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Found 202 Software Packages (Results 1–100)

LISREL

Software Authors:   Scientific Software International, Inc.,Skokie, IL 60077
Referenced in: 290 Publications (1979–2022)
Related Software: EQS; Mplus; R; Amos; PRELIS; lavaan; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Operations research, mathematical programming (90-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
Referenced 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)

limma

Software Authors:   Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK
Referenced in: 48 Publications (2005–2022)
Related Software: Bioconductor; gcrma; R; edgeR; Voom; DEseq; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

DAISY

Software Authors:   Giuseppina Bellu , Maria Pia Saccomani, Stefania Audoly , Leontina D’Angiò
Referenced in: 53 Publications (2008–2022)
Related Software: COMBOS; GenSSI; SIAN; BLAD; ObservabilityTest; MESSI; …
Main Fields: Commutative algebra (13-XX); Ordinary differential equations (34-XX); Statistics (62-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)

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)

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)

CellML

Software Authors:   Hedley, Warren J.; Nelson, Melanie R.; Bullivant, David P.; Nielsen, Poul F.
Referenced in: 17 Publications (2001–2021)
Related Software: Chaste; COPASI; SUNDIALS; CellSys; R; Python; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Computer science (68-XX)

GNA

Software Authors:   Hidde de Jong, Johannes Geiselmann, Céline Hernandez, Michel Page
Referenced in: 25 Publications (2006–2021)
Related Software: BIOCHAM; Ginsim; Celldesigner; KEGG; RoVerGeNe; DiVinE; …
Main Fields: Mathematical logic and foundations (03-XX); Ordinary differential equations (34-XX); Computer science (68-XX)

VAMPnets

Software Authors:   Andreas Mardt, Luca Pasquali, Hao Wu, Frank Noé
Referenced in: 22 Publications (2019–2022)
Related Software: PDE-Net; torchdiffeq; TensorFlow; SINDy; GAIO; PRMLT; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Operator theory (47-XX); Numerical analysis (65-XX)

PyDSTool

Software Authors:   Clewley RH, Sherwood WE, LaMar MD, Guckenheimer JM
Referenced in: 17 Publications (2012–2021)
Related Software: MATCONT; Matlab; AUTO; XPPAUT; DDE-BIFTOOL; COCO; …
Main Fields: Ordinary differential equations (34-XX); Partial differential equations (35-XX); Dynamical systems and ergodic theory (37-XX)

Scicos

Software Authors:   INRIA
Referenced in: 19 Publications (2006–2019)
Related Software: Scilab; ScicosLab; FreeFem++; Modelica; Chaos; GPOPS; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX); Computer science (68-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)

ROCKET

Software Authors:   Barber, Rina Foygel; Kolar, Mladen
Referenced in: 13 Publications (2016–2021)
Related Software: glasso; covTest; TETRAD; huge; Knorm; limma; …
Main Fields: Statistics (62-XX); Computer science (68-XX)

ZIFA

Software Authors:   Pierson, E.; Yau, C.
Referenced in: 13 Publications (2018–2021)
Related Software: CIDR; t-SNE; MAST; SNN-Cliq; zinbwave; DESeq2; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

NFsim

Software Authors:   Sneddon MW, Faeder JR, Emonet T
Referenced 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)

Spikenet

Software Authors:   Arnaud Delorme; Simon J Thorpe
Referenced in: 8 Publications (2005–2014)
Related Software: NEURON; XPPAUT; UniProt; WebGestalt; KDDONTO; Protege; …
Main Fields: General and overarching topics; collections (00-XX); Numerical analysis (65-XX); Computer science (68-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)

Nengo

Software Authors:   T. Bekolay, J. Bergstra, E. Hunsberger, T. DeWolf, T. C. Stewart, D. Rasmussen, X. Choo, A. R. Voelker, C. Eliasmith
Referenced in: 9 Publications (2015–2021)
Related Software: Pynn; TensorFlow; Python; Brian; NEST; PyTorch; …
Main Fields: Partial differential equations (35-XX); Computer science (68-XX); Biology and other natural sciences (92-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)

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)

GGMselect

Software Authors:   Giraud, Christophe; Huet, Sylvie; Verzelen, Nicolas
Referenced in: 9 Publications (2012–2022)
Related Software: glasso; igraph; huge; QUIC; R; CAPUSHE; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

INDELible

Software Authors:   Fletcher W, Yang ZH
Referenced in: 7 Publications (2012–2021)
Related Software: SimPhy; ASTRID; DendroPy; RAxML; OCTAL; FastMe; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Computer science (68-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)

