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Found 461 Software Packages (Results 1–100)

Matlab

Software Authors:   MathWorks Inc
Referenced in: 12,950 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)

PMA

Software Authors:   Daniela Witten, Rob Tibshirani, Sam Gross, Balasubramanian Narasimhan
Referenced in: 136 Publications (2009–2022)
Related Software: R; glasso; ElemStatLearn; glmnet; GitHub; YALMIP; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

DSTool

Software Authors:   J Guckenheimer, BA Meloon, MR Myers, FJ Wicklin, Michael Patra
Referenced in: 103 Publications (1992–2021)
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)

SHOGUN

Software Authors:   Sonnenburg, Sören; Rätsch, Gunnar; Schäfer, Christin; Schölkopf, Bernhard; Henschel, Sebastian; Widmer, Christian; Behr, Jonas; Zien, Alexander; De Bona, Fabio; Binder, Alexander; Gehl, Christian; Franc, Vojtěch
Referenced in: 85 Publications (2005–2022)
Related Software: SimpleMKL; LIBSVM; UCI-ml; Mosek; SpicyMKL; Matlab; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

PHYLIP

Software Authors:   Felsenstein, J.
Referenced in: 87 Publications (1996–2021)
Related Software: ClustalW; PAUP*; MrBayes; fastDNAml; R; PAML; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

Cell-PLoc

Software Authors:   Chou, K. C.; Shen, H. B.
Referenced in: 82 Publications (2008–2019)
Related Software: Euk-mPLoc; LIBSVM; iLoc-Euk; Memtype-2L; Plant-mPLoc; iLoc-Hum; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

DAVID

Software Authors:   Huang DW, Sherman BT, Tan Q et al
Referenced in: 44 Publications (2007–2022)
Related Software: KEGG; Bioconductor; R; Cytoscape; STRING; limma; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Numerical analysis (65-XX)

PAUP*

Software Authors:   David Swofford
Referenced in: 49 Publications (1987–2021)
Related Software: PHYLIP; RAxML; MrBayes; ClustalW; PAML; fastDNAml; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

Chaste

Software Authors:   Bernabeu, Miguel O.; Bordas, Rafel; Pathmanathan, Pras; Pitt-Francis, Joe; Cooper, Jonathan; Garny, Alan; Gavaghan, David J.; Rodriguez, Blanca; Southern, James A.; Whiteley, Jonathan P.
Referenced in: 52 Publications (2009–2022)
Related Software: CellML; PhysiCell; PETSc; CellSys; Biocellion; Matlab; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Mechanics of deformable solids (74-XX)

RegulonDB

Software Authors:   Gama-Castro, S.; Jimenez-Jacinto, V.; Peralta-Gil, M.; Santos-Zavaleta, A.; Peñaloza-Spinola, M.I.; Contreras-Moreira, B.; Segura-Salazar, J.; Muñiz-Rascado, L.; Martinez-Flores, I.; Salgado, H.; Bonavides-Martinez, C.; Abreu-Goodger, C.; Rodríguez-Penagos, C.; Miranda-Ríos, J.; Morett, E.; Merino, E.; Huerta, A.M.; Treviño-Quintanilla, L.; Collado-Vides, J.
Referenced in: 30 Publications (2002–2020)
Related Software: KEGG; ARACNE; GeneNetWeaver; R; WebLogo; JASPAR; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-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: 43 Publications (2005–2021)
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)

STAMP

Software Authors:   Koopman, S. J.; Harvey, A. C.; Doornik, J. A.; Shephard, A.
Referenced in: 36 Publications (1998–2019)
Related Software: SsfPack; Ox; R; Matlab; SAS; Stata; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Game theory, economics, finance, and other social and behavioral sciences (91-XX)

MUMMER

Software Authors:   S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, S.L. Salzberg
Referenced in: 29 Publications (2003–2022)
Related Software: LAGAN; REPuter; BLASTZ; PatternHunter; AVID; DIALIGN; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Computer science (68-XX)

Pse-in-One

Software Authors:   Liu, B.; Liu, F.; Wang, X.; Chen, J.; Fang, L.; Chou, K. -C.:
Referenced in: 41 Publications (2015–2019)
Related Software: iRSpot-PseDNC; PseKNC; iPro54-PseKNC; pLoc-mEuk; iRNA-PseColl; pLoc-mAnimal; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-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)

DSPCA

Software Authors:   Alexandre d'Aspremont, Laurent El Ghaoui, Michael I. Jordan, Gert R. G. Lanckriet, Ronny Luss
Referenced in: 35 Publications (2005–2015)
Related Software: SeDuMi; SDPT3; SDPLR; Yale Face; Human Mortality; CAPTAIN; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

