Tools Comparison 2022
From BioUML platform
Revision as of 13:50, 28 March 2022 by Ilya Kiselev (Talk | contribs)
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) | |
| | ||||||||
|---|---|---|---|---|---|---|---|---|
| 1. Model creation | visual\text-based | via tables | visual | visual | text-based | via tables | via direct API | |
| 2. Simulation | + | + | + | + | + | + | + | |
| 3. Parameter fitting | + | + | - | - | +/- (3rd party python libraries) |
+ | via python/Julia | |
| 4. Model analysis | + | + | + | - | + | + | + | |
| 5. Unique or rare features | Parameter identifiability, Manual parameter fitting |
Generic nonlinear optimization | Markov Chain analysis using state-based abstraction |
Provides a special notation for biochemical reaction networks (i.e. CellDesigner notation) |
MopheusML language for multicellular and multiscale modeling, spatial models, Cellular Potts models |
|||
| 6. Database access | + | - | + | + | +/- (3rd party python libraries) |
- | - | |
| 7. Jupyter notebooks | + | + | + | - | + | - | + | |
| 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 | + | - | + | - | - | + | - | |
| 11. Cellular Potts Models | - | - | - | - | - | + | - | |
| Systems Biology Markup Language | ||||||||
| 1. level and version | l3v2 (all tests passed) | l3v2 except algebraic |
l3v2 | l2v4 | l3v2, except algebraic, delay |
l3v2, except algebraic |
l3v2 except algebraic, delay | |
| 2. comp | fully (all tests passed) | import | fully (all tests passed) | - | partially | partially | partially | |
| 3. fbc | + | - | + | - | - | - | - | |
| 4. arrays | - | - | + | - | - | - | - | |
| 5. distrib | - | - | + | - | - | - | - | |
| 6. layout | - | - | + | - | - | - | - | |
| Other Standards | ||||||||
| 1. SBGN PD | + | export | - | + | - | - | - | |
| 2. SBGN-ML | + | - | - | + | - | - | - | |
| 3. SedML | + | + | + | + | + | - | - | |
| 4. Combine archive | + | + | + | - | + | - | - | |
| 5. SBOL | - | - | + | - | +/- (3rd party python libraries) |
- | - | |
| 6. Antimony | + | - | - | - | + | - | - | |
| 7. Bionetgen | + (standalone) | - | - | - | - | - | - | |
| 8. BioPAX | + | - | - | + | - | - | - | |
| Availability | ||||||||
| 1. Windows | + | + | + | + | + | + | + | |
| 2. Linux | + | + | + | + | + | + | + | |
| 3. MacOS | + | + | + | + | + | + | + | |
| 4. Web application | + | + | - | - | via Colab | - | via Colab | |
| Programming Language | Java | C++ | Java/С | Java | Python/Julia | C++ | C/C++/Pyhton/Julia | |
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.
- ↑ 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
- ↑ 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
- ↑ 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.
