Gromacs Software Authors: Mark James Abraham; Teemu Murtola; Roland Schulz; Szilárd Páll; Jeremy C.Smith; Berk Hess; Erik Lindahl Cited in: 99 Publications (2002–2022) Related Software: NAMD; CHARMM; LINCS; AMBER; VMD; LAMMPS; … Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)
Bio-PEPA Software Authors: Federica Ciocchetta, Maria Luisa Guerriero, Vashti Galpin, Jane Hillston, Giulio Caravagna, Allan Clark, Andrea Degasperi, Adam Duguid, Kanimozhi Ellavarason, Stephen Gilmore, Laurence Loewe, Dimitrios Milios Cited in: 91 Publications (2008–2022) Related Software: PEPA; PRISM; BIOCHAM; BioNetGen; BlenX; LBS; … Main Fields: Ordinary differential equations (34-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)
BIOCHAM Software Authors: Chabrier, N., Fages, F., Soliman, S. Cited in: 45 Publications (2005–2022) Related Software: Bio-PEPA; PRISM; PEPA; BioNetGen; LBS; GNA; … Main Fields: Mathematical logic and foundations (03-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)
BioModels Software Authors: Le Novere, N., Bornstein, B., Broicher, A., Courtot, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B., Snoep, J.L., Hucka, M Cited in: 30 Publications (2008–2022) Related Software: COPASI; KEGG; Celldesigner; PoCaB; Bio-PEPA; PRISM; … Main Fields: Ordinary differential equations (34-XX); Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX)
GEPASI Software Authors: P. Mendes Cited in: 28 Publications (1996–2013) Related Software: E-CELL; Virtual Cell; SCAMP; MCELL; MetaModel; ODEPACK; … Main Fields: Ordinary differential equations (34-XX); Numerical analysis (65-XX); Computer science (68-XX)
BioBayes Software Authors: Mark Girolami; Vladislav Vyshemirsky Cited in: 20 Publications (2008–2022) Related Software: PRMLT; deGradInfer; BayesDA; ABC-SysBio; R; PMTK; … Main Fields: Ordinary differential equations (34-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)
Möbius Software Authors: William H. Sanders Cited in: 19 Publications (2001–2021) Related Software: SMART_; PEPA; SHARPE; PRISM; GreatSPN 1.7; SPNP; … Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)
Celldesigner Software Authors: Funahashi, A., Morohashi, M., Kitano, H., Tanimura, N. Cited in: 17 Publications (2007–2019) Related Software: KEGG; MetaCyc; BIOCHAM; Reactome; BioModels; COPASI; … Main Fields: Ordinary differential equations (34-XX); Numerical analysis (65-XX); Computer science (68-XX)
sbtoolbox Software Authors: Henning Schmidt; Mats Jirstrand Cited in: 12 Publications (2009–2019) Related Software: Matlab; SBML-SAT; libSBML; Sbmltoolbox; SymPy; Python; … Main Fields: Ordinary differential equations (34-XX); Dynamical systems and ergodic theory (37-XX); Calculus of variations and optimal control; optimization (49-XX)
LBS Software Authors: Pedersen, Michael; Plotkin, Gordon D. Cited in: 15 Publications (2010–2022) Related Software: Bio-PEPA; BioNetGen; BIOCHAM; PRISM; BlenX; NFsim; … Main Fields: Ordinary differential equations (34-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)
Paramotopy Software Authors: Daniel Bates; D. Brake; M. Niemerg Cited in: 13 Publications (2013–2023) Related Software: Bertini; PHCpack; HOM4PS; alphaCertified; NumericalAlgebraicGeometry; Macaulay2; … Main Fields: Commutative algebra (13-XX); Algebraic geometry (14-XX); Numerical analysis (65-XX)
STOCKS Software Authors: Andrzej M. Kierzek Cited in: 12 Publications (2008–2019) Related Software: PROPhESY; PARAM; MRMC; Bio-PEPA; PRISM; SPPARKS; … Main Fields: Probability theory and stochastic processes (60-XX); Numerical analysis (65-XX); Computer science (68-XX)
Data2Dynamics Software Authors: Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, et al Cited in: 8 Publications (2018–2021) Related Software: AMIGO; PESTO; PEtab; COPASI; SUNDIALS; R; … Main Fields: Ordinary differential equations (34-XX); Partial differential equations (35-XX); Probability theory and stochastic processes (60-XX)
