×

Found 188 Software Packages (Results 1–100)

Matlab

Software Authors:   MathWorks Inc
Referenced in: 12,958 Publications (1982–2024)
Related Software: Simulink; LMI toolbox; Maple; MATLAB ODE suite; ode23; ode45; …
Main Fields: Ordinary differential equations (34-XX); Partial differential equations (35-XX); Numerical analysis (65-XX)

CGAL

Software Authors:   CGAL Editorial Board
Referenced in: 370 Publications (2000–2022)
Related Software: LEDA; 2D triangulations; 2D Arrangement; Triangle; Boost; Qhull; …
Main Fields: Convex and discrete geometry (52-XX); Numerical analysis (65-XX); Computer science (68-XX)

FGb

Software Authors:   J.-C. Faugère
Referenced in: 244 Publications (1998–2022)
Related Software: Magma; SINGULAR; Maple; ISOLATE; Kronecker; FLASH; …
Main Fields: Commutative algebra (13-XX); Algebraic geometry (14-XX); Numerical analysis (65-XX)

DSTool

Software Authors:   J Guckenheimer, BA Meloon, MR Myers, FJ Wicklin, Michael Patra
Referenced in: 104 Publications (1992–2022)
Related Software: AUTO; AUTO-86; HomCont; PITCON; MATCONT; LOCBIF; …
Main Fields: Ordinary differential equations (34-XX); Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX)

Bocop

Software Authors:   Bonnans, F.J., Martinon, P., Grélard, V.
Referenced in: 51 Publications (2013–2022)
Related Software: Ipopt; SOCS; minpack; HamPath; GloptiPoly; GitHub; …
Main Fields: Calculus of variations and optimal control; optimization (49-XX); Numerical analysis (65-XX); Mechanics of particles and systems (70-XX)

BIOCHAM

Software Authors:   Chabrier, N., Fages, F., Soliman, S.
Referenced 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)

iLoc-Euk

Software Authors:   Chou, K. -C.; Wu, Z. -C.; Xiao, X.
Referenced in: 37 Publications (2011–2019)
Related Software: iLoc-Hum; Cell-PLoc; iLoc-Virus; Plant-mPLoc; iLoc-Gpos; LIBSVM; …
Main Fields: Harmonic analysis on Euclidean spaces (42-XX); Statistics (62-XX); Computer science (68-XX)

PDB2PQR

Software Authors:   T. Dolinsky, J. Nielsen, A. McCammon, N. Baker
Referenced in: 33 Publications (2006–2022)
Related Software: APBS; MIBPB; TABI; tabipb; CHARMM; PBEQ-Solver; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Optics, electromagnetic theory (78-XX)

Knut

Software Authors:   Szalai, Robert
Referenced in: 31 Publications (2007–2022)
Related Software: DDE-BIFTOOL; PDDE-CONT; MATCONT; AUTO; dde23; COCO; …
Main Fields: Ordinary differential equations (34-XX); Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX)

REVEAL

Software Authors:   Liang, S., Fuhrman, S., Somogyi, R
Referenced in: 22 Publications (2003–2022)
Related Software: KEGG; R; BoolNet; E-CELL; GEPASI; Macaulay2; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

Breach

Software Authors:   Alexandre Donzé
Referenced in: 26 Publications (2011–2022)
Related Software: S-TaLiRo; Flow*; SpaceEx; Matlab; KeYmaera; C2e2; …
Main Fields: Mathematical logic and foundations (03-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

Plant-mPLoc

Software Authors:   Chou, K. -C.; Shen, H. -B.
Referenced in: 26 Publications (2010–2019)
Related Software: Cell-PLoc; Euk-mPLoc; iLoc-Euk; iLoc-Virus; GPCR-2L; iLoc-Hum; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

BioBayes

Software Authors:   Mark Girolami; Vladislav Vyshemirsky
Referenced 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)

Reactome

Software Authors:   G. Joshi-Tope M. Gillespie; I. Vastrik; P. D'Eustachio; E. Schmidt; B. de Bono; B. Jassal; G.R. Gopinath; G.R. Wu; L. Matthews; S. Lewis; E. Birney; L. Stein
Referenced in: 13 Publications (2008–2022)
Related Software: KEGG; Bioconductor; MetaCyc; Celldesigner; BioGRID; Cytoscape; …
Main Fields: Combinatorics (05-XX); Partial differential equations (35-XX); Statistics (62-XX)

