Difference between revisions of "Tools Comparison 2022"

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| text-based
 
| text-based
 
| via tables
 
| via tables
|
+
| -
 
|-
 
|-
 
|2. Simulation
 
|2. Simulation
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| -
 
| -
 
| -
 
| -
|
+
| -
 
|-
 
|-
 
|4. Model analysis
 
|4. Model analysis
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| +
 
| +
 
| +
 
| +
|
+
| +
 
|-
 
|-
 
|5. Database access
 
|5. Database access
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| -
 
| -
 
| -
 
| -
|
+
| -
 
|-
 
|-
 
|6. Jupyter notebooks
 
|6. Jupyter notebooks
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| -
 
| -
 
| -
 
| -
|
+
| -
 
|-
 
|-
 
!colspan="9"|<center>'''Model formalism'''</center>
 
!colspan="9"|<center>'''Model formalism'''</center>
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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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| -
 
| -
 
| -
 
| -
|
+
| -
 
|-
 
|-
 
!colspan="9"|'''Standards'''
 
!colspan="9"|'''Standards'''
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|1. SBML
 
|1. SBML
 
| l3v2, all tests passed
 
| l3v2, all tests passed
| l3v1 except algebraic
+
| l3v1 except<br>algebraic
 
| l3v1
 
| l3v1
 
| l3v1
 
| l3v1
 
| l3v1
 
| l3v1
 
| l3v1, partially
 
| l3v1, partially
|
+
| l3v1 except<br>algebraic, delay
 
|-
 
|-
 
|2. SBML comp
 
|2. SBML comp
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| partially
 
| partially
 
| partially
 
| partially
|
+
| partially
 
|-
 
|-
 
|3. SBML fbc
 
|3. SBML fbc
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|  
 
|  
 
|  
 
|  
|
+
| -
 
|-
 
|-
 
|4. SBGN PD
 
|4. SBGN PD
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| -
 
| -
 
| -
 
| -
|
+
| -
 
|-
 
|-
 
|5. SBGN-ML
 
|5. SBGN-ML
 +
| +
 
|  
 
|  
 
|  
 
|  
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|  
 
|  
 
|  
 
|  
|  
+
| -
|
+
 
|-
 
|-
 
|6. SedML
 
|6. SedML
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| -
 
| -
 
| -
 
| -
|
+
| -
 
|-
 
|-
 
|9. Antimony
 
|9. Antimony
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| -
 
| -
 
| -
 
| -
|
+
| -
 
|-
 
|-
 
|11. BioPAX
 
|11. BioPAX
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| -
 
| -
 
| -
 
| -
|
+
| -
 
|-
 
|-
 
!colspan="9"|'''Availability'''
 
!colspan="9"|'''Availability'''
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| -
 
| -
 
| -
 
| -
|
+
| -
 
|-
 
|-
 
|'''Programming Language'''
 
|'''Programming Language'''

Revision as of 17:48, 7 February 2022

Here we collect information about similar software and their features in comparison with BioUML.

Comparisons made by third parties

  • Support of SBML standard can be measured by percentage of passed tests from test suite presented on SBML web site.
  • Extensive comparison of different simulators according to their speed and percentage of passed SBML tests was performed by Maggioli et al.[1]

Modeling tools comparison

This comparison was made in February 2022. Previous was done in 2019 and is available at separate page Tools Comparison.

BioUML [2] COPASI [3] iBioSim [4]. CellDesigner [5] Tellurium[6] Morpheus[7] libRoadRunner
Current version
(stable)
2021.3
(Sep 2021)
4.34
(Aug 2021)
3.0.0
(Sep 2017)
4.4.2
(Jun 2020)
2.2.0
(Dec 2019)
2.2.6
(Feb 2022)
1.4.18
(May 2017)
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 + - + + - - -
6. Jupyter notebooks + - + + - - -
Model 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 l3v1 except
algebraic, delay
2. SBML comp fully, all tests passed - partially - partially partially partially
3. SBML fbc fully, all tests passed -
4. SBGN PD + export - + - - -
5. SBGN-ML + -
6. SedML + + - - + -
7. Combine archive
8. SBOL - - + - - - -
9. Antimony + (in standalone) - - - + -
10. Bionetgen + (in standalone) - - - - - -
11. BioPAX + - - + - - -
Availability
1. Windows + + + + + + +
2. Linux + + + + + + +
3. MacOS + + + + + + +
4. Web application + - - - - - -
Programming Language Java C++ Java Java Python C++ C/C++

References

  1. Maggioli, F., Mancini, T., Tronci, E. (2020). SBML2Modelica: integrating biochemical models within open-sThis comparison was made in February 2022. Previous was done in 2019 and is available at separate page Tools Comparison.tandard simulation ecosystems. Bioinformatics, 36(7), 2165-2172. doi:https://doi.org/10.1093/bioinformatics/btz860
  2. Kolpakov, F., Akberdin, I., Kashapov, T., Kiselev, L., Kolmykov, S., Kondrakhin, Y., Kutumova, E., Mandrik, N., Pintus, S., Ryabova, A. and Sharipov, R. (2019). BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. Nucleic acids research, 47(W1), W225-W233. doi:https://doi.org/10.1093/nar/gkz440
  3. Hoops S., Sahle S., Gauges R., Lee C., Pahle J., Simus N., Singhal M., Xu L., Mendes P. and Kummer U. (2006). COPASI: a COmplex PAthway SImulator. Bioinformatics 22, 3067-74.
  4. Watanabe, L., Nguyen, T., Zhang, M., Zundel, Z., Zhang, Z., Madsen, C., Roehner, N., Myers, C. (2018). iBioSim 3: a tool for model-based genetic circuit design. ACS synthetic biology, 8(7), 1560-1563. doi:https://doi.org/10.1021/acssynbio.8b00078
  5. Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H., CellDesigner: a process diagram editor for gene-regulatory and biochemical networks, BIOSILICO, 1:159-162, 2003
  6. Choi K., Medley K., König M., Stocking K., Smith L., Gu S., Sauro, H.M. Tellurium: An extensible python-based modeling environment for systems and synthetic biology, Biosystems, Volume 171, 2018, Pages 74-79. doi:https://doi.org/10.1016/j.biosystems.2018.07.006.
  7. J. Starruß, W. de Back, L. Brusch and A. Deutsch. Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology. Bioinformatics, 30 (9): 1331-1332, 2014.
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