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)

booleannet

Software Authors:   Albert, I.; Thakar, J.; Li, S.; Zhang, R.; Albert, R.
Referenced in: 7 Publications (2010–2020)
Related Software: PANET; CANA; Python; Cellnoptr; Graphviz; XPPAUT; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

Bubbles

Software Authors:   Aapo Hyvärinen; Jarmo Hurri; Jaakko Väyrynen
Referenced in: 8 Publications (2005–2014)
Related Software: LIBSVM; MNIST; sfa; R; JPEG2000
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)

KEGGgraph

Software Authors:   Jitao David Zhang; Stefan Wiemann
Referenced in: 7 Publications (2011–2015)
Related Software: Bioconductor; KEGG; Reactome; igraph; clipper; graphite; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

MeCoSim

Software Authors:   Pérez-Hurtado, I.; Valencia-Cabrera, L.; Pérez-Jiménez, M. J.; Colomer, M. A.; Riscos-Núñez, A.
Referenced in: 8 Publications (2012–2020)
Related Software: P-Lingua; PMCGPU; CuSNP; gCol; jSpin; SPIN; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

BioShape

Software Authors:   Buti, F.; Cacciagrano, D.; Corradini, F.; Merelli, E.; Tesei, L.; Pani, M.
Referenced in: 4 Publications (2010–2014)
Related Software: Bio-PEPA; BioNetGen; BioAmbient Machine; PathSim; PEPA; StochKit; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Convex and discrete geometry (52-XX); Computer science (68-XX)

Cell Illustrator

Software Authors:   Matsuno, Hiroshi; Nagasaki, Masao; Miyano, Satoru; University of Tokyo.
Referenced in: 5 Publications (2009–2018)
Related Software: SNOOPY; SUNDIALS; CPN Assistant; ViennaRNA; MrBayes; tYNA; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

HMMmix

Software Authors:   Stevenn Volant; Caroline Berard
Referenced in: 5 Publications (2014–2021)
Related Software: CAPUSHE; CMA-ES; TAHMMAnnot; mclust; R; CRAN
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Statistical mechanics, structure of matter (82-XX)

HysterSoft

Software Authors:   Dimian, Mihai; Andrei, Petru
Referenced in: 6 Publications (2014–2022)
Related Software: GitHub; KronFit
Main Fields: Dynamical systems and ergodic theory (37-XX); Mechanics of particles and systems (70-XX); Statistical mechanics, structure of matter (82-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)

PROSPERous

Software Authors:   Jiangning Song, Fuyi Li, André Leier, Tatiana T Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I Webb, Robert N Pike
Referenced in: 6 Publications (2018–2021)
Related Software: 2L-piRNA; iDNA6mA-PseKNC; pLoc-mHum; iRNA-3typeA; pLoc-mGneg; iPromoter-2L; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

SQUAD

Software Authors:   Akram Méndez; Carlos Ramírez; Mauricio Pérez Martínez; Luis Mendoza
Referenced in: 5 Publications (2010–2021)
Related Software: C-ImmSim; CoLoMoTo; PyBoolNet; ERODE; Ginsim; z3; …
Main Fields: Biology and other natural sciences (92-XX); Systems theory; control (93-XX)

TRNSYS

Software Authors:   Thermal Energy System Specialists, LLC
Referenced in: 5 Publications (2001–2019)
Related Software: Matlab; EnergyPlus
Main Fields: Numerical analysis (65-XX); Fluid mechanics (76-XX); Classical thermodynamics, heat transfer (80-XX)

Ace

Software Authors:   Barton, J.P., De Leonardis E., Coucke A., Cocco S.
Referenced in: 5 Publications (2016–2021)
Related Software: Alakazam; Change-O; DeepTCR; repgenHMM; OLGA; SoDA2; …
Main Fields: Quantum theory (81-XX); Statistical mechanics, structure of matter (82-XX); Biology and other natural sciences (92-XX)

Antimony

Software Authors:   Lucian P. Smith, Frank T. Bergmann, Deepak Chandran, Herbert M. Sauro
Referenced in: 1 Publication (2010)
Related Software: Python; PEtab; Data2Dynamics; COPASI; SimpleSBML; libSBML; …
Main Fields: Probability theory and stochastic processes (60-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

Bio-PEPAd

Software Authors:   Caravagna, Giulio; Hillston, Jane
Referenced in: 4 Publications (2012–2015)
Related Software: Bio-PEPA; LBS; PRISM; BIOCHAM; UMDES; BlenX; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

