS + + + + + +
Web application + - - - - -
Programming Language Java C++ Java/C Java Python C++
Retrieved from "https://wiki.biouml.org/index.php?title=Tools_Comparison&oldid=9491"
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