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Found 177 Software Packages (Results 1–100)

KEGG

Software Authors:   Minoru Kanehisa; Susumu Goto
Cited in: 194 Publications (2003–2022)
Related Software: Bioconductor; R; UniProt; MetaCyc; Cytoscape; Reactome; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Numerical analysis (65-XX)

Bio-PEPA

Software Authors:   Federica Ciocchetta, Maria Luisa Guerriero, Vashti Galpin, Jane Hillston, Giulio Caravagna, Allan Clark, Andrea Degasperi, Adam Duguid, Kanimozhi Ellavarason, Stephen Gilmore, Laurence Loewe, Dimitrios Milios
Cited in: 91 Publications (2008–2022)
Related Software: PEPA; PRISM; BIOCHAM; BlenX; BioNetGen; LBS; …
Main Fields: Ordinary differential equations (34-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

REVEAL

Software Authors:   Liang, S., Fuhrman, S., Somogyi, R
Cited in: 22 Publications (2003–2022)
Related Software:
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

GNA

Software Authors:   Hidde de Jong, Johannes Geiselmann, Céline Hernandez, Michel Page
Cited 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)

CFinder

Software Authors:   Balázs Adamcsek; Gergely Palla; Illés J. Farkas; Imre Derényi; Tamás Vicsek
Cited in: 16 Publications (2006–2020)
Related Software: MCODE; BioGRID; R; Cytoscape; KEGG; igraph; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

MESSI

Software Authors:   Mercedes Pérez Millán, Alicia Dickenstein
Cited in: 22 Publications (2018–2022)
Related Software: REDLOG; QEPCAD; Maple; Binomials.m2; DAISY; Mathematica; …
Main Fields: Commutative algebra (13-XX); Algebraic geometry (14-XX); Ordinary differential equations (34-XX)

VAMPnets

Software Authors:   Andreas Mardt, Luca Pasquali, Hao Wu, Frank Noé
Cited 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)

FANMOD

Software Authors:   Wernicke, S.; Rasche, F.
Cited in: 17 Publications (2010–2021)
Related Software: Kavosh; MAVisto; MODA; KEGG; NeMoFinder; MetaCyc; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

iPPBS-Opt

Software Authors:   Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K. -C.
Cited in: 16 Publications (2016–2019)
Related Software: pSuc-Lys; iPro54-PseKNC; Pse-in-One; iRSpot-EL; iSuc-PseOpt; iDNA-Methyl; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

BiNGO

Software Authors:   Maere S., Heymans K., Kuiper M.
Cited in: 8 Publications (2010–2019)
Related Software: KEGG; Cytoscape; GOstat; GOLEM; R; GOPET; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

poroelasticity

Software Authors:   Lee, J. J.; Piersanti, E.; Mardal, K.-A.; Rognes, M. E.
Cited in: 13 Publications (2019–2022)
Related Software: FEniCS; NGSolve; Netgen; MUMPS; PCPATCH; hypre; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Mechanics of deformable solids (74-XX)

Kavosh

Software Authors:   Kashani ZR, Ahrabian H, Elahi E, Nowzari-Dalini A, Ansari ES, Asadi S, Mohammadi S, Schreiber F, Masoudi-Nejad A
Cited in: 9 Publications (2012–2021)
Related Software: FANMOD; MODA; NeMoFinder; gSpan; MetaCyc; MAVisto; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

PhyloNet

Software Authors:   Than, C., Ruths, D., Nakhleh, L.
Cited in: 10 Publications (2010–2022)
Related Software: PhyloNetworks; MSCquartets; RIATA-HGT; iGTP; DupTree; ASTRAL-II; …
Main Fields: Combinatorics (05-XX); Convex and discrete geometry (52-XX); Operations research, mathematical programming (90-XX)

RAMAS

Software Authors:   Kloetzer, Marius; Belta, Calin
Cited in: 12 Publications (2006–2013)
Related Software: RoVerGeNe; HyTech; PHAVer; SpaceEx; HSolver; Benchmarks; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

Spikenet

Software Authors:   Arnaud Delorme; Simon J Thorpe
Cited 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)

SA-cluster

Software Authors:   Cheng, Hong; Zhou, Yang; Huang, Xin; Yu, Jeffrey Xu
Cited in: 10 Publications (2012–2022)
Related Software: Inc-cluster; SimRank; DAVID; AppliedPredictiveModeling; igraph; GraRep; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

SW1PerS

Software Authors:   J. A. Perea, A. Deckard, S. B. Haase, J. Harer
Cited in: 10 Publications (2015–2022)
Related Software: Ripser; javaPlex; TDA; PersistenceImages; TopologyNet; GitHub; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Algebraic topology (55-XX); Statistics (62-XX)

GGMselect

Software Authors:   Giraud, Christophe; Huet, Sylvie; Verzelen, Nicolas
Cited 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)

StochPy

Software Authors:   Maarleveld, T. R.; Olivier, B. G.; Bruggeman, F. J.
Cited 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)

TIGRESS

Software Authors:   Haury, A.C., Mordelet, F., Vera-Licona, P., Vert, J.P.
Cited in: 9 Publications (2013–2019)
Related Software: SIRENE; ARACNE; glasso; JASPAR; BioGRID; glmnet; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Game theory, economics, finance, and other social and behavioral sciences (91-XX)

ADAM

Software Authors:   Hinkelmann F, Brandon M, Guang B, McNeill R, Blekherman G, Veliz-Cuba A, Laubenbacher R
Cited 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.
Cited 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)

DNA

Software Authors:   Gill, R., Datta, S., Datta, S.
Cited in: 7 Publications (2013–2021)
Related Software: WGCNA; GlobalMIT; slingshot; SNN-Cliq; MrTADFinder; CIDR; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

KEGGgraph

Software Authors:   Jitao David Zhang; Stefan Wiemann
Cited 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)

MCINTYRE

Software Authors:   Riguzzi, F.
Cited in: 7 Publications (2015–2019)
Related Software: ProbLog; PITA; CP-logic; PRISM; cplint; SWI-Prolog; …
Main Fields: Computer science (68-XX)

NETWORKINFERENCE

Software Authors:   Smith, V.Anne; Jarvis, Erich D.; Hartemink, Alexander J.
Cited in: 8 Publications (2002–2020)
Related Software: Brain Connectivity Toolbox; Figaro; PRISM; KEGG; Church; TETRAD; …
Main Fields: Ordinary differential equations (34-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

TopologyNet

Software Authors:   Zixuan Cang, Guo-Wei Wei
Cited in: 8 Publications (2020–2022)
Related Software: Ripser; PersistenceImages; javaPlex; Dionysus; PHAT; Gudhi; …
Main Fields: Combinatorics (05-XX); Differential geometry (53-XX); Algebraic topology (55-XX)

jHoles

Software Authors:   Binchi, Jacopo; Merelli, Emanuela; Rucco, Matteo; Petri, Giovanni; Vaccarino, Francesco
Cited in: 7 Publications (2014–2021)
Related Software: javaPlex; PHAT; Perseus; Gudhi; Ripser; GitHub; …
Main Fields: Algebraic topology (55-XX); Numerical analysis (65-XX); Quantum theory (81-XX)

parest_dae

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

PoCaB

Software Authors:   Samal, Satya Swarup; Errami, Hassan; Weber, Andreas
Cited 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)

SABRE

Software Authors:   Didier, F., Henzinger, T.A., Mateescu, M., Wolf, V
Cited in: 5 Publications (2011–2016)
Related Software: PRISM; MARCIE; Bio-PEPA; SBML Test Suite; INFAMY; MRMC; …
Main Fields: Probability theory and stochastic processes (60-XX); Numerical analysis (65-XX); Computer science (68-XX)

GADDI

Software Authors:   S. Zhang, S. Li, J. Yang
Cited in: 4 Publications (2014–2019)
Related Software: Fg-index; TALE; SAPPER; GraphGrep; SAGA; GString; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX)

GHOST

Software Authors:   Rob Patro; Carl Kingsford
Cited in: 6 Publications (2013–2021)
Related Software: IsoRank; SPINAL; L-GRAAL; IsoRankN; NETAL; HubAlign; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

Polynome

Software Authors:   Dimitrova, Elena; García-Puente, Luis David; Hinkelmann, Franziska; Jarrah, Abdul S.; Laubenbacher, Reinhard; Stigler, Brandilyn; Stillman, Michael; Vera-Licona, Paola
Cited 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)

SQUAD

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

Antimony

Software Authors:   Lucian P. Smith, Frank T. Bergmann, Deepak Chandran, Herbert M. Sauro
Cited 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)

BioNet

Software Authors:   Beisser, D.; Klau, G. W.; Dandekar, T.; Mueller, T., Dittrich, M
Cited in: 4 Publications (2014–2018)
Related Software: Bioconductor; miRecords; STRING; TopHat; Cytoscape; igraph; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

Diffcorr

Software Authors:   Atsushi Fukushima, Kozo Nishida
Cited in: 3 Publications (2016–2018)
Related Software: R; bc3net; igraph; DCGL; VCNet; edgeR; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