DREAM4

Software Authors:   Greenfield, A., A. Madar, H. Ostrer, R. Bonneau
Referenced in: 4 Publications (2015–2020)
Related Software: graphite; TRANSFAC; Biopython; WGCNA; pcalg; GeneNetWeaver; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)

ESMERALDA

Software Authors:   Gernot A. Fink, Thomas Plötz
Referenced in: 2 Publications (2006–2013)
Related Software: IAM; StreamKM++; k-means++; UCI-ml; SIFT; IAM-OnDB; …
Main Fields: Statistics (62-XX); Computer science (68-XX)

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)

SReach

Software Authors:   Q. Wang, P. Zuliani, S. Kong, S. Gao, E. M. Clarke
Referenced in: 4 Publications (2015–2020)
Related Software: ProbReach; dReal; StocHy; AMYTISS; pFaces; SReachTools; …
Main Fields: Mathematical logic and foundations (03-XX); Ordinary differential equations (34-XX); Computer science (68-XX)

tellurium

Software Authors:   Kiri Choi, J Kyle Medley, Matthias König, Kaylene Stocking, Caroline Cannistra, Michal Galdzicki, Herbert Sauro
Referenced in: 1 Publication (2018)
Related Software: Python; COPASI; libRoadRunner; SUNDIALS; MEIGO; BioNetGen; …
Main Fields: Biology and other natural sciences (92-XX)

Biocellion

Software Authors:   Kang, S., Kahan, S., McDermott, J., Flann, N., Shmulevich, I.
Referenced in: 3 Publications (2020–2021)
Related Software: PhysiCell; Chaste; CellSys; Morpheus; Microvessel Chaste; EmbryoMaker; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

BioGAP

Software Authors:   Attila Egry-Nagy; Andrew Francis; Volker Gebhardt
Referenced in: 4 Publications (2014–2019)
Related Software: Mauve; GAP; GitHub; VIZ; TikZ; Graphviz
Main Fields: Combinatorics (05-XX); Order, lattices, ordered algebraic structures (06-XX); Group theory and generalizations (20-XX)

ChromHMM

Software Authors:   Ernst, J., Kellis, M.
Referenced in: 4 Publications (2017–2021)
Related Software: Bowtie 2; KEGG; edgeR; GitHub; STAR; intePareto; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-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)

GSVA

Software Authors:   Hänzelmann S, Castelo R, Guinney J
Referenced in: 4 Publications (2014–2021)
Related Software: Bioconductor; MSigDB; ROAST; DAVID; KEGG; edgeR; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

mmLib

Software Authors:   Ethan Merritt; Jay Painter
Referenced in: 3 Publications (2009–2017)
Related Software: PyClimate; pyMPI; Parallel netCDF; SciTools; Python; ACTS; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

multi2boolean

Software Authors:   Fauré, Adrien; Kaji, Shizuo
Referenced in: 4 Publications (2018–2019)
Related Software: Ginsim; YalSAT; Lingeling; Splatz; GRAT; Treengeling; …
Main Fields: Combinatorics (05-XX); Order, lattices, ordered algebraic structures (06-XX); Biology and other natural sciences (92-XX)

Psim

Software Authors:   Bianco, L., Manca, V., Marchetti, L., Petterlini, M.
Referenced in: 4 Publications (2007–2013)
Related Software: P-Lingua; pLinguaCore; gnuplot; BioSPI; PRISM
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

SERB

Software Authors:   Larkin, Timothy S.; Carruthers, Raymond I.; Soper, Richard S.
Referenced in: 4 Publications (1988–2006)
Related Software: Smalltalk; SIMSCRIPT; DYNAMO
Main Fields: Numerical analysis (65-XX); Computer science (68-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)

VirtualLeaf

Software Authors:   Merks, R., Guravage, M., Inzé, D., Beemster, G
Referenced in: 3 Publications (2015–2019)
Related Software: PhysiCell; CellSys; Microvessel Chaste; EmbryoMaker; CompuCell3D; Morpheus; …
Main Fields: Biology and other natural sciences (92-XX)

Yifei2020Dimensionality

Software Authors:   Li, Yifei; Johnston, Stuart T.; Buenzli, Pascal R.; van Heijster, Peter; Simpson, Matthew J.
Referenced in: 4 Publications (2021–2022)
Related Software: NeuralPDE.jl; DifferentialEquations.jl; GitHub
Main Fields: Partial differential equations (35-XX); Difference and functional equations (39-XX); Biology and other natural sciences (92-XX)

