examples

Example COMBINE/OMEX archives

This directory is a collection of example COMBINE/OMEX archives that describe simulations of biological models. As detailed below, the archives in this directory involve a variety of modeling frameworks (e.g., logical, constraint-based), simulation algorithms (e.g., CVODE, SSA), and model formats (e.g., BNGL, SBML). All of the simulations in the archives in this directory are described using the Simulation Experiment Description Markup Language (SED-ML).

The purpose of this directory is two-fold:

• This directory serves as a reference for the community.
• The directory serves as a test suite for the BioSimulators registry of biosimulation tools. Tools submitted to the registry are validated using the software in this repository and the examples in this directory.

Modeling frameworks employed by the example archives

The archives in this directory involve the following modeling frameworks:

Name	SBO id
flux balance	SBO_0000624
hybrid flux balance-continous	SBO_0000684
logical	SBO_0000234
non-spatial continuous	SBO_0000293
non-spatial discrete	SBO_0000295
resource balance	SBO_0000692
spatial discrete	SBO_0000294

Simulation algorithms employed by the example archives

The archives in this directory involve numerous simulation algorithms such as:

Name	Acronym	KiSAO id
Code Value Ordinary Differential Equation Solver	CVODE	KISAO_0000019
Stochastic Simulation Algorithm	SSA	KISAO_0000029

Model formats employed by the example archives

The archives in this directory involve the following model formats:

Name	Acronym	EDAM id
BioNetGen Language	BNGL	format_3972
CellML		format_3240
NeuroML/Low Entropy Model Specification Language	LEMS
RBA TSV/XML format
Smoldyn Language
Systems Biology Markup Language (core)	SBML	format_2585
SBML flux balance constraints package	SBML-fbc	format_2585
SBML qualitative modeling package	SBML-qual	format_2585
SBML MASS schema
Virtual Cell Markup Language	VCML
XPP ODE format

Note, more specific EDAM terms have SBML-fbc, SBML-qual, and other formats have been requested.

Formats for the example data visualizations for the results of the example archives

The archives in this directory involve the following model formats:

Name	EDAM id
SED-ML	format_3685
Vega	format_3969

Compatibility of the example archives with simulation tools

Because each simulation tool only supports a limited number of modeling frameworks, simulation algorithms, and model formats, no simulation tool is capable of executing all of the archives in this directory. The BioSimulators registry of biosimulation tools contains detailed information about the modeling frameworks, simulation algorithms, and model formats supported by each registered tool. This information can be used to determine which tools are capable of executing a given archive.

Below is information about the compatibility of a selection of archives.

Source	Archive	Results	Data visualization (Vega)	Modeling framework (SBO id)	Simulation algorithm (KiSAO id)	Model format (EDAM id)	Compatibile simulators
Bordbar Cell Syst	.omex	.h5		non-spatial continuous (0000293)	CVODE (0000019)	SBML (format_2585)	tellurium
Caravagna J Theor Biol	.omex	.h5		non-spatial continuous (0000293)	CVODE (0000019)	SBML (format_2585)	PySCeS, tellurium, VCell
Chaouiya BMC Syst Biol	.omex	.h5		logical (0000234)	synchronous updating (0000449)	SBML qual (format_2585)	BoolNet, GINsim
Ciliberto J Cell Biol	.omex	.h5	.json	non-spatial continuous (0000295)	CVODE (0000019)	SBML (format_2585)	PySCeS, tellurium, VCell
Ciliberto J Cell Biol	.omex	.h5		non-spatial continuous (0000295)	Fehlberg (0000086)	SBML (format_2585)	libSBMLSim, tellurium, VCell
Dolan PLoS Comput Biol	.omex	.h5		non-spatial discrete (0000295)	NFsim (0000263)	BNGL (format_3972)	BioNetGen
E. coli core metabolism (COBRApy Team)	.omex	.h5	.json	flux balance (0000624)	FBA (0000437)	SBML fbc (format_2585)	COBRApy, CBMPy
E. coli resource allocation	.omex	.h5	.json	resource balance (0000692)	RBA (0000669)	RBA	RBApy
Edelstein Biol Cybern	.omex	.h5	.json	non-spatial continuous (0000293)	LSODA (0000088)	SBML (format_2585)	GillesPy2, PySCeS
Elowitz Nature	.omex	.h5	.json	non-spatial continuous (0000293)	CVODE (0000019)	CellML (format_3240)	OpenCOR
Elowitz Nature	.omex	.h5	.json	non-spatial continuous (0000293)	CVODE (0000019)	SBML (format_2585)	PySCeS, tellurium, VCell
Hodgkin-Huxley dynamics	.omex	.h5		non-spatial continuous (0000293)	CVODE (0000019)	NeuroML/LEMS	NEURON, NetPyNe
Hodgkin-Huxley dynamics	.omex	.h5		non-spatial continuous (0000293)	Euler forward method (0000030)	NeuroML/LEMS	pyNeuroML
Irons J Theor Biol	.omex	.h5	.json	logical (0000234)	synchronous updating (0000449)	SBML qual (format_2585)	BoolNet, GINsim
Lorenz system	.omex	.h5		non-spatial continuous (0000293)	CVODE (0000019)	OpenCOR	OpenCOR
Lotka-Volterra model (Smoldyn Team)	.omex	.h5		spatial discrete (0000294)	Smoluchowski method (0000057)	Smoldyn	Smoldyn
Parmar BMC Syst Biol	.omex	.h5		non-spatial continuous (0000293)	CVODE (0000019)	SBML (format_2585)	PySCeS, tellurium, VCell
Powers Pflugers Arch	.omex			non-spatial continuous (0000293)	CVODE (0000019)	VCML	VCell
Szymanska J Theor Biol	.omex	.h5		non-spatial continuous (0000293)	CVODES (0000496)	SBML (format_2585)	AMICI
Tomida EMBO J	.omex	.h5	.json	non-spatial continuous (0000293)	LSODA/LSODAR (0000560)	SBML (format_2585)	COPASI
Saglam toy gene regulatory network	.omex	.h5		non-spatial continuous (0000293)	CVODE (0000019)	BNGL (format_3972)	BioNetGen
Varusai Sci Rep	.omex	.h5		non-spatial continuous (0000293)	LSODA/LSODAR (0000560)	SBML (format_2585)	COPASI
Vilar PNAS	.omex			non-spatial continuous (0000293), non-spatial discrete (0000295)	CVODE (0000019) and NRM (0000027)	SBML (format_2585)	VCell
Wu Biochem Pharmacol	.omex			non-spatial continuous (0000293)	CVODE (0000019)	XPP ODE	XPP