View source for Tools Comparison 2022

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

== Comparisons made by third parties ==
<ul>
<li>Support of SBML standard can be measured by percentage of passed tests from test suite presented on SBML [http://raterule.caltech.edu/Facilities/Database/Simulator web site].
<li>Extensive comparison of different simulators according to their speed and percentage of passed SBML tests was performed by Maggioli et al.<ref>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}}</ref>
</ul>

== Modeling tools comparison ==

This comparison was made in February 2022. Previous was done in 2019 and is available at separate page [[Tools Comparison]].<br>

{| class="wikitable"
|+
|
|[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}}
</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] <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}}</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.
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]
|-
| Current version<br>(stable)
| 2021.3<br> (Sep 2021)
| 4.34<br> (Aug 2021)
| 3.0.0<br> (Sep 2017)
| 4.4.2<br> (Jun 2020)
| 2.2.0<br> (Dec 2019)
| 2.2.6<br> (Feb 2022)
| 1.4.18<br> (May 2017)
|-
!colspan="9"| <center>'''Capabilities'''</center>
|-
|1. Model creation
| visual\text-based
| via tables
| visual
| visual
| text-based
| via tables
| via direct API
|-
|2. Simulation
| +
| +
| +
| +
| +
| +
| +
|-
|3. Parameter fitting
| +
| +
| - 
| -
| +/- (3rd party<br>python libraries)
| +
| via python/Julia
|-
|4. Model analysis
| +
| +
| +
| -
| +
| +
| +
|-
|5. Unique or rare features
| Parameter identifiability,<br>Manual parameter fitting
| Generic nonlinear optimization
| Markov Chain analysis<br> using state-based abstraction
| Provides a special notation<br>for biochemical reaction networks<br> (i.e. CellDesigner notation)
| 
| MopheusML language for<br> multicellular and multiscale modeling,<br>spatial models,<br>Cellular Potts models
| 
|-
|6. Database access
| +
| -
| +
| +
| +/- (3rd party<br>python libraries)
| -
| -
|-
|7. Jupyter notebooks
| +
| +
| +
| -
| +
| -
| +
|-
!colspan="9"|<center>'''Model formalism'''</center>
|-
|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
| -
| -
| -
| -
| -
| +
| -
|-
!colspan="9"|'''Systems Biology Markup Language'''
|-
|1. level and version
| l3v2 (all tests passed)
| l3v2 except<br>algebraic
| l3v2
| l2v4
| l3v2, except<br>algebraic, delay
| l3v2, except<br>algebraic
| l3v2 except<br>algebraic, delay
|-
|2. comp
| fully (all tests passed)
| import
| fully (all tests passed)
| -
| partially
| partially
| partially
|-
|3. fbc
| +
| -
| +
| -
| -
| -
| -
|-
|4. arrays
| -
| -
| +
| -
| -
| -
| -
|-
|5. distrib
| -
| -
| +
| -
| -
| -
| -
|-
|6. layout
| -
| -
| +
| -
| -
| -
| -
|-
!colspan="9"|'''Other Standards'''
|-
|1. SBGN PD
| +
| export
| -
| +
| -
| -
| -
|-
|2. SBGN-ML
| +
| -
| -
| +
| -
| -
| -
|-
|3. SedML
| +
| +
| +
| +
| +
| -
| -
|-
|4. Combine archive
| +
| +
| +
| -
| +
| -
| -
|-
|5. SBOL
| -
| -
| +
| -
| +/- (3rd party<br>python libraries)
| -
| -
|-
|6. Antimony
| +
| -
| -
| -
| +
| -
| -
|-
|7. Bionetgen
| + (standalone)
| -
| -
| -
| -
| -
| -
|-
|8. BioPAX
| +
| -
| -
| +
| -
| -
| -
|-
!colspan="9"|'''Availability'''
|-
|1. Windows
| +
| +
| +
| +
| +
| +
| +
|-
|2. Linux
| +
| + 
| +
| +
| +
| +
| +
|-
|3. MacOS
| +
| + 
| +
| +
| +
| +
| +
|-
|4. Web application
| +
| [http://shiny.copasi.org +]
| -
| -
| via Colab
| -
| via Colab
|-
|'''Programming Language'''
| Java
| C++
| Java/С
| Java
| Python/Julia
| C++
| C/C++/Pyhton/Julia
|}

==References==

<references/>
<References/>