SIESTA

Software Authors:   Soler J.S., Artacho E., Gale J.D., Garcia A., Junquera J., Ordejon P., Sanchez-Portal D
Referenced in: 22 Publications (2006–2022)
Related Software: ONETEP; CASTEP; ABINIT; OCTOPUS; CONQUEST; ScaLAPACK; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Mechanics of deformable solids (74-XX)

BlenX

Software Authors:   Lorenzo Dematté; Corrado Priami; Alessandro Romanel
Referenced in: 18 Publications (2008–2020)
Related Software: Bio-PEPA; PRISM; PEPA; BioNetGen; LBS; BioModels; …
Main Fields: Mathematical logic and foundations (03-XX); Category theory; homological algebra (18-XX); Computer science (68-XX)

Celldesigner

Software Authors:   Funahashi, A., Morohashi, M., Kitano, H., Tanimura, N.
Referenced 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)

iLoc-Animal

Software Authors:   Lin, W. -Z.; Fang, J. -A.; Xiao, X.; Chou, K. -C.
Referenced in: 20 Publications (2013–2019)
Related Software: iLoc-Hum; iRSpot-PseDNC; iLoc-Virus; iLoc-Euk; iAMP-2L; iSNO-PseAAC; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

iLoc-Plant

Software Authors:   Wu, Z. -C.; Xiao, X.; Chou, K. -C.
Referenced in: 18 Publications (2012–2019)
Related Software: iLoc-Virus; iLoc-Euk; iLoc-Hum; iLoc-Gpos; Cell-PLoc; iLoc-Animal; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

sbtoolbox

Software Authors:   Henning Schmidt; Mats Jirstrand
Referenced 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)

ESPResSo

Software Authors:   Limbach, H.-J.; Arnold, A.; Mann, B. A.; Holm, C
Referenced in: 14 Publications (2008–2021)
Related Software: NAMD; Gromacs; ESPResSo++; AdResS; MMM2D; Python; …
Main Fields: Numerical analysis (65-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

GenSSI

Software Authors:   Chis O, Banga J, Balsa-Canto E
Referenced in: 14 Publications (2013–2022)
Related Software: DAISY; SIAN; AMIGO; COMBOS; ObservabilityTest; GitHub; …
Main Fields: Ordinary differential equations (34-XX); Dynamical systems and ergodic theory (37-XX); Statistics (62-XX)

libSBML

Software Authors:   B. J. Bornstein, S. M. Keating, A. Jouraku, M. Hucka
Referenced in: 3 Publications (2009–2018)
Related Software: SimpleSBML; Python; COPASI; sbtoolbox; Antimony; StochKit2; …
Main Fields: Ordinary differential equations (34-XX); Numerical analysis (65-XX); Operations research, mathematical programming (90-XX)

Siconos

Software Authors:   Siconos development team
Referenced in: 13 Publications (2010–2022)
Related Software: PATH Solver; CasADi; Ipopt; ZQPCVX; Meschach; RODAS; …
Main Fields: Numerical analysis (65-XX); Mechanics of particles and systems (70-XX); Mechanics of deformable solids (74-XX)

Data2Dynamics

Software Authors:   Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, et al
Referenced 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)

SW1PerS

Software Authors:   J. A. Perea, A. Deckard, S. B. Haase, J. Harer
Referenced in: 12 Publications (2015–2022)
Related Software: TDA; Ripser; javaPlex; Persistence Landscape; PersistenceImages; TopologyNet; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Algebraic topology (55-XX); Statistics (62-XX)

COMBOS

Software Authors:   Nicolette Meshkat, Christine Er-zhen Kuo, Joseph DiStefano, III
Referenced in: 11 Publications (2017–2022)
Related Software: DAISY; SIAN; GenSSI; BLAD; ObservabilityTest; Maple; …
Main Fields: Ordinary differential equations (34-XX); Partial differential equations (35-XX); Statistics (62-XX)