BiMAT

Software Authors:   Cesar O. Flores, Timothée Poisot, Sergi Valverde, Joshua S. Weitz
Referenced in: 2 Publications (2018–2019)
Related Software: LightGraphs.jl; EcologicalNetworks.jl; cheddar; bipartite; igraph; Julia; …
Main Fields: Statistical mechanics, structure of matter (82-XX)

BioModelAnalyzer

Software Authors:   Ahmed, Zara; Benque, David; Berezin, Sergey; Dahl, Anna Caroline E.; Fisher, Jasmin; Hall, Benjamin A.; Ishtiaq, Samin; Nanavati, Jay; Piterman, Nir; Riechert, Maik; Skoblov, Nikita
Referenced in: 2 Publications (2017–2021)
Related Software: Cytoscape.js; ATLANTIS; Aeon; PyBoolNet; ASSA-PBN; Ginsim; …
Main Fields: Mathematical logic and foundations (03-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

Bisulfighter

Software Authors:   Saito, Y., J. Tsuji, T. Mituyama
Referenced in: 3 Publications (2016)
Related Software: MethylSig; HMM-Fisher; MOABS; HMM-DM; BSmooth; methylKit; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

CellTrack

Software Authors:   Sacan, A., Ferhatosmanoglu, H., Coskun, H.
Referenced in: 2 Publications (2011–2012)
Related Software:
Main Fields: Dynamical systems and ergodic theory (37-XX); Computer science (68-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)

deBInfer

Software Authors:   Philipp H Boersch-Supan, Leah R Johnson
Referenced in: 2 Publications (2018–2021)
Related Software: R; Stan; deSolve; devtools; PBSddesolve; pomp; …
Main Fields: Ordinary differential equations (34-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

FluxSimulator

Software Authors:   Thomas W. Binsl, Katharine M. Mullen, Ivo H. M. van Stokkum, Jaap Heringa, Johannes H. G. M. van Beek
Referenced in: 0 Publications
Related Software: R; VCNet; edgeR; ARACNE; DEseq; JDINAC; …
Main Fields:

MoVisPP

Software Authors:   Chen, Ming; Hariharaputran, Sridhar; Hofestädt, Ralf; Kormeier, Benjamin
Referenced in: 3 Publications (2011)
Related Software: COPASI; SNOOPY; VisANT; Virtual Cell; Bio-SPICE; KEGG; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

netgwas

Software Authors:   Pariya Behrouzi, Ernst C. Wit
Referenced in: 1 Publication (2019)
Related Software: Matrix; R; igraph; MASS (R); onemap; Rbgl; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

OCTOPUS

Software Authors:   Håkan Viklund, Arne Elofsson
Referenced in: 1 Publication (2013)
Related Software: Phobius; pSLIP; clusfind; AAindex; PseAAC-Builder; PROSITE; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

PICS

Software Authors:   Zhang, Xuekui; Robertson, Gordon; Krzywinski, Martin; Ning, Kaida; Droit, Arnaud; Jones, Steven; Gottardo, Raphael
Referenced in: 3 Publications (2011–2015)
Related Software: nucleoSim; PuFFIN; nucleR; consensusSeekeR; VennDiagram; FindPeaks; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

Pomelo II

Software Authors:   Edward R. Morrissey; Ramón Diaz-Uriarte
Referenced in: 2 Publications (2010–2013)
Related Software: MetaPCA; AAPL; kerfdr; OrderedList; Bioconductor; R; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-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)

PyMix

Software Authors:   Georgi, B., Costa, I.G., Schliep, A
Referenced in: 2 Publications (2013–2021)
Related Software: BClass; pyMEF; Mixmod; JASPAR
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX); Information and communication theory, circuits (94-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)

Simbody

Software Authors:   Seth, Ajay; Sherman, Michael; Eastman, Peter; Delp, Scott
Referenced in: 2 Publications (2010–2015)
Related Software: OpenSim; Puppeteer; Simox; RBDL; Matlab; Octave; …
Main Fields: Mechanics of particles and systems (70-XX); Biology and other natural sciences (92-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)

VaxiJen

Software Authors:   Doytchinova, I.A.; Flower, D.R.
Referenced in: 3 Publications (2009–2017)
Related Software: I-TASSER; SVM-Prot; HIVcleave; EzyPred; Signal-3L; MITOPRED; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

ADMC++

Software Authors:   Phipps, Eric; Casey, Richard; Guckenheimer, John
Referenced in: 2 Publications (2006–2007)
Related Software: Matlab
Main Fields: Dynamical systems and ergodic theory (37-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

