Difference between revisions of "Tools Comparison"

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|Model creation
 
|Model creation
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| visual\text-based
 
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|Simulation
 
|Simulation
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|Parameter fitting
 
|Parameter fitting
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|Model analysis
 
|Model analysis
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|Database access
 
|Database access
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|ODE
 
|ODE
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|Stochastic
 
|Stochastic
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|Algebraic
 
|Algebraic
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| -
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|Discrete
 
|Discrete
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|Modular modeling
 
|Modular modeling
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| -
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| -
 
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|Agent-based
 
|Agent-based
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| -
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| +
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| -
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| -
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| -
 
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|Rule-based
 
|Rule-based
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| -
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| -
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| -
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| -
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| -
 
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|Population-based
 
|Population-based
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| -
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| ?
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| -
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|'''Standards'''
 
|'''Standards'''
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|SBML
 
|SBML
 +
| l3v1 import\export, all tests passed
 +
| l3v1 import\export partially
 +
| l3v1
 
|
 
|
 
|
 
|
 
|
 
|
 +
|-
 +
|SBML comp
 +
| import\export, all tests passed
 +
| -
 +
| import\export, all tests passed
 
|
 
|
 
|
 
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|SBGN
 
|SBGN
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+
| +
 
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|SedML
 
|SedML
−
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+
| +
 
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|Antimony
 
|Antimony
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| + (in standalone)
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+
| -
−
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+
| -
 
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|Bionetgen
 
|Bionetgen
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| + (in standalone)
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+
| -
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|
+
| -
 
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|BioPAX
 
|BioPAX
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+
| +
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+
| -
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+
| -
 
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|Windows
 
|Windows
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+
|+
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|+
−
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+
|+
 
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|
 
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|-
 
|Linux
 
|Linux
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| +
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+
| +
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+
| +
 
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|
 
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|-
 
|-
 
|MacOS
 
|MacOS
−
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+
| +
−
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+
| +
−
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+
| +
 
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|
 
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|-
 
|-
 
|Web application
 
|Web application
−
|
+
| +
−
|
+
| -
−
|
+
| -
 
|
 
|
 
|
 
|
 
|
 
|
 
|-
 
|-
−
|'''Platform'''
+
|'''Programming Language'''
−
|
+
| Java
−
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+
| C
−
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+
| Java
 
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|}
 
|}

Revision as of 22:16, 2 May 2019

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
Simulation + + +
Parameter fitting + +
Model analysis + +
Database access + -
Formalism
ODE + + + + + +
Stochastic + + +
Algebraic + - +
Discrete + + +
Modular modeling + - + -
Agent-based + - + - - -
Rule-based + - - - - -
Population-based + -  ? - - -
Standards
SBML l3v1 import\export, all tests passed l3v1 import\export partially l3v1
SBML comp import\export, all tests passed - import\export, all tests passed
SBGN +
SedML +
Antimony + (in standalone) - -
Bionetgen + (in standalone) - -
BioPAX + - -
Availability
Windows
Linux + + +
MacOS + + +
Web application + - -
Programming Language Java C Java
Retrieved from "https://wiki.biouml.org/index.php?title=Tools_Comparison&oldid=8404"
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