NFsim Software Authors: Sneddon MW, Faeder JR, Emonet T Cited in: 11 Publications (2011–2021) Related Software: BioNetGen; GitHub; LBS; Bio-PEPA; ERODE; BIOCHAM; … Main Fields: Ordinary differential equations (34-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)
PhysiCell Software Authors: Ghaffarizadeh, A.; Heiland, R.; Friedman, SH; Mumenthaler, SM; Macklin, P. Cited in: 10 Publications (2019–2022) Related Software: Chaste; Biocellion; CellSys; CompuCell3D; Python; Morpheus; … Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)
PySB Software Authors: Lopez, C. F., Muhlich, J. L., Bachman, J. A., Sorger, P. K. Cited in: 10 Publications (2014–2021) Related Software: BioNetGen; Smoldyn; STEPS; MesoRD; URDME; COPASI; … Main Fields: Partial differential equations (35-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)
StochKit2 Software Authors: Sanft KR, Wu S, Roh M, Fu J, Lim RK, Petzold LR Cited in: 8 Publications (2012–2021) Related Software: StochKit; Python; GillesPy2; ppsim; libSBML; COPASI; … Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)
SCAMP Software Authors: Sauro, Herbert M.; Fell, David A. Cited in: 7 Publications (1991–2011) Related Software: GEPASI; Virtual Cell; E-CELL; MetaModel; MEG; TABASCO; … Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)
BiGG Software Authors: J. Schellenberger, J.O. Park, T.M. Conrad, B.O. Palsson Cited in: 9 Publications (2011–2020) Related Software: KEGG; efmtool; Metatool; R; DIAMOnD; COBRA Toolbox; … Main Fields: Ordinary differential equations (34-XX); Numerical analysis (65-XX); Computer science (68-XX)
SpiCO Software Authors: Kuttler, Céline; Lhoussaine, Cédric; Niehren, Joachim Cited in: 10 Publications (2007–2020) Related Software: Bio-PEPA; BioNetGen; BlenX; PEPA; Dizzy; StochPy; … Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)
Sobol Software Authors: Zhang, X.-Y., Trame, M. N., Lesko, L. J., Schmidt, S Cited in: 8 Publications (2018–2022) Related Software: Matlab; NumPy; MOEA; DifferentialEquations.jl; eFAST; Plots.jl; … Main Fields: Statistics (62-XX); Fluid mechanics (76-XX); Operations research, mathematical programming (90-XX)
Cellerator Software Authors: Shapiro, B.E., Levchenko, A., Meyerowitz, E.M., Wold, B.J., Mjolsness, E.D. Cited in: 7 Publications (2005–2019) Related Software: Mathematica; BIOCHAM; STOCHSIM; Matlab; Python; CplexA; … Main Fields: Combinatorics (05-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)
BioSPI Software Authors: – Cited in: 7 Publications (2004–2011) Related Software: PRISM; MGS; Psim; P-Lingua; Dizzy; BioModels; … Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)
SABRE Software Authors: Didier, F., Henzinger, T.A., Mateescu, M., Wolf, V Cited in: 5 Publications (2011–2016) Related Software: PRISM; MARCIE; Bio-PEPA; SBML Test Suite; INFAMY; MRMC; … Main Fields: Probability theory and stochastic processes (60-XX); Numerical analysis (65-XX); Computer science (68-XX)
SBML-SAT Software Authors: Zi Z1, Zheng Y, Rundell AE, Klipp E. Cited in: 7 Publications (2009–2021) Related Software: SensSB; sbtoolbox; Matlab; PottersWheel; Sobol; CRAN; … Main Fields: Ordinary differential equations (34-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)
DFBAlab Software Authors: Gomez, J; Höffner, K; Barton, P, Cited in: 5 Publications (2016–2018) Related Software: Matlab; CPLEX; COBRApy; METRADE; MoNeRe; COBRA Toolbox; … Main Fields: Numerical analysis (65-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)
HRSSA Software Authors: Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong Cited in: 6 Publications (2016–2019) Related Software: HSimulator; COPASI; STEPS; SHAVE; CERENA Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Operations research, mathematical programming (90-XX)
KinFitSim Software Authors: Irina Svir; Oleksiy Klymenko Cited in: 6 Publications (2005–2015) Related Software: KINFIT; DynaFit Main Fields: Partial differential equations (35-XX); Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX)
sbioPN Software Authors: Roberto Bertolusso; Marek Kimmel Cited in: 6 Publications (2012–2022) Related Software: SPPARKS Main Fields: Ordinary differential equations (34-XX); Partial differential equations (35-XX); Biology and other natural sciences (92-XX)
smfsb Software Authors: Darren Wilkinson Cited in: 3 Publications (2012–2019) Related Software: pomp; R; Matlab; CollocInfer; deSolve; vSMC; … Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Numerical analysis (65-XX)
CRNreals Software Authors: G. Szederkényi, J.R. Banga, A.A. Alonso Cited in: 5 Publications (2014–2022) Related Software: GLPK; YALMIP; CLP; SCIP; Matlab Main Fields: Ordinary differential equations (34-XX); Dynamical systems and ergodic theory (37-XX); Classical thermodynamics, heat transfer (80-XX)
WinBEST-KIT Software Authors: Sekiguchi, T.; Okamoto, M. Cited in: 3 Publications (2008–2013) Related Software: ESSYNS; Simpathica; SoftCADS; PLMaddon; MetMAP; MACSYMA; … Main Fields: Statistics (62-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)
Charlie Software Authors: Heiner, Monika; Schwarick, Martin; Wegener, Jan-Thierry Cited in: 2 Publications (2015–2017) Related Software: SNOOPY; SNAKES; ANDy; ZBDD; SABRE; MARCIE; … Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)
Path2Models Software Authors: Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van˜Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Novére NL Cited in: 4 Publications (2015–2019) Related Software: PRMLT; SINDy; Hybrid-SINDy; GitHub; GeneNetWeaver; SOSlib; … Main Fields: Dynamical systems and ergodic theory (37-XX); Statistics (62-XX); Numerical analysis (65-XX)
JSBML Software Authors: Dräger, A., Rodriguez, N., Dumousseau, M., Dörr, A., Wrzodek, C., Novère, N.L., Zell, A., Hucka, M. Cited in: 3 Publications (2012–2021) Related Software: KEGG; MetaCyc; polymake; ERODE; UniProt; z3; … Main Fields: Ordinary differential equations (34-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)
MetMAP Software Authors: Vera, J.; Torres, N. V. Cited in: 3 Publications (2010–2013) Related Software: PLAS; Simpathica; SoftCADS; WinBEST-KIT; PLMaddon; ESSYNS; … Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)
MoVisPP Software Authors: Chen, Ming; Hariharaputran, Sridhar; Hofestädt, Ralf; Kormeier, Benjamin Cited in: 3 Publications (2011) Related Software: COPASI; SNOOPY; Virtual Cell; VisANT; Bio-SPICE; KEGG; … Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)
rBioNet Software Authors: Thorleifsson, S.G.; Thiele, I. Cited in: 2 Publications (2012–2016) Related Software: COBRA Toolbox; Sbmltoolbox Main Fields: Biology and other natural sciences (92-XX)
ANDy Software Authors: Franck Delaplace, Cinzia Di Giusto, Jean-Louis Giavitto, Hanna Klaudel Cited in: 1 Publication (2018) Related Software: Charlie; SNOOPY; SNAKES Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)
BOSS Software Authors: Jorgensen, W. L.; Tirado-Rives, J. Cited in: 0 Publications Related Software: VMD; Cassandra; RASPA; FEASST; Etomica; Towhee; … Main Fields: –
CANA Software Authors: Rion Brattig Correia; Alexander J. Gates; Xuan Wang; Luis M. Rocha Cited in: 1 Publication (2020) Related Software: multistatepdscontrol; GitHub; ADAM; Ginsim; Macaulay2; PANET; … Main Fields: Biology and other natural sciences (92-XX); Systems theory; control (93-XX)
Cell++ Software Authors: Chris Sanford, Matthew L.K. Yip, Carl White, John Parkinson Cited in: 1 Publication (2011) Related Software: Smoldyn; MesoRD Main Fields: Partial differential equations (35-XX); Statistical mechanics, structure of matter (82-XX)
GillesPy Software Authors: J. H. Abel, B. Drawert, A. Hellander, and L. R. Petzold Cited in: 2 Publications (2021–2022) Related Software: StochPy; VODE Main Fields: Approximations and expansions (41-XX); Probability theory and stochastic processes (60-XX); Biology and other natural sciences (92-XX)
GillesPy2 Software Authors: Sean Matthew; et al. Cited in: 1 Publication (2021) Related Software: StochKit2; ppsim; Jupyter; Python; StochKit; GitHub Main Fields: Biology and other natural sciences (92-XX)
HSimulator Software Authors: Marchetti, Luca; Lombardo, Rosario; Priami, Corrado Cited in: 2 Publications (2017–2019) Related Software: HRSSA; STEPS; COPASI Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)
libSRES Software Authors: X. Ji; Y.. Xu Cited in: 1 Publication (2015) Related Software: SBML-PET Main Fields: Numerical analysis (65-XX); Biology and other natural sciences (92-XX)
PathSim Software Authors: N.F. Polys, D.A. Bowman, C. North, R.C. Laubenbacher, K. Duca Cited in: 0 Publications Related Software: BioAmbient Machine; BioShape; Bio-PEPA; MASyV; BioWar Main Fields: –
BMCSER Software Authors: Kyurkchiev, Nikolay; Markov, Svetoslav; Mincheva, Maya Cited in: 1 Publication (2016) Related Software: Mathematica Main Fields: Combinatorics (05-XX); Ordinary differential equations (34-XX); Biology and other natural sciences (92-XX)
BSTLab Software Authors: Schwacke, J., Voit, E.O. Cited in: 1 Publication (2004) Related Software: – Main Fields: Biology and other natural sciences (92-XX)
CHEPROO Software Authors: Bea, S.; Carrera, J.; Ayora, C.; Batlle, F.; Saaltink, M. Cited in: 1 Publication (2020) Related Software: TOUGHREACT Main Fields: Numerical analysis (65-XX); Fluid mechanics (76-XX); Geophysics (86-XX)
Compartor Software Authors: Pietzsch, T., Duso, L., Zechner, C. Cited in: 0 Publications Related Software: Catalyst.jl; MEANS; CERENA; ModelingToolkit.jl; DifferentialEquations.jl; Julia; … Main Fields: –
COVAIN Software Authors: Sun X.; Weckwerth W. Cited in: 1 Publication (2014) Related Software: Algorithm 432; KEGGtranslator; KEGG; Sbmltoolbox; SDE Toolbox Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)
DYVIPAC Software Authors: Lan K. Nguyen, Andrea Degasperi, Philip Cotter, Boris N. Kholodenko Cited in: 0 Publications Related Software: SBW; LibSBMLSim; RunBioSimulations; PySCeS; SOSlib; LLVM; … Main Fields: –
Facile Software Authors: Siso-Nadal, F., Ollivier, J.F., Swain, P.S. Cited in: 1 Publication (2015) Related Software: LOCA; VirtualLeaf; PyPTS; PyNCT; Python; sbtoolbox; … Main Fields: Biology and other natural sciences (92-XX)
LASSIE Software Authors: Tangherloni A, Nobile MS, Besozzi D, Mauri G, Cazzaniga P Cited in: 1 Publication (2019) Related Software: GeneNetWeaver; Path2Models; SOSlib; BioPreDyn-bench; MMG; sgnesR; … Main Fields: Biology and other natural sciences (92-XX)
LNA++ Software Authors: Feigelman, Justin; Weindl, Daniel; Theis, Fabian J.; Marr, Carsten; Hasenauer, Jan Cited in: 1 Publication (2018) Related Software: GitHub; CERENA; iNA; Python; StochKit2; StochSens; … Main Fields: Biology and other natural sciences (92-XX)
MomentClosure.jl Software Authors: Augustinas Sukys, Ramon Grima Cited in: 0 Publications Related Software: Catalyst.jl; MEANS; CERENA; ModelingToolkit.jl; Compartor; DifferentialEquations.jl; … Main Fields: –
PathMiner Software Authors: D.C. McShan, S. Rao, I. Shah Cited in: 1 Publication (2009) Related Software: CPLEX Main Fields: Combinatorics (05-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)
SBMLDiagrams Software Authors: Jin Xu, Jessie Jiang, Herbert M. Sauro Cited in: 0 Publications Related Software: libSBML; SimpleSBML; Python Main Fields: –
SBtab Software Authors: Timo Lubitz, Elad Noor, Jens Hahn, Frank Bergmann Cited in: 0 Publications Related Software: phraSED-ML; AMIGO; tellurium; CellML; MEIGO; BioNetGen; … Main Fields: –
scala-smfsb Software Authors: Wilkinson, Darren J. Cited in: 1 Publication (2019) Related Software: SBML-shorthand; smfsbSBML; smfsb; Scala; R Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)
pauwels2014 Software Authors: Edouard Pauwels Cited in: 0 Publications Related Software: – Main Fields: –
SeQuaiA Software Authors: Češka, Milan; Chau, Calvin; Křetínský, Jan Cited in: 0 Publications Related Software: – Main Fields: –