AGL-Score

Software Authors:   D. Nguyen; G.-W. Wei
Referenced in: 2 Publications (2021)
Related Software: TopologyNet; DioDe; HERMES; CliqueTop; DIPHA; Ripser; …
Main Fields: Algebraic geometry (14-XX); Differential geometry (53-XX); Algebraic topology (55-XX)

ALF

Software Authors:   Daniel A. Dalquen, Maria Anisimova, Gaston H. Gonnet, Christophe Dessimoz
Referenced in: 2 Publications (2016–2020)
Related Software: SimPhy; TTA Lynx; CodonTest; xREI; RevTrans; MACSE; …
Main Fields: Biology and other natural sciences (92-XX)

Altruist

Software Authors:   Agner Fog
Referenced in: 2 Publications (2003–2009)
Related Software: Triangle; MersenneTwister; XFEM
Main Fields: Mechanics of deformable solids (74-XX); Biology and other natural sciences (92-XX)

AMICI

Software Authors:   Fröhlich, F., Weindl, D., Schälte, Y., Pathirana, D., Paszkowski, Ł., Lines, G. T., Stapor, P., Hasenauer, J.
Referenced in: 1 Publication (2019)
Related Software: PEtab; Data2Dynamics; COPASI; ScrumPy; Antimony; MOCCASIN; …
Main Fields: Partial differential equations (35-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

ARSyN

Software Authors:   Nueda, Maria J.; Ferrer, Alberto; Conesa, Ana
Referenced in: 2 Publications (2012–2018)
Related Software: HaploReg; MapSplice; eSNV-detect; Strelka; Salmon; ZOOM; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

BATMAN

Software Authors:   Jie Hao, William Astle, Maria De Iorio, Timothy Ebbels
Referenced in: 2 Publications (2020–2021)
Related Software: BioMagResBank; SpinCouple; Nmrglue; Dolphin; Rtwalk; t-walk; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX)

BClass

Software Authors:   Arturo Medrano-Soto; J. Andres Christen; Julio Collado-vides
Referenced in: 1 Publication (2021)
Related Software: AutoClass; LISP-STAT; PyMix
Main Fields: Statistics (62-XX)

BicNET

Software Authors:   Henriques, R.; Madeira, SC
Referenced in: 1 Publication (2018)
Related Software: FABIA; BicPAMS; BicAT; EXPANDER; BicOverlapper; bibench; …
Main Fields: Statistics (62-XX)

BioLQM

Software Authors:   Naldi, A.
Referenced in: 1 Publication (2022)
Related Software: BoolNet; Pint; PyBoolNet; usefun; MaBoSS; Cellnoptr; …
Main Fields: Order, lattices, ordered algebraic structures (06-XX); Biology and other natural sciences (92-XX)

Biomine

Software Authors:   Lauri Eronen; Hannu Toivonen
Referenced in: 1 Publication (2019)
Related Software: PL-ranking; SEGS; SegMine; NCDawareRank; Fr-ONT; NetSDM; …
Main Fields: Computer science (68-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)

BIOSIM

Software Authors:   Bergdoll, Stefan; Koch, Uwe T.
Referenced in: 1 Publication (1995)
Related Software:
Main Fields: 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:

DEXUS

Software Authors:   Klambauer G, Unterthiner T, Hochreiter S.
Referenced in: 2 Publications (2016–2017)
Related Software: missForest; recount; HTSeq; impute; VIM; STAR; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

DIMM-SC

Software Authors:   Sun, Z., Wang, T., Deng, K., XF, W., Lafyatis, R., Ding, Y. et al.
Referenced in: 0 Publications
Related Software: umap; pcaReduce; DESeq2; SNN-Cliq; ZIFA; CIDR; …
Main Fields: Statistics (62-XX)

Filzbach

Software Authors:   D. Purves; V. Lyutsarev
Referenced in: 2 Publications (2013)
Related Software: trueskill; FACTORIE; Church; IBAL; CUDD
Main Fields: Computer science (68-XX)

Genoviz

Software Authors:   Helt GA, Nicol JW, Erwin E, Blossom E, Blanchard SG, Chervitz SA et al
Referenced in: 1 Publication (2016)
Related Software: Galaxy; ROAST; featureCounts; Rsubread; recount; PROPER; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

GillesPy2

Software Authors:   Sean Matthew; et al.
Referenced in: 1 Publication (2021)
Related Software: StochKit2; ppsim; Jupyter; Python; GitHub; StochKit
Main Fields: Biology and other natural sciences (92-XX)