Difference between revisions of "Tools Comparison"

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|Model creation
 
|Model creation
 
| visual\text-based
 
| visual\text-based
−
|
+
| via tables
−
|
+
| visual
−
|
+
| visual
−
|
+
| text-based
−
|
+
| via tables
 
|-
 
|-
 
|Simulation
 
|Simulation
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| +
 
| +
 
| +
 
| +
−
|
+
| via ext.tools
−
|
+
| +
−
|
+
| +
 
|-
 
|-
 
|Parameter fitting
 
|Parameter fitting
 
| +
 
| +
 
| +
 
| +
−
|  
+
| -
−
|
+
| -
−
|
+
| -
−
|
+
| -
 
|-
 
|-
 
|Model analysis
 
|Model analysis
 
| +
 
| +
 
| +
 
| +
−
|  
+
| +
−
|
+
| -
−
|
+
| +
−
|
+
| +
 
|-
 
|-
 
|Database access
 
|Database access
 
| +
 
| +
 
| -
 
| -
−
|
+
| +
−
|
+
| +
−
|
+
| -
−
|
+
| -
 
|-
 
|-
 
|'''Formalism'''
 
|'''Formalism'''
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| +
 
| +
 
|-
 
|-
−
|Stochastic
+
|Stochastic Gillespie-type
 +
| +
 +
| +
 +
| +
 
| +
 
| +
 
| +
 
| +
 
| +
 
| +
−
|
 
−
|
 
−
|
 
 
|-
 
|-
 
|Algebraic
 
|Algebraic
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| -
 
| -
 
| +
 
| +
−
|
+
| -
−
|
+
| +
−
|
+
| +
 
|-
 
|-
 
|Discrete
 
|Discrete
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| +
 
| +
 
| +
 
| +
−
|
+
| +
−
|
+
| +
−
|
+
| +
 
|-
 
|-
 
|Modular modeling
 
|Modular modeling
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| +
 
| +
 
| -  
 
| -  
−
|
+
| +
−
|
+
| +
 +
|-
 +
|Combined formalisms
 +
| +
 +
| -
 +
| +
 +
| -
 +
| -
 +
| +
 
|-
 
|-
 
|Agent-based
 
|Agent-based
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| +
 
| +
 
| -
 
| -
−
| ?
+
| +
 
| -
 
| -
 
| -
 
| -
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|-
 
|-
 
|SBML
 
|SBML
−
| l3v1 import\export, all tests passed
+
| l3v2, all tests passed
−
| l3v1 import\export partially
+
| l3v1 except algebraic
 +
| l3v2
 
| l3v1
 
| l3v1
−
|
+
| l3v1
−
|
+
| l3v1, partially
−
|
+
 
|-
 
|-
 
|SBML comp
 
|SBML comp
−
| import\export, all tests passed
+
| fully, all tests passed
 
| -
 
| -
−
| import\export, all tests passed
+
| +
−
|
+
| -
−
|
+
| partially
−
|
+
| partially
 
|-
 
|-
 
|SBGN
 
|SBGN
 
| +
 
| +
−
|
+
| export
−
|
+
| -
−
|
+
| +
−
|
+
| -
−
|
+
| -
 
|-
 
|-
 
|SedML
 
|SedML
 
| +
 
| +
−
|
+
| -
−
|
+
| +
−
|
+
| -
−
|
+
| +
−
|
+
| -
 +
|-
 +
|SBOL
 +
| -
 +
| -
 +
| +
 +
| -
 +
| -
 +
| -
 
|-
 
|-
 
|Antimony
 
|Antimony
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| -
 
| -
 
| -
 
| -
−
|
+
| -
−
|
+
| +
−
|
+
| -
 
|-
 
|-
 
|Bionetgen
 
|Bionetgen
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| -
 
| -
 
| -
 
| -
−
|
+
| -
−
|
+
| -
−
|
+
| -
 
|-
 
|-
 
|BioPAX
 
|BioPAX
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| -
 
| -
 
| -
 
| -
−
|
+
| +
−
|
+
| -
−
|
+
| -
 
|-
 
|-
 
|'''Availability'''
 
|'''Availability'''
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|-
 
|-
 
|Windows
 
|Windows
−
|+
+
| +
−
|+
+
| +
−
|+
+
| +
−
|
+
| +
−
|
+
| +
−
|
+
| +
 
|-
 
|-
 
|Linux
 
|Linux
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| +  
 
| +  
 
| +
 
| +
−
|
+
| +
−
|
+
| +
−
|
+
| +
 
|-
 
|-
 
|MacOS
 
|MacOS
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| +  
 
| +  
 
| +
 
| +
−
|
+
| +
−
|
+
| +
−
|
+
| +
 
|-
 
|-
 
|Web application
 
|Web application
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| -
 
| -
 
| -
 
| -
−
|
+
| -
−
|
+
| -
−
|
+
| -
 
|-
 
|-
 
|'''Programming Language'''
 
|'''Programming Language'''
 
| Java
 
| Java
−
| C
+
| C++
 +
| Java/C
 
| Java
 
| Java
−
|
+
| Python
−
|
+
| 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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