Difference between revisions of "Tools Comparison 2022"

From BioUML platform
Jump to: navigation, search
Line 14: Line 14:
 
|+
 
|+
 
|
 
|
−
|BioUML
+
|[http://wiki.biouml.org/ BioUML] <ref>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}}
−
|COPASI
+
</ref>
−
|iBioSim
+
|[http://copasi.org/ COPASI] <ref>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.</ref>
−
|CellDesigner
+
|[https://async.ece.utah.edu/tools/ibiosim/ iBioSim]
−
|Tellurium
+
|[https://www.celldesigner.org/ CellDesigner] <ref>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</ref>
−
|Morpheus
+
|[http://libroadrunner.org/ Tellurium]<ref>Choi K., Medley K., König M., Stocking K., Smith L., Gu S., Sauro, H.M.
−
|libRoadRunner
+
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}}.</ref>
 +
|[https://morpheus.gitlab.io/ Morpheus]<ref>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.</ref>
 +
|[http://libroadrunner.org/ libRoadRunner]
 
|-
 
|-
−
|'''Link'''
+
| '''Current version'''
−
| http://wiki.biouml.org/
+
| 2021.3<br> (Sep 2021)
−
| http://copasi.org/
+
| 4.34<br> (Aug 2021)
−
| https://async.ece.utah.edu/tools/ibiosim/
+
| 3.0.0<br> (Sep 2017)
−
| https://www.celldesigner.org/
+
| 4.4.2<br> (Jun 2020)
−
| https://tellurium.analogmachine.org/
+
| 2.2.0<br> (Dec 2019)
−
| https://morpheus.gitlab.io/
+
| 2.2.6<br> (Feb 2022)
−
| http://libroadrunner.org/
+
| 1.4.16<br> (Feb 2022)
 
|-
 
|-
 
|'''Capabilities'''
 
|'''Capabilities'''

Revision as of 17:18, 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.

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 2022

BioUML [2] COPASI [3] iBioSim CellDesigner [4] Tellurium[5] Morpheus[6] libRoadRunner
Current version 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) 		1.4.16
(Feb 2022)
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
2. SBML comp fully, all tests passed - 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++

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. ↑ 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
  5. ↑ 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.
  6. ↑ 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.
Retrieved from "https://wiki.biouml.org/index.php?title=Tools_Comparison_2022&oldid=9465"
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox