×

Found 63 Software Packages (Results 1–63)

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: