List of systems biology modeling software

Last updated

Systems biology relies heavily on building mathematical models to help understand and make predictions of biological processes. Specialized software to assist in building models has been developed since the arrival of the first digital computers. [1] [2] [3] [4] The following list gives the currently supported software applications available to researchers.

Contents

The vast majority of modern systems biology modeling software support SBML, which is the de facto standard for exchanging models of biological cellular processes. Some tools also support CellML, a standard used for representing physiological processes. The advantage of using standard formats is that even though a particular software application may eventually become unsupported and even unusable, the models developed by that application can be easily transferred to more modern equivalents. This allows scientific research to be reproducible long after the original publication of the work.

To obtain more information about a particular tool, click on the name of the tool. This will direct you either to a peer-reviewed publication or, in some rare cases, to a dedicated Wikipedia page.

Actively supported open-source software applications

General information

When an entry in the SBML column states "Yes, but only for reactions.", it means that the tool only supports the reaction component of SBML. For example, rules, events, etc. are not supported.

NameDescription/NotabilityOSLicenseSite SBML Support
iBioSim iBioSim [5] [6] is a computer-aided design (CAD) tool for the modeling, analysis, and design of genetic circuits.multiplatform (Java/C++) Apache License Yes
CompuCell3D GUI/Scripting tool [7] for building and simulating multicellular models.multiplatform (C++/Python) MIT Yes, but only for reactions.
COPASI GUI tool [8] [9] for analyzing and simulating SBML models.multiplatform (C++)Artistic License Yes
Cytosim Spatial simulator for flexible cytoskeletal filaments and motor proteins [10] Mac, Linux, Cygwin (C++) GPL3 Not applicable
libroadrunner High-performance software library for simulation and analysis of SBML models [11] [12] multiplatform (C/C++) Apache License Yes
massPy Simulation tool [13] [14] that can work with COBRApy [15] multiplatform (Python) MIT Yes
MCell GUI tool for particle-based spatial stochastic simulation with individual molecules [16] [17] [18] multiplatform MIT and GPLv2 Not applicable
OpenCOR A cross-platform modelling environment, which is aimed at organizing, editing, simulating, and analysing CellML files on Windows, Linux and macOS.multiplatform (C++/Python) GPLv3 Uses CellML
PhysiBoSS A specialized form of the PhysiCell agent-based modeling platform that directly integrates Boolean signaling networks into cell Agents [19] multiplatform (C++) BSD-3 Yes, but only for reactions
PhysiCell A agent-based [20] modeling framework for multicellular systems biology.multiplatform (C++) BSD-3 Yes, but only for reactions
PySCeS Python tool for modeling and analyzing SBML models [21] [22] [23] multiplatform (Python) BSD-3 Yes
pySB Python-based [24] platform with specialization in rule-based models.multiplatform (Python) BSD-3 Partial
ReaDDy Particle-based spatial simulator with intermolecular potentials [25] Linux and MacCustom Not applicable
SBSCL Java library [26] [27] with efficient and exhaustive support for SBMLmultiplatform (Java) LGPL Yes
SBW (software) A distributed workbench [28] [29] that includes many modeling toolsmultiplatform (C/C++) BSD-3 Yes
Smoldyn Particle-based simulator for spatial stochastic simulations with individual molecules [30] [31] [32] [33] multiplatform (C/C++/Python) LGPL Not applicable
Spatiocyte Spatial modeling software that uses a fine lattice with up to one molecule per site [34] [35] multiplatformUnknown Not applicable
SpringSaLaD Particle-based spatial simulator in which molecules are spheres that are linked by springs [36] multiplatformUnknown Not applicable
STEPS Stochastic reaction-diffusion and membrane potential solver on distributed meshes [37] [38] [39] [40] multiplatform (C++/Python) GPLv2 Partial
Tellurium (software) Simulation environment, [41] [42] that packages multiple libraries into one platform.multiplatform (Python) Apache License Yes
URDME Stochastic reaction-diffusion simulation on unstructured meshes [43] MatLab on Mac, LinuxGPL3 Not applicable
VCell Comprehensive modeling platform [44] [45] for non-spatial, spatial, deterministic and stochastic simulations, including both reaction networks and reaction rules.multiplatform (Java) MIT Yes

Specialist Tools

The following table lists specialist tools that cannot be grouped with the modeling tools.