AMIGO

Software Authors:   Eva Balsa-Canto; Julio R. Banga
Referenced in: 7 Publications (2015–2021)
Related Software: Data2Dynamics; PESTO; COPASI; R; pyPESTO; PEtab; …
Main Fields: Ordinary differential equations (34-XX); Numerical analysis (65-XX); Operations research, mathematical programming (90-XX)

BiGG

Software Authors:   J. Schellenberger, J.O. Park, T.M. Conrad, B.O. Palsson
Referenced 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)

Bio-SPICE

Software Authors:   Garvey TD, Lincoln P, Pedersen CJ et al
Referenced in: 8 Publications (2005–2014)
Related Software: COPASI; BioModels; Taverna; GEPASI; KEGG; Celldesigner; …
Main Fields: History and biography (01-XX); Numerical analysis (65-XX); Computer science (68-XX)

IDP3

Software Authors:   Bruynooghe, Maurice; Blockeel, Hendrik; Bogaerts, Bart; De Cat, Broes; De Pooter, Stef; Jansen, Joachim; Labarre, Anthony; Ramon, Jan; Denecker, Marc; Verwer, Sicco
Referenced in: 9 Publications (2015–2020)
Related Software: clasp; WASP; DLV; Clingo; Cmodels; DLV2; …
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX)

SpiCO

Software Authors:   Kuttler, Céline; Lhoussaine, Cédric; Niehren, Joachim
Referenced 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)

ABC-SysBio

Software Authors:   Liepe, J., Barnes, C., Cule, E., Erguler, K., Kirk, P., Toni, T., Stumpf, M. P. H.
Referenced in: 6 Publications (2012–2022)
Related Software: BioBayes; astroABC; EasyABC; SciPy; Python; BCM; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Numerical analysis (65-XX)

ADAM

Software Authors:   Hinkelmann F, Brandon M, Guang B, McNeill R, Blekherman G, Veliz-Cuba A, Laubenbacher R
Referenced in: 8 Publications (2011–2020)
Related Software: Ginsim; Macaulay2; BoolNet; SNOOPY; Polynome; multistatepdscontrol; …
Main Fields: Algebraic geometry (14-XX); Linear and multilinear algebra; matrix theory (15-XX); Biology and other natural sciences (92-XX)

MultiLoc2

Software Authors:   Blum, T.; Briesemeister, S.; Kohlbacher, O.
Referenced in: 6 Publications (2011–2014)
Related Software: MultiLoc; Cell-PLoc; iLoc-Euk; Euk-mPLoc; Plant-mPLoc; Euk-PLoc; …
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
Referenced in: 7 Publications (2018–2022)
Related Software: Matlab; MOEA; DifferentialEquations.jl; eFAST; Plots.jl; Makie.jl; …
Main Fields: Statistics (62-XX); Mechanics of deformable solids (74-XX); Fluid mechanics (76-XX)

HybridSal

Software Authors:   Tiwari, A.
Referenced in: 4 Publications (2009–2020)
Related Software: HSolver; RSOLVER; Yices; Breach; HyLAA; SpaceEx; …
Main Fields: Mathematical logic and foundations (03-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

pLoc_bal-mGneg

Software Authors:   Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen
Referenced in: 7 Publications (2018–2019)
Related Software: pLoc-mGneg; iPromoter-2L; iRSpot-EL; iRNA-PseColl; pLoc-mAnimal; iEnhancer-2L; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

PoCaB

Software Authors:   Samal, Satya Swarup; Errami, Hassan; Weber, Andreas
Referenced in: 7 Publications (2012–2015)
Related Software: BioModels; polymake; z3; KEGG; REDLOG; SDeval; …
Main Fields: Algebraic geometry (14-XX); Ordinary differential equations (34-XX); Numerical analysis (65-XX)

RuleBender

Software Authors:   Xu, W., Smith, A. M., Faeder, J. R., Marai, G. E.
Referenced in: 5 Publications (2015–2021)
Related Software: BioNetGen; GROOVE; MOSBIE; Tulip; PORGY; Dask; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

SBML-SAT

Software Authors:   Zi Z1, Zheng Y, Rundell AE, Klipp E.
Referenced 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)

