Difference between revisions of "Tools Comparison 2022"

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|Tellurium
 
|Tellurium
 
|Morpheus
 
|Morpheus
 +
|libRoadRunner
 
|-
 
|-
 
|'''Capabilities'''
 
|'''Capabilities'''
 +
|
 
|
 
|
 
|
 
|
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| text-based
 
| text-based
 
| via tables
 
| via tables
 +
|
 
|-
 
|-
 
|2. Simulation
 
|2. Simulation
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| +
 
| +
 
| via ext.tools
 
| via ext.tools
 +
| +
 
| +
 
| +
 
| +
 
| +
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| -
 
| -
 
| -
 
| -
 +
|
 
|-
 
|-
 
|4. Model analysis
 
|4. Model analysis
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| +
 
| +
 
| +
 
| +
 +
|
 
|-
 
|-
 
|5. Database access
 
|5. Database access
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| -
 
| -
 
| -
 
| -
 +
|
 
|-
 
|-
 
|'''Formalism'''
 
|'''Formalism'''
 +
|
 
|
 
|
 
|
 
|
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|-
 
|-
 
|1. ODE
 
|1. ODE
 +
| +
 
| +
 
| +
 
| +
 
| +
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| +
 
| +
 
| -
 
| -
 +
| +
 
| +
 
| +
 
| +
 
| +
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| +
 
| +
 
| +
 
| +
 +
|
 
|-
 
|-
 
|4. Discrete
 
|4. Discrete
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| +
 
| +
 
| +
 
| +
 +
|
 
|-
 
|-
 
|5. Flux balance
 
|5. Flux balance
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|  
 
|  
 
|  
 
|  
 +
|
 
|-
 
|-
 
|6. Modular modeling
 
|6. Modular modeling
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| +
 
| +
 
| +
 
| +
 +
|
 
|-
 
|-
 
|7. Mixed formalisms
 
|7. Mixed formalisms
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| -
 
| -
 
| +
 
| +
 +
|
 
|-
 
|-
 
|8. Agent-based
 
|8. Agent-based
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| -
 
| -
 
| -
 
| -
 +
|
 
|-
 
|-
 
|9. Rule-based
 
|9. Rule-based
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| -
 
| -
 
| -
 
| -
 +
|
 
|-
 
|-
 
|10. Population-based
 
|10. Population-based
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| -
 
| -
 
| -
 
| -
 +
|
 
|-
 
|-
 
|'''Standards'''
 
|'''Standards'''
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|  
 
|  
 
|  
 
|  
 +
|
 
|
 
|
 
|
 
|
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| l3v1
 
| l3v1
 
| l3v1, partially
 
| l3v1, partially
 +
|
 
|-
 
|-
 
|2. SBML comp
 
|2. SBML comp
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| partially
 
| partially
 
| partially
 
| partially
 +
|
 
|-
 
|-
 
|3. SBGN
 
|3. SBGN
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| -
 
| -
 
| -
 
| -
 +
|
 
|-
 
|-
 
|4. SedML
 
|4. SedML
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| +
 
| +
 
| -
 
| -
 +
|
 
|-
 
|-
 
|5. Combine archive
 
|5. Combine archive
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|  
 
|  
 
|  
 
|  
 +
|
 
|-
 
|-
 
|6. SBOL
 
|6. SBOL
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| -
 
| -
 
| -
 
| -
 +
|
 
|-
 
|-
 
|7. Antimony
 
|7. Antimony
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| +
 
| +
 
| -
 
| -
 +
|
 
|-
 
|-
 
|8. Bionetgen
 
|8. Bionetgen
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| -
 
| -
 
| -
 
| -
 +
|
 
|-
 
|-
 
|9. BioPAX
 
|9. BioPAX
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| -
 
| -
 
| -
 
| -
 +
|
 
|-
 
|-
 
|'''Availability'''
 
|'''Availability'''
 +
|
 
|
 
|
 
|
 
|
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| +
 
| +
 
| +
 
| +
 +
|
 
|-
 
|-
 
|2. Linux
 
|2. Linux
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| +
 
| +
 
| +
 
| +
 +
|
 
|-
 
|-
 
|3. MacOS
 
|3. MacOS
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| +
 
| +
 
| +
 
| +
 +
|
 
|-
 
|-
 
|4. Web application
 
|4. Web application
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| -
 
| -
 
| -
 
| -
 +
|
 
|-
 
|-
 
|'''Programming Language'''
 
|'''Programming Language'''
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| Python
 
| Python
 
| C++
 
| C++
 +
|
 
|}
 
|}

Revision as of 15:47, 7 February 2022

Here we collect information about similar software and their features in comparison with BioUML.
This comparison was made in February 2022. Previous was done in 2019 and is available at separate page Tools Comparison.

BioUML COPASI iBioSim CellDesigner Tellurium Morpheus libRoadRunner
Capabilities
1. Model creation visual\text-based via tables visual visual text-based via tables
2. Simulation + + + via ext.tools + + +
3. Parameter fitting + + - - - -
4. Model analysis + + + - + +
5. Database access + - + + - -
Formalism
1. ODE + + + + + + +
2. Stochastic Gillespie-type + + - + + + +
3. Algebraic + - + - + +
4. Discrete + + + + + +
5. Flux balance
6. Modular modeling + - + - + +
7. Mixed formalisms + - - - - +
8. Agent-based + - + - - -
9. Rule-based + - - - - -
10. Population-based + - - - - -
Standards
1. SBML l3v2, all tests passed l3v1 except algebraic l3v1 l3v1 l3v1 l3v1, partially
2. SBML comp fully, all tests passed - partially - partially partially
3. SBGN + export - + - -
4. SedML + + - - + -
5. Combine archive
6. SBOL - - + - - -
7. Antimony + (in standalone) - - - + -
8. Bionetgen + (in standalone) - - - - -
9. BioPAX + - - + - -
Availability
1. Windows + + + + + +
2. Linux + + + + + +
3. MacOS + + + + + +
4. Web application + - - - - -
Programming Language Java C++ Java Java Python C++
Retrieved from "https://wiki.biouml.org/index.php?title=Tools_Comparison_2022&oldid=9457"
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