NameDescription/NotabilityOSLicenseSite
PySCeSToolbox PySCeSToolbox [46] is a set of metabolic model analysis tools. Among other features, it can be used to generate the control analysis equations that relate the elasticities to the control coefficients. The package is cross-platform and requires PySCeS and Maxima to operate.multiplatform (C++/Python) BSD-3

Feature Tables

Supported modeling paradigms

NameODEConstraint basedStochasticLogicalAgent basedSpatial (particle)Spatial (continuous)
iBioSimYesNoYesNoLimitedNoNo
CompuCell3DYesNoNoNoYesNoYes
COPASIYesNoYesNoNoNoNo
CytosimNoNoYesNo ?Yes ?
libroadrunnerYesNoYesNoNoNoNo
massPyUses libroadrunnerUses COBRApyNoNoNoNo
MCellNoNoYesNoNoYesNo
OpenCORYesNoNoNoNoNoNo
PhysiBoSS
PhysiCellUses libroadrunnerNoNoNoYes ?Yes
PySCeSYesNo ?NoNoNoNo
pySBYesNoNoNoNoNoNo
ReaDDy
SBSCLYes ? ?NoNoNoNo
SBWYesNoYesNoNoNoNo
SmoldynNoNoYesNoNoYesNo
Spatiocyte
SpringSaLaD
STEPS
Tellurium (software)Uses libroadrunner
URDME
VCellYesNo ?NoNoNoSingle Cell

Differential equation specific features

NameNon-stiff solverStiff solverSteady-state solverSteady-state sensitivitiesTime-dependent sensitivitiesBifurcation Analysis
iBioSimYesYesNoNo ?No
CompuCell3DUses libroadrunnerNA
COPASIYesYesYesYes ?Limited
libroadrunnerYesYesYesYesYesvia AUTO2000 plugin
masspyUses libroadrunner
OpenCORYesYes ? ? ?No
PhysiBoSS
PhysiCellUses libroadrunner
PySCeSYesYesYesYes ?Limited+
pySBYesNoNoNoNoNo
SBSCL
SBWUses C# edition of roadrunnerYes
Tellurium (software)Uses libroadrunner
VCellYesYesNoNoNoNo

File format support and interface type

NameImportExportPrimary InterfaceNetwork visualization (editing)
iBioSimSBMLSBMLGUIYes (Yes)
CompuCell3DNative XML specification format and SBMLNative XMLGUI/Python scriptingNo
COPASINative XML specification format and SBMLNative XML and SBMLGUIYes (No)
libroadrunnerSBMLSBMLPython scriptingNo
masspySBMLSBMLPython scriptingNo

Advanced features (where applicable)

NameStoichiometry matrixReduced stoich matrixConserved moiety analysisJacobianMCA
COPASIYesYesYesYesYes
libroadrunnerYesYesYesYesYes
masspyvia libroadrunner
PySCeSYesYesYesYesYes
VCell ? ? ? ?Limited

Other features

NameParameter EstimationDAE supportUnits support
iBioSimNo ? ?
ComputeCell3DNANA ?
COPASIYesLimitedYes
libroadrunnervia Python packagesLimitedYes
masspyvia Python packagesLimitedYes

Particle-based simulators

Particle based simulators treat each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions. [47]

Comparison of particle-based simulators

The following list compares the features for several particle-based simulators. This table is edited from a version that was originally published in the Encyclopedia of Computational Neuroscience. [48] System boundaries codes: R = reflecting, A = absorbing, T = transmitting, P = periodic, and I = interacting. * Algorithm is exact but software produced incorrect results at the time of original table compilation. † These benchmark run times are not comparable with others due to differing levels of detail.