STOCHSIMGPU

Software Authors:   Klingbeil, G.; Erban, R.; Giles, M.; Maini, P. K.
Referenced in: 6 Publications (2012–2022)
Related Software: BayesDA; MLMCandMultifidelityForABC; AABC; Smoldyn; MesoRD; STEPS; …
Main Fields: Partial differential equations (35-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

ABNER

Software Authors:   Burr Settles
Referenced in: 0 Publications
Related Software: iHOP; ProMiner; GENIA corpus; KEGG; RelEx; OpenDMAP; …
Main Fields:

AgentCell

Software Authors:   Thierry Emonet, Charles M. Macal, Michael J. North, Charles E. Wickersham, Philippe Cluzel
Referenced in: 6 Publications (2007–2020)
Related Software: BacSim; FreeFem++; STOCHSIM
Main Fields: Partial differential equations (35-XX); Biology and other natural sciences (92-XX)

HRSSA

Software Authors:   Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong
Referenced 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)

Lyap

Software Authors:   F. Sattin
Referenced in: 6 Publications (1997–2021)
Related Software: Matlab; mctoolbox; SLICOT; LAPACK
Main Fields: Ordinary differential equations (34-XX); Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX)

MEIGO

Software Authors:   Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J.
Referenced in: 2 Publications (2010–2019)
Related Software: COPASI; R; AMIGO; tellurium; BioNetGen; PyBioNetFit; …
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

Polynome

Software Authors:   Dimitrova, Elena; García-Puente, Luis David; Hinkelmann, Franziska; Jarrah, Abdul S.; Laubenbacher, Reinhard; Stigler, Brandilyn; Stillman, Michael; Vera-Licona, Paola
Referenced in: 6 Publications (2010–2017)
Related Software: ADAM; Macaulay2; Ginsim; SageMath; TIGRESS; SNOOPY
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

ProMoT

Software Authors:   F Tränkle, M Zeitz, M Ginkel; Waschler, Roland; Angeles-Palacios, Odon; Ginkel, Martin; Kienle, Achim
Referenced in: 5 Publications (2000–2021)
Related Software: TABASCO; lpSolve; SUNDIALS; SciPy; SynBioSS; BioJADE; …
Main Fields: General and overarching topics; collections (00-XX); History and biography (01-XX); Partial differential equations (35-XX)

Sbmltoolbox

Software Authors:   Sarah M. Keating; Benjamin J. Bornstein; Andrew Finney; Michael Hucka
Referenced in: 4 Publications (2010–2016)
Related Software: sbtoolbox; COBRA Toolbox; SBMLSim; SBML Test Suite; Sostools; libSBML; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

smfsb

Software Authors:   Darren Wilkinson
Referenced 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)

Bioclipse

Software Authors:   Spjuth O, Alvarsson J, Berg A, Eklund M, Kuhn S, Masak C, Torrance G, Wagener J, Willighagen E, Steinbeck C, Wikberg J.
Referenced in: 0 Publications
Related Software: CDK; Taverna; BioMOBY; Screensaver; Spring; BIRT; …
Main Fields:

CRNreals

Software Authors:   G. Szederkényi, J.R. Banga, A.A. Alonso
Referenced 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)

ProbCD

Software Authors:   Ricardo Vêncio, Ilya Shmulevich
Referenced in: 0 Publications
Related Software: GOPET; BayGO; Gaggle; GOLEM; GOtcha; BiNGO; …
Main Fields:

SensSB

Software Authors:   Rodriguez-Fernandez, M., Banga, J.R.
Referenced in: 4 Publications (2012–2020)
Related Software: Matlab; SBML-SAT; COPASI; sbtoolbox; SPSens; StochSens; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX); Systems theory; control (93-XX)

SOSlib

Software Authors:   Lu J, Muller S, Machné R, Flamm C
Referenced in: 3 Publications (2012–2019)
Related Software: SUNDIALS; COPASI; BioBayes; R; SBW; LibSBMLSim; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Biology and other natural sciences (92-XX)