DREAM4

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

Inc-cluster

Software Authors:   Cheng, Hong; Zhou, Yang; Huang, Xin; Yu, Jeffrey Xu
Cited in: 5 Publications (2012–2020)
Related Software: SA-cluster; GraRep; node2vec; AS 136; APCluster; apcluster; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

MODA

Software Authors:   Omidi S, Schreiber F, Masoudi-Nejad A
Cited in: 3 Publications (2014–2020)
Related Software: Kavosh; NeMoFinder; FANMOD; Graemlin; gSpan; STAMP; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

NeMoFinder

Software Authors:   Chen J, Hsu M, Lee L, Ng SK
Cited in: 5 Publications (2009–2020)
Related Software: MODA; Kavosh; FANMOD; Graemlin; KEGG; gSpan; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

SING

Software Authors:   Raffaele Di Natale, Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dennis Shasha
Cited in: 4 Publications (2014–2018)
Related Software: GraphGrep; SAGA; GADDI; SAPPER; Fg-index; TALE; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

Tanglegrams

Software Authors:   Scornavacca, C.; Zickman, F.; Huson, D.
Cited in: 5 Publications (2012–2022)
Related Software: OEIS; SylvX; GDToolkit; SPRSupertrees
Main Fields: Combinatorics (05-XX); Order, lattices, ordered algebraic structures (06-XX); Computer science (68-XX)

tellurium

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

C-GRAAL

Software Authors:   Vesna Memisevic; Natasa Przulj
Cited in: 4 Publications (2013–2022)
Related Software: GEDEVO; SPINAL; CVX; SDPT3; MultiPhyl; PathBLAST; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

CoLoMoTo

Software Authors:   Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé
Cited in: 4 Publications (2019–2022)
Related Software: Ginsim; PyBoolNet; SQUAD; ERODE; z3; caspo; …
Main Fields: Order, lattices, ordered algebraic structures (06-XX); Biology and other natural sciences (92-XX); Information and communication theory, circuits (94-XX)

GSNCA

Software Authors:   Rahmatallah, Y.; Emmert-Streib, F.; Glazko, G.,
Cited in: 4 Publications (2016–2021)
Related Software: copula; CDVine; copula; PINALOG; NETAL; HubAlign; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

MAVisto

Software Authors:   Schreiber F, Schwöbbermeyer H.
Cited in: 4 Publications (2011–2015)
Related Software: FANMOD; KEGG; PathBLAST; Kavosh; ClustalW; GOrilla; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Statistics (62-XX)

MMG

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

multi2boolean

Software Authors:   Fauré, Adrien; Kaji, Shizuo
Cited 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)

TinkerCell

Software Authors:   Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro
Cited 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
Cited in: 3 Publications (2015–2019)
Related Software: PhysiCell; CellSys; Microvessel Chaste; EmbryoMaker; CompuCell3D; Morpheus; …
Main Fields: Biology and other natural sciences (92-XX)

BiMAT

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

BiNoM

Software Authors:   Andrei Zinovyev; Eric Viara; Laurence Calzone; Emmanuel Barillot
Cited in: 2 Publications (2012–2015)
Related Software: CellPublisher; Pathway Commons; Ginsim; elmap
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-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
Cited in: 2 Publications (2017–2021)
Related Software: ATLANTIS; Aeon; PyBoolNet; ASSA-PBN; Cytoscape.js; Ginsim; …
Main Fields: Mathematical logic and foundations (03-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

CentiServer

Software Authors:   Jalili, M., Salehzadeh-Yazdi, A., Asgari, Y., Arab, S.S., Yaghmaie, M., Ghavamzadeh, A., et al.
Cited in: 2 Publications (2016–2022)
Related Software: igraph; sna; ggraph; influenceR; CINNA; R; …
Main Fields: Combinatorics (05-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

CGBayesNets

Software Authors:   McGeachie, M. J.; Chang, H. -H.; Weiss, S. T.
Cited in: 2 Publications (2016)
Related Software: bnlearn; UCI-ml; caret; gRain; deal; mlr; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

ChordLink

Software Authors:   Angori, Lorenzo; Didimo, Walter; Montecchiani, Fabrizio; Pagliuca, Daniele; Tappini, Alessandra
Cited in: 3 Publications (2019–2021)
Related Software: NodeTrix; GitHub
Main Fields: Computer science (68-XX)