FeatureMCellSmoldyneGFRDSpringSaLaDReaDDy
Time steps~1 usns to msevent-based~10 ns~0.1 ns to us
Moleculespointspoints, spheresspheresmulti-spheresmulti-spheres
Dimensions2,31,2,3333
System boundariesR,A,P,TR,A,P,TPRP,I
Surfacestriangle meshmany primitives-1 flat surfaceplane, sphere
Surface molecules1/tile, 2 statesunlimited, 4 states-unlimited, 3 states-
Excluded volume-excellentexactgoodexcellent
Multimersstates onlyrule-based model-explicitexplicit
Allostery-yes-yes-
Reaction accuracyvery goodexcellentexact*excellentexcellent
Dissociation productsstochasticfixed separationadjacentadjacentadjacent
Molecule-surface interactionsgoodexcellent-to sites onlypotentials
Long-range interactions-yes--yes
Benchmark run time67 s22 s13 days†9.1 months†13 minutes
Distributionexecutableexecutableself-compileJava fileself-compile
User interfaceGUI, texttexttextGUIPython script
Graphical outputexcellentgoodpartial supportpartial supportgood
Library interfacePythonC/C++, Python--Python
References

[49] [50] [51]

[52] [53] [54] [55] [56] [57] [58]

Model calibration software

Model calibration is a key activity when developing systems biology models. This table highlights some of the current model calibration tools available to systems biology modelers. The first table list tools that are SBML compatible.

ToolPEtab CompatibleP1P2
pyPESTO [59] YesNANA
COPASIYesNANA

PEtab [60] is a community standard for specifying model calibration runs.

Legacy open-source software applications

The following list some very early software for modeling biochemical systems that were developed pre-1980s There are listed for historical interest.

NameDescription/NotabilityLanguageTerminus ante quem [61]
BIOSIM [62] The first ever recorded digital simulator of biochemical networks (by David Garfinkel)FORTRAN IV1968
KDF 9 [63] First simulator to support MCA. Developed by the late Jim Burns in EdinburghEarly form of FORTRAN1968
METASIM [64] Early simulator by Park and WrightPL/11973

The following list shows some of the software modeling applications that were developed in the 1980s and 1990s. There are listed for historical interest.

NameDescription/NotabilityLanguage SBML SupportTerminus ante quem [65]
COR [66] First public CellML-based environment.Object PascalUses CellML 2010
DBsolve [67] Early GUI based simulation platform.C/C++No1999
E-Cell [68] One of the earliest attempts at a whole-cell modeling platform.C/C++No1999
Gepasi [69] First GUI application that supported metabolic control analysis and parameter estimation.C/C++Yes1993
Jarnac [70] First GUI based application to support scripting in systems biology modeling.Object PascalYes2000
JSim [71] First Java-based systems biology modeling platformJavaYes2003
MetaMod [72] One of the first PC-based systems biology simulatorsBBC MicroNo1986
MetaModel [73] Early PC-based systems biology simulatorTurbo Pascal 5.0No1991
MIST [74] GUI based simulatorBorland Pascal 7.0No1995
SCAMP [75] First application to support metabolic control analysis and simulation on a PCPascal, later in CNo1985 (Thesis)

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References

  1. ↑ Chance, Britton; Garfinkel, David; Higgins, Joseph; Hess, Benno; Chance, E.M. (August 1960). "Metabolic Control Mechanisms". Journal of Biological Chemistry. 235 (8): 2426–2439. doi: 10.1016/S0021-9258(18)64638-1 .
  2. ↑ Chance, Britton; Higgins, Joseph; Garfinkel, David (1962). Analogue and digital computer representations of biochemical processes. Federation of American Societies for Experimental Biology..: Federation Proceedings, Vol 12. No. 1-2. p. 75.
  3. ↑ Burns, Jim (1 March 1973). Metabolic Control Analysis. Thesis (Thesis). doi:10.5281/zenodo.7240738.
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  5. ↑ Watanabe, Leandro; Nguyen, Tramy; Zhang, Michael; Zundel, Zach; Zhang, Zhen; Madsen, Curtis; Roehner, Nicholas; Myers, Chris (19 July 2019). "iBioSim3: A Tool for Model-Based Genetic Circuit Design". ACS Synthetic Biology. 8 (7): 1560–1563. doi:10.1021/acssynbio.8b00078. PMID   29944839. S2CID   49429947.
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