DOTcvpSB

Software Authors:   Tomáš Hirmajer; Eva Balsa-Canto; Julio R Banga
Referenced in: 3 Publications (2014–2017)
Related Software: DOTcvp
Main Fields: Calculus of variations and optimal control; optimization (49-XX); Biology and other natural sciences (92-XX); Systems theory; control (93-XX)

EPE

Software Authors:   Demin, Oleg; Goryanin, Igor
Referenced in: 4 Publications (2009–2015)
Related Software: DBSolve
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Statistical mechanics, structure of matter (82-XX)

Gaggle

Software Authors:   P.T. Shannon, D.J. Reiss, R. Bonneau, N.S. Baliga
Referenced in: 0 Publications
Related Software: GOPET; BayGO; GOLEM; GOtcha; BiNGO; ProbCD; …
Main Fields:

HybridSystemsLab

Software Authors:   Sanfelice, Ricardo G.
Referenced in: 4 Publications (2021–2022)
Related Software: HyEQ; YALMIP; Matlab
Main Fields: Systems theory; control (93-XX)

libRoadRunner

Software Authors:   Somogyi, E. T. et al.
Referenced in: 1 Publication (2017)
Related Software: tellurium; Python; SUNDIALS; COPASI; SBW; LibSBMLSim; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

MABSys

Software Authors:   Lemaire, François; Ürgüplü, Asli
Referenced in: 4 Publications (2010–2016)
Related Software: RegularChains; Indiff; AIDA; Maple; DIFFALG; ExpandedLiePointSymmetry
Main Fields: Commutative algebra (13-XX); Real functions (26-XX); Ordinary differential equations (34-XX)

MMG

Software Authors:   Sanguinetti G, Noirel J, Wright PC
Referenced in: 1 Publication (2019)
Related Software: GeneNetWeaver; Path2Models; SOSlib; LASSIE; BioPreDyn-bench; sgnesR; …
Main Fields: Biology and other natural sciences (92-XX)

OPERAS

Software Authors:   Stamatopoulou, Ioanna; Kefalas, Petros; Gheorghe, Marian
Referenced in: 2 Publications (2009–2017)
Related Software: NetLogo
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX); Game theory, economics, finance, and other social and behavioral sciences (91-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
Referenced 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)

PEtab

Software Authors:   Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul L. Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl
Referenced in: 1 Publication (2020)
Related Software: Data2Dynamics; COPASI; AMIGO; pyPESTO; Antimony; Python; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX)

QNSTOP

Software Authors:   B. D. Amos, D. R. Easterling, L. T. Watson, W. I. Thacker, B. S. Castle, M. W. Trosset
Referenced in: 4 Publications (2016–2020)
Related Software: UOBYQA; DELAUNAYSPARSE; Algorithm 587; DeWall; LAPACK; VTDIRECT95; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Operations research, mathematical programming (90-XX)

TinkerCell

Software Authors:   Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro
Referenced in: 2 Publications (2014–2015)
Related Software: TABASCO; lpSolve; SUNDIALS; SciPy; ProMoT; SynBioSS; …
Main Fields: Ordinary differential equations (34-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

ARACNe-AP

Software Authors:   Lachmann A, Giorgi FM, Lopez G, Califano A.
Referenced in: 2 Publications (2018–2019)
Related Software: pycit; infotheory; IDTxl; MDEntropy; SciPy; NumPy; …
Main Fields: Biology and other natural sciences (92-XX)

BiNoM

Software Authors:   Andrei Zinovyev; Eric Viara; Laurence Calzone; Emmanuel Barillot
Referenced in: 2 Publications (2012–2015)
Related Software: CellPublisher; Pathway Commons; Ginsim; elmap
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

CMBSlib

Software Authors:   Sylvian Soliman, François Fages
Referenced in: 3 Publications (2005–2008)
Related Software: BIOCHAM; KEGG; Cellerator; CSPLib
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX); Systems theory; control (93-XX)

COBRApy

Software Authors:   Ali Ebrahim, Joshua A Lerman, Bernhard O Palsson, Daniel R Hyduke
Referenced in: 2 Publications (2015–2019)
Related Software: METRADE; DFBAlab; MoNeRe; COBRA Toolbox; fastGapFill; meneco; …
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