EMBOSS

Software Authors:   Rice, P.; Longden, I.; Bleasby, A.
Referenced in: 19 Publications (2004–2019)
Related Software: BLAST; ClustalW; PSI-BLAST; UniProt; Cd-hit; KEGG; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Statistics (62-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)

Fiji

Software Authors:   Schindelin, J., et al
Referenced in: 22 Publications (2016–2021)
Related Software: ImageJ; CellProfiler; R; Python; COMSOL; FFTW; …
Main Fields: Partial differential equations (35-XX); Statistics (62-XX); Computer science (68-XX)

Knut

Software Authors:   Szalai, Robert
Referenced in: 30 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)

DESeq2

Software Authors:   Michael Love, Constantin Ahlmann-Eltze, Kwame Forbes, Simon Anders, Wolfgang Huber
Referenced in: 26 Publications (2015–2022)
Related Software: Bioconductor; edgeR; R; DEseq; Voom; BaySeq; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Numerical analysis (65-XX)

CompuCell3D

Software Authors:   Popławski, Nikodem J.; Shirinifard, Abbas; Swat, Maciej; Glazier, James A.
Referenced in: 24 Publications (2008–2022)
Related Software: PhysiCell; Chaste; EmbryoMaker; ParaView; CellSys; Microvessel Chaste; …
Main Fields: Partial differential equations (35-XX); Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-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)

Khan Academy

Software Authors:   Khan Academy
Referenced in: 12 Publications (2009–2021)
Related Software: realmath; Tenmarks; Mathegym; IXL; abfrager; bettermarks; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-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)

Biopython

Software Authors:   Cock, P. J. A.; Antao, T.; Chang, J. T.; Chapman, B. A.; Cox, C. J.; Dalke, A.; Friedberg, I.; Hamelryck, T.; Kauff, F.; Wilczynski, B.; De Hoon, M. J.
Referenced in: 7 Publications (2009–2019)
Related Software: Python; bioperl; BioJava; DendroPy; TRANSFAC; UniProt; …
Main Fields: General and overarching topics; collections (00-XX); Mathematical logic and foundations (03-XX); Statistics (62-XX)

BLAD

Software Authors:   Boulier, François
Referenced in: 20 Publications (2007–2022)
Related Software: Maple; DAISY; DIFFALG; RegularChains; Epsilon; SIAN; …
Main Fields: Field theory and polynomials (12-XX); Commutative algebra (13-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)

SfePy

Software Authors:   R. Cimrman et al.
Referenced in: 18 Publications (2012–2022)
Related Software: Python; FEniCS; SciPy; petsc4py; mpi4py; Matlab; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Mechanics of deformable solids (74-XX)

CLUTO

Software Authors:   university of Minnesota; Karypis G
Referenced in: 12 Publications (2003–2020)
Related Software: UCI-ml; skmeans; Scikit; Python; R; clue; …
Main Fields: Linear and multilinear algebra; matrix theory (15-XX); Statistics (62-XX); Computer science (68-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)

Mesquite

Software Authors:   Maddison, W.P.;D.R. Maddison
Referenced in: 12 Publications (2006–2021)
Related Software: R; kdetrees; ape; Castor; ggtree; IcyTree; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

MemHyb

Software Authors:   Hayat, Maqsood; Khan, Asifullah
Referenced in: 15 Publications (2012–2019)
Related Software: Memtype-2L; iLoc-Hum; iRSpot-PseDNC; Pse-in-One; iLoc-Euk; iDNA-Methyl; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

phytools

Software Authors:   Liam J. Revell
Referenced in: 10 Publications (2014–2021)
Related Software: R; ape; GEIGER; MrBayes; BEAUti; phangorn; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-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)

Nuc-ploc

Software Authors:   Hong-Bin Shen, Kuo-Chen Chou
Referenced in: 13 Publications (2009–2018)
Related Software: PseAAC; Cell-PLoc; Euk-PLoc; Memtype-2L; iLoc-Hum; iRSpot-PseDNC; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

drc

Software Authors:   Christian Ritz, Jens Strebig
Referenced in: 8 Publications (1996–2020)
Related Software: R; nlstools; nlme; sandwich; nls2; nlrwr; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Numerical analysis (65-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)

PermutMatrix

Software Authors:   G. Caraux; S. Pinloche
Referenced in: 10 Publications (2009–2019)
Related Software: seriation; GAP; R; TSP; Matlab; PQSER; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Numerical analysis (65-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)