COBRApy

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

CplexA

Software Authors:   J. M. G. Vilar, L. Saiz
Cited in: 2 Publications (2016–2019)
Related Software: Cellerator; STOCHSIM; Matlab; Python; Mathematica; RegulonDB
Main Fields: Biology and other natural sciences (92-XX)

CrossNets

Software Authors:   Türel, Özgür; Likharev, Konstantin
Cited in: 3 Publications (2003–2011)
Related Software:
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX); Information and communication theory, circuits (94-XX)

FluxSimulator

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

GEDEVO

Software Authors:   Ibragimov, Rashid; Malek, Maximilian; Guo, Jiong; Baumbach, Jan
Cited in: 2 Publications (2013–2022)
Related Software: C-GRAAL; GREAT; BioGRID; IGLOO; CVX; SDPT3; …
Main Fields: Combinatorics (05-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

GenePath

Software Authors:   Zupan, B.; Demsar, J.; Bratko, I.; Juvan, P.; Halter, J. A.; Kuspa, A.; Shaulsky, G.
Cited in: 2 Publications (2006–2013)
Related Software: KEGG; TopLog; SOLAR
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

GeNGe

Software Authors:   Hache H, Wierling C, Lehrach H, Herwig R
Cited in: 1 Publication (2019)
Related Software: ARACNE; DINGO; glasso; SynTReN; GeneNetWeaver; RegulonDB; …
Main Fields: Biology and other natural sciences (92-XX)

GlobalMIT

Software Authors:   Vinh, N.X., Chetty, M., Coppel, R., Wangikar, P.P.
Cited in: 3 Publications (2015–2021)
Related Software: ARACNE; KEGG; slingshot; SNN-Cliq; MrTADFinder; CIDR; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

L-GRAAL

Software Authors:   Noël Malod-Dognin; Nataša Pržulj
Cited in: 3 Publications (2015–2021)
Related Software: IsoRank; GHOST; MAGNA++; SPINAL; PrimAlign; IsoRankN; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

LinkProt

Software Authors:   P. Dabrowski-Tumanski, A. Jarmolinksa, W. Niemyska, E. Rawdon, K.C. Millett, J.I. Sulkowksa
Cited in: 3 Publications (2017–2020)
Related Software: KnotProt; LassoProt; PyLasso; PyLink; pKNOT
Main Fields: Manifolds and cell complexes (57-XX); Quantum theory (81-XX); Statistical mechanics, structure of matter (82-XX)

MI-GRAAL

Software Authors:   Oleksii Kuchaiev; Natasa Przulj
Cited 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)

MoVisPP

Software Authors:   Chen, Ming; Hariharaputran, Sridhar; Hofestädt, Ralf; Kormeier, Benjamin
Cited 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)

NETAL

Software Authors:   Neyshabur, B.; Khadem, A.; Hashemifar, S.; Arab, S.S.
Cited in: 3 Publications (2014–2016)
Related Software: KEGG; HubAlign; GHOST; SPINAL; PathBLAST; BLAST; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

netgwas

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

OCTOPUS

Software Authors:   Håkan Viklund, Arne Elofsson
Cited 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)

SpectralNET

Software Authors:   Forman JJ1, Clemons PA, Schreiber SL, Haggarty SJ.
Cited in: 2 Publications (2011)
Related Software: Graph Investigator; StOCNET; LAPACK; GeneRAGE; ProClust; BLAST; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

SynBioSS

Software Authors:   Hill A, Tomshine J, Weeding E, Sotiropoulos V, Kaznessis Y
Cited in: 1 Publication (2017)
Related Software: TABASCO; lpSolve; SUNDIALS; SciPy; ProMoT; BioJADE; …
Main Fields: Partial differential equations (35-XX); Biology and other natural sciences (92-XX)

ANDy

Software Authors:   Franck Delaplace, Cinzia Di Giusto, Jean-Louis Giavitto, Hanna Klaudel
Cited in: 1 Publication (2018)
Related Software: Charlie; SNOOPY; SNAKES
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

ANIMO

Software Authors:   Schivo S, Scholma J, van der Vet PE et al
Cited in: 2 Publications (2014–2018)
Related Software: STRINGdb; PRS; NET-SYNTHESIS; SMPDB; PathCellNet; GNAT; …
Main Fields: Biology and other natural sciences (92-XX)

ATLANTIS

Software Authors:   Shah, O. S.; Chaudhary, M. F.A.; Awan, H. A.; Fatima, F.; Arshad, Z.; Amina, B.; Ahmed, M.; Hameed, H.; Furqan, M.; Khalid, S.
Cited in: 2 Publications (2019–2021)
Related Software: Ginsim; BoolNet; Aeon; PyBoolNet; ASSA-PBN; Cytoscape.js; …
Main Fields: Algebraic geometry (14-XX); Linear and multilinear algebra; matrix theory (15-XX); Biology and other natural sciences (92-XX)