JSBML

Software Authors:   Dräger, A., Rodriguez, N., Dumousseau, M., Dörr, A., Wrzodek, C., Novère, N.L., Zell, A., Hucka, M.
Referenced 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)

MI-GRAAL

Software Authors:   Oleksii Kuchaiev; Natasa Przulj
Referenced in: 2 Publications (2013–2020)
Related Software: IsoRankN; IsoRank; Natalie; GHOST; NABEECO; SPINAL; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

ModSpec

Software Authors:   D. Amsallem; J. Roychowdhury
Referenced in: 3 Publications (2013–2016)
Related Software: Rallpacks
Main Fields: Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

NETASA

Software Authors:   Ahmad, S.; Gromiha, M. M.
Referenced in: 3 Publications (2005–2018)
Related Software: RBSURFpred; OnD-CRF; Hum-mPLoc; Euk-mPLoc; iRSpot-EL; iRNA-PseColl; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX); Information and communication theory, circuits (94-XX)

NIMEFI

Software Authors:   Ruyssinck, J., Huynh-Thu, V.A., Geurts, P., Dhaene, T., Demeester, P., Saeys, Y.
Referenced in: 2 Publications (2017–2020)
Related Software: Espresso; InterpretML; Alibi Explain; auto-sklearn; dalex; AI Explainability 360; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

OKVAR-Boost

Software Authors:   Lim N, Senbabaoglu Y, Michailidis G, d'Alché-Buc F.
Referenced in: 3 Publications (2013–2016)
Related Software: ARACNE; fda (R); GeneNetWeaver; G1DBN; UNLocBoX; TIGRESS; …
Main Fields: Operator theory (47-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

PyBioNetFit

Software Authors:   Mitra, ED; Suderman, R.; Colvin, J.; Ionkov, A.; Hu, A.; Sauro, HM; Posner, RG; Hlavacek, WS
Referenced in: 1 Publication (2020)
Related Software: COPASI; AMIGO; tellurium; MEIGO; BioNetGen; Data2Dynamics; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX)

PyNCT

Software Authors:   Draelants, Delphine; Kłosiewicz, Przemysław; Broeckhove, Jan; Vanroose, Wim
Referenced in: 3 Publications (2015–2021)
Related Software: LOCA; NumPy; Python; AUTO; MATCONT; Trilinos; …
Main Fields: Partial differential equations (35-XX); Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX)

pyPESTO

Software Authors:   Schmiester, Leonard; Weindl, Daniel; Hasenauer, Jan
Referenced in: 1 Publication (2020)
Related Software: AMIGO; Data2Dynamics; PEtab; COPASI; PyBioNetFit; PESTO; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX)

rBioNet

Software Authors:   Thorleifsson, S.G.; Thiele, I.
Referenced in: 2 Publications (2012–2016)
Related Software: COBRA Toolbox; Sbmltoolbox
Main Fields: Biology and other natural sciences (92-XX)

SBRML

Software Authors:   Dada, JO; Spasić, I; Paton, NW; Mendes, P
Referenced in: 1 Publication (2013)
Related Software: Virtual Cell; KEGG; COPASI; Octave; CellSys; cPath; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Biology and other natural sciences (92-XX)

SloppyCell

Software Authors:   Ryan Gutenkunst
Referenced in: 3 Publications (2009–2016)
Related Software: ObservabilityTest; Python; GenSSI; DAISY; tn; BioModels; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Biology and other natural sciences (92-XX); Systems theory; control (93-XX)

SwisTrack

Software Authors:   Lochmatter, T., Roduit, P., Cianci, C., Correll, N., Jacot, J., Martinoli, A.
Referenced in: 3 Publications (2008–2016)
Related Software: COPL_DSDP
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

SYSBIONS

Software Authors:   Johnson, R, Kirk, P, Stumpf, M P
Referenced in: 2 Publications (2018–2019)
Related Software: BioBayes; abc; BCM; PyMC; ABC-SysBio; SciPy; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

anNET

Software Authors:   Nicola Zamboni, Anne Kümmel, Matthias Heinemann
Referenced in: 1 Publication (2011)
Related Software: expa; COBRA Toolbox; Bio-SPICE; Metatool; Celldesigner; LINDO; …
Main Fields: Numerical analysis (65-XX); Classical thermodynamics, heat transfer (80-XX)

