Tools Comparison 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.

Modeling tools comparison 2022

	BioUML	COPASI	iBioSim	CellDesigner	Tellurium	Morpheus	libRoadRunner
Link	http://wiki.biouml.org/	http://copasi.org/	https://async.ece.utah.edu/tools/ibiosim/	https://www.celldesigner.org/	https://tellurium.analogmachine.org/	https://morpheus.gitlab.io/	http://libroadrunner.org/
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++