BicNET

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

BicPAMS

Software Authors:   Henriques, R.; Ferreira, FL; Madeira, SC
Cited in: 1 Publication (2018)
Related Software: FABIA; BicNET; BicAT; bibench; CoClust; MTBA; …
Main Fields: Statistics (62-XX)

BioGrapher

Software Authors:   Viswanathan, Rama; Liang, Sijia; Yang, Yang; Jungck, John R.
Cited 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)

BioLQM

Software Authors:   Naldi, A.
Cited 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)

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
Cited 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)

BisoGenet

Software Authors:   Martin, A., Ochagavia, M. E., Rabasa, L. C., Miranda, J., Fernandez‐de Cossio, J., Bringas, R.
Cited in: 1 Publication (2018)
Related Software:
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

BRTSim

Software Authors:   Federico Maggi
Cited in: 2 Publications (2020)
Related Software: TOUGHREACT
Main Fields: Biology and other natural sciences (92-XX)

CellPublisher

Software Authors:   L.A. Flórez, C.R. Lammers, R. Michna, J. Stülke
Cited 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)

CytoNCA

Software Authors:   Tang, Y.; Li, M.; Wang, J.; Pan, Y.; Wu, F.X
Cited in: 2 Publications (2018–2019)
Related Software:
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

DPClus

Software Authors:   Md. Altaf-Ul-Amin, Hisashi Tsuji, Ken Kurokawa, Hiroko Asahi, Yoko Shinbo, Shigehiko Kanaya
Cited in: 1 Publication (2012)
Related Software: KNApSAcK database; DPClusOST; DPClusSBO; MCODE; GOstats
Main Fields: Combinatorics (05-XX); Biology and other natural sciences (92-XX)

DyNetViewer

Software Authors:   Li, M.; Yang, J.; Wu, F. -X.; Pan, Y.; Wang, J.
Cited in: 2 Publications (2019)
Related Software: Cytoscape; CytoCtrlAnalyser; CytoNCA; IntAct; UniProt
Main Fields: Statistical mechanics, structure of matter (82-XX); Biology and other natural sciences (92-XX)

FLAR

Software Authors:   Mirabedini, Seyed Javad; Teshnehlab, Mohammad; Shenasa, Mohammad Hassan; Rahmani, Amir Masoud
Cited in: 2 Publications (2008)
Related Software: AntHocNet; AntNet
Main Fields: Operations research, mathematical programming (90-XX); Systems theory; control (93-XX); Information and communication theory, circuits (94-XX)

GENeVis

Software Authors:   Westenberg, Michel A.; van Hijum, Sacha A.F.T.; Lulko, Andrzej T.; Kuipers, Oscar P.; Roerdink, Jos B.T.M.
Cited in: 2 Publications (2008–2021)
Related Software: DeepWalk; graph2vec; node2vec; TopoLayout; Prefuse; GVF
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

Graph Investigator

Software Authors:   Czech, Wojciech; Dzwinel, Witold; Goryczka, Sławomir; Arodź, Tomasz; Dudek, Arkadiusz Z.
Cited in: 2 Publications (2011–2016)
Related Software: SpectralNET; StOCNET
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

GraphWeb

Software Authors:   J. Reimand, L. Tooming, H. Peterson, P. Adler, J. Vilo
Cited in: 1 Publication (2010)
Related Software: g Profiler; KEGGanim
Main Fields: Biology and other natural sciences (92-XX)

hiPathDB

Software Authors:   Yu, N.; Seo, J.; Rho, K.; Jang, Y.; Park, J.; Kim, W.K.; Lee, S
Cited in: 2 Publications (2015–2017)
Related Software: GNA; PREMER; DREAMTools; GeneNetWeaver; Clingo
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

HSimulator

Software Authors:   Marchetti, Luca; Lombardo, Rosario; Priami, Corrado
Cited in: 2 Publications (2017–2019)
Related Software: HRSSA; STEPS; COPASI
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

IGLOO

Software Authors:   Lei Meng, Aaron Striegel, Tijana Milenkovic
Cited in: 1 Publication (2017)
Related Software: GEDEVO; GREAT; BioGRID; IGLOO; GLESP; Healpix
Main Fields: Relativity and gravitational theory (83-XX)

JGL

Software Authors:   Patrick Danaher
Cited in: 1 