Difference between revisions of "Tools Comparison"

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{| class="wikitable"
 
{| class="wikitable"
−
|+Simulation and modeling tools
+
|+
−
|Name
+
|
−
|Standards
+
−
|Capabilities
+
−
|Formalisms
+
−
|Type
+
−
|-
+
 
|BioUML
 
|BioUML
 +
|COPASI
 +
|iBioSim
 +
|CellDesigner
 +
|Tellurium
 +
|Morpheus
 +
|-
 +
|'''Capabilities'''
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|
 
|
−
|Standalone\web
 
 
|-
 
|-
−
|COPASI
+
|Model creation
 +
| visual\text-based
 +
| via tables
 +
| visual
 +
| visual
 +
| text-based
 +
| via tables
 +
|-
 +
|Simulation
 +
| +
 +
| +
 +
| +
 +
| via ext.tools
 +
| +
 +
| +
 +
|-
 +
|Parameter fitting
 +
| +
 +
| +
 +
| -
 +
| -
 +
| -
 +
| -
 +
|-
 +
|Model analysis
 +
| +
 +
| +
 +
| +
 +
| -
 +
| +
 +
| +
 +
|-
 +
|Database access
 +
| +
 +
| -
 +
| +
 +
| +
 +
| -
 +
| -
 +
|-
 +
|'''Formalism'''
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|
 
|
−
|Standalone
 
 
|-
 
|-
−
|iBioSim
+
|ODE
 +
| +
 +
| +
 +
| +
 +
| +
 +
| +
 +
| +
 +
|-
 +
|Stochastic Gillespie-type
 +
| +
 +
| +
 +
| +
 +
| +
 +
| +
 +
| +
 +
|-
 +
|Algebraic
 +
| +
 +
| -
 +
| +
 +
| -
 +
| +
 +
| +
 +
|-
 +
|Discrete
 +
| +
 +
| +
 +
| +
 +
| +
 +
| +
 +
| +
 +
|-
 +
|Modular modeling
 +
| +
 +
| -
 +
| +
 +
| -
 +
| +
 +
| +
 +
|-
 +
|Combined formalisms
 +
| +
 +
| -
 +
| +
 +
| -
 +
| -
 +
| +
 +
|-
 +
|Agent-based
 +
| +
 +
| -
 +
| +
 +
| -
 +
| -
 +
| -
 +
|-
 +
|Rule-based
 +
| +
 +
| -
 +
| -
 +
| -
 +
| -
 +
| -
 +
|-
 +
|Population-based
 +
| +
 +
| -
 +
| +
 +
| -
 +
| -
 +
| -
 +
|-
 +
|'''Standards'''
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|
 
|
−
|Standalone
+
|-
 +
|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++
 
|}
 
|}

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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