AutoClass@IJM

Software Authors:   Achcar, Fiona; Camadro, Jean-Michel; Mestivier, Denis
Referenced in: 1 Publication (2018)
Related Software: ZIFA; AutoClass; t-SNE; SpectralCAT; BayesLCA
Main Fields: Statistics (62-XX); Computer science (68-XX)

BioGrapher

Software Authors:   Viswanathan, Rama; Liang, Sijia; Yang, Yang; Jungck, John R.
Referenced in: 2 Publications (2015–2016)
Related Software: JavaBENZER; Excel; VBA; Visual Basic; Graphviz
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

BioPreDyn-bench

Software Authors:   Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR
Referenced in: 2 Publications (2019–2021)
Related Software: PESTO; Data2Dynamics; SUNDIALS; EvA2; Qlopt; AMIGO; …
Main Fields: Ordinary differential equations (34-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

BioSimulator.jl

Software Authors:   Alfonso Landeros, Timothy Stutz, Kevin L. Keys, Alexander Alekseyenko, Janet S. Sinsheimer, Kenneth Lange, Mary Sehl
Referenced in: 0 Publications
Related Software: DifferentialEquations.jl; Julia; DiffEqFlux; Flux; GR Framework; epinet; …
Main Fields:

BioTapestry

Software Authors:   Institute for Systems Biology (ISB); William Longabaugh; Eric Davidson; Hamid Bolouri; et al.
Referenced in: 2 Publications (2011–2020)
Related Software: Virtual Cell; Bio-PEPA; ViennaRNA; MrBayes; tYNA; PhyNav; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

CellMiner

Software Authors:   Reinhold WC, Sunshine M, Liu H, Varma S, Kohn KW, Morris J, Doroshow J, Pommier Y
Referenced in: 1 Publication (2016)
Related Software: R; enetLTS; pense; robustHD; Galaxy; ROAST; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

CellPublisher

Software Authors:   L.A. Flórez, C.R. Lammers, R. Michna, J. Stülke
Referenced in: 1 Publication (2015)
Related Software: Pathway Commons; BiNoM; Ginsim; elmap; Google Maps API; GBrowse; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

Cryo-EM

Software Authors:   Eva Nogales, Sjors H.W. Scheres
Referenced in: 2 Publications (2020–2022)
Related Software: RELION; cryoSPARC; FINUFFT; FREALIGN; NFFT3; EMan; …
Main Fields: Numerical analysis (65-XX); Biology and other natural sciences (92-XX); Information and communication theory, circuits (94-XX)

DBSolve

Software Authors:   –
Referenced in: 2 Publications (2009–2016)
Related Software: GNA; COPASI; EPE
Main Fields: Computer science (68-XX); Game theory, economics, finance, and other social and behavioral sciences (91-XX); Biology and other natural sciences (92-XX)

explorase

Software Authors:   Michael Lawrence, Eun-kyung Lee, Dianne Cook, Jihong Kim, Hogeun An, Dongshin Kim
Referenced in: 0 Publications
Related Software: R; rattle; GTK+; limma; RGtk2; GGobi; …
Main Fields:

Gillespie.jl

Software Authors:   Frost, Simon D.W.
Referenced in: 0 Publications
Related Software: GillespieSSA; Julia; JuMP; libSBML; DifferentialEquations.jl; COPASI; …
Main Fields:

GillesPy

Software Authors:   J. H. Abel, B. Drawert, A. Hellander, and L. R. Petzold
Referenced 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)

GReTA

Software Authors:   Alessandro Attanasi, Andrea Cavagna, Lorenzo Del Castello, Irene Giardina, Asja Jelic, Stefania Melillo, Leonardo Parisi, Fabio Pellacini, Edward Shen, Edmondo Silvestri, Massimiliano Viale
Referenced in: 1 Publication (2018)
Related Software: Trackpy; TracTrac; OpenLPT; OpenPTV; Python; MyPTV
Main Fields: Ordinary differential equations (34-XX); Partial differential equations (35-XX); Statistical mechanics, structure of matter (82-XX)