ForceAtlas2

Software Authors:   Jacomy, M.; Venturini, T.; Heymann, S.; Bastian, M.
Referenced in: 12 Publications (2017–2022)
Related Software: Gephi; GitHub; Supracentrality; CHAMP; GenLouvain; UMAP; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

SW1PerS

Software Authors:   J. A. Perea, A. Deckard, S. B. Haase, J. Harer
Referenced in: 10 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)

blockcluster

Software Authors:   Serge Iovleff, Parmeet Singh Bhatia, Josselin Demont, Gerard Goavert, Vincent Brault, Christophe Biernacki, Gilles Celeux
Referenced in: 8 Publications (2017–2022)
Related Software: biclust; BicAT; R; clustMD; BiGGEsTS; UCI-ml; …
Main Fields: Order, lattices, ordered algebraic structures (06-XX); Statistics (62-XX)

ChEMBL

Software Authors:   Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP
Referenced in: 7 Publications (2012–2022)
Related Software: DrugBank; KEGG; PubChem; CDK; MovieLens; BindingDB; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

GEOquery

Software Authors:   Sean D, Meltzer PS
Referenced in: 7 Publications (2016–2021)
Related Software: R; Bioconductor; shiny; WEKA; adaptMT; AdaPT; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-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)

Lynx

Software Authors:   Ganesh, V., O’Donnell, C.W., Soos, M., Devadas, S., Rinard, M.C., Solar-Lezama, A.
Referenced in: 9 Publications (2013–2021)
Related Software: MathCheck; Maple; FFTW; SMT-LIB; Mathematica; z3; …
Main Fields: Combinatorics (05-XX); Number theory (11-XX); Geometry (51-XX)

PESTO

Software Authors:   Stapor, P.; et al
Referenced in: 9 Publications (2018–2022)
Related Software: Data2Dynamics; AMIGO; COPASI; SUNDIALS; MEIGO; R; …
Main Fields: Ordinary differential equations (34-XX); Partial differential equations (35-XX); Numerical analysis (65-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)

HMDB

Software Authors:   Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al.
Referenced in: 2 Publications (2020–2021)
Related Software: Cytoscape; plotly; Highcharter; shiny; OOMPA; hgu133plus2.db; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

pLoc_bal-mHum

Software Authors:   Chou, K.-C.; Cheng, X.; Xiao, X
Referenced in: 9 Publications (2019)
Related Software: pLoc-mGneg; iPromoter-2L; iRSpot-EL; iRNA-PseColl; pLoc-mEuk; pLoc-mAnimal; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

Segmentor3IsBack

Software Authors:   Alice Cleynen, Michel Koskas, Emilie Lebarbier, Guillem Rigaill, Stephane Robin
Referenced in: 5 Publications (2017–2021)
Related Software: changepoint; wbs; R; FDRSeg; stepR; not; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX)

StochPy

Software Authors:   Maarleveld, T. R.; Olivier, B. G.; Bruggeman, F. J.
Referenced in: 8 Publications (2017–2022)
Related Software: COPASI; BioNetGen; StochKit2; JuMP; libSBML; DifferentialEquations.jl; …
Main Fields: Ordinary differential equations (34-XX); Approximations and expansions (41-XX); Probability theory and stochastic processes (60-XX)

TAMBIS

Software Authors:   Stevens, R.; Baker, P.; Bechhofer, S.; Ng, G.; Jacoby, A.; Paton, N.W.; Goble, C.A.; Brass, A.
Referenced in: 2 Publications (2001–2006)
Related Software: UniProt; KEGG; caGrid; Soap; Eiffel; i*; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

TWILIGHT

Software Authors:   Scheid, Stefanie; Spang, Rainer
Referenced in: 6 Publications (2005–2012)
Related Software: twilight; Bioconductor; R; COBS; DAVID; compdiagTools; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Numerical analysis (65-XX)

Virtual Cell

Software Authors:   Loew, L. M.; Schaff, J. C.
Referenced in: 7 Publications (2003–2020)
Related Software: GEPASI; E-CELL; SCAMP; KEGG; COPASI; MEG; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Computer science (68-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)

GeneMark

Software Authors:   Besemer, J., Borodovsky, M.
Referenced in: 6 Publications (1993–2016)
Related Software: FragGeneScan; SUMO; Pfam; GeneMarkS; UniProt; InterProScan; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Probability theory and stochastic processes (60-XX); Statistics (62-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)

SECT

Software Authors:   Crawford, Lorin; Monod, Anthea; Chen, Andrew X.; Mukherjee, Sayan; Rabadán, Raúl
Referenced in: 8 Publications (2020–2021)
Related Software: PersistenceImages; TDA; kernelTDA; Holes; Gudhi; Morpho; …
Main Fields: Algebraic topology (55-XX); Probability theory and stochastic processes (60-XX); Statistics (62-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)

Biota

Software Authors:   B. Jones,W. Werner, J. Schrank
Referenced in: 7 Publications (1994–2005)
Related Software: NADA; MINITAB; BioQUEST
Main Fields: Dynamical systems and ergodic theory (37-XX); Statistics (62-XX); Classical thermodynamics, heat transfer (80-XX)

CCP4

Software Authors:   Winn, M.D.; Ballard, C.C.; Cowtan, K.D.; Dodson, E.J.; Emsley, P.
Referenced in: 4 Publications (2005–2019)
Related Software: Coot; UglyMol; UniProt; MOLREP; EXI; molstack; …
Main Fields: General and overarching topics; collections (00-XX); Statistical mechanics, structure of matter (82-XX); Operations research, mathematical programming (90-XX)

COXPRESdb

Software Authors:   Obayashi, T.; Hayashi, S.; Shibaoka, M.; Saeki, M.; Ohta, H.; Kinoshita, K.
Referenced in: 3 Publications (2011–2022)
Related Software: KEGG; ArrayExpress; Cytoscape; Symmetric NMTF; QPLIB; STRING; …
Main Fields: Statistics (62-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

Dotplot

Software Authors:   Church, K., Helfman, I.
Referenced in: 4 Publications (2005–2017)
Related Software: CCFinder; CP-miner; DECKARD; Winnowing; UMLDiff; ArgoUML; …
Main Fields: Linear and multilinear algebra; matrix theory (15-XX); Dynamical systems and ergodic theory (37-XX); Statistics (62-XX)

GlobPlot

Software Authors:   Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson
Referenced in: 4 Publications (2008–2019)
Related Software: IUPred; RONN; FoldIndex; FoldUnfold; DISOPRED; ELM; …
Main Fields: Mathematical logic and foundations (03-XX); Statistics (62-XX); Biology and other natural sciences (92-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)

MAPPFinder

Software Authors:   Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, Conklin BR
Referenced in: 4 Publications (2006–2011)
Related Software: GenMAPP; KEGG; Bioconductor; DAVID; FatiGO; Reactome; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Numerical analysis (65-XX)

MCFDR

Software Authors:   Sandve, G., Ferkingstad, E.; Nygard, S
Referenced in: 7 Publications (2014–2020)
Related Software: MMCTest; ORIOGEN; simctest; QuickMMCTest; iBBiG; bootlib; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Numerical analysis (65-XX)

MUSCOP

Software Authors:   Potschka, Andreas
Referenced in: 7 Publications (2001–2021)
Related Software: NewtonLib; ADOL-C; UFL; FEniCS; DOLFIN; MUMPS; …
Main Fields: Partial differential equations (35-XX); Calculus of variations and optimal control; optimization (49-XX); Global analysis, analysis on manifolds (58-XX)

parest_dae

Software Authors:   Casian Pantea, Ankur Gupta, James B. Rawlings, Gheorghe Craciun
Referenced in: 7 Publications (2014–2020)
Related Software: SINGULAR; neural ideal; GitHub; Ginsim; Macaulay2; DAISY; …
Main Fields: Field theory and polynomials (12-XX); Commutative algebra (13-XX); Algebraic geometry (14-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)

RIATA-HGT

Software Authors:   Nakhleh, Luay; Ruths, Derek; Wang, Li-San
Referenced in: 7 Publications (2005–2021)
Related Software: PhyloNet; PAUP*; T-REX; MSCquartets; PhyloNetworks; Macaulay2; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-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)

bioNMF

Software Authors:   Montano A, Saez P, Chagoyen M, Tirado F, Carazo JM, Marqui RD
Referenced in: 5 Publications (2008–2020)
Related Software: FABIA; DAVID; Wenxiang; MEGAN; ONE; RAST; …
Main Fields: Linear and multilinear algebra; matrix theory (15-XX); Statistics (62-XX); Numerical analysis (65-XX)

ConsensusPathDB

Software Authors:   Kamburov A, Pentchev K, Galicka H et al
Referenced in: 4 Publications (2011–2018)
Related Software: IntAct; BioGRID; igraph; STRINGdb; ANIMO; PRS; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

DDLab

Software Authors:   Wuensche, Andrew
Referenced in: 5 Publications (2011–2021)
Related Software: ConwayLife; Boids
Main Fields: Dynamical systems and ergodic theory (37-XX); Computer science (68-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)