Difference between revisions of "Tools Comparison 2022"
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|[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> | |[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> | ||
| − | |[https://async.ece.utah.edu/tools/ibiosim/ iBioSim] | + | |[https://async.ece.utah.edu/tools/ibiosim/ iBioSim] <ref>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}}. |
| + | |||
|[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> | |[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> | ||
|[http://libroadrunner.org/ Tellurium]<ref>Choi K., Medley K., König M., Stocking K., Smith L., Gu S., Sauro, H.M. | |[http://libroadrunner.org/ Tellurium]<ref>Choi K., Medley K., König M., Stocking K., Smith L., Gu S., Sauro, H.M. | ||
Revision as of 17:20, 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 Cite error: Closing </ref> missing for <ref> tag
|
Tellurium[4] | Morpheus[5] | 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) |
1.4.16 (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
- ↑ 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
- ↑ 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
- ↑ 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.
- ↑ 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.
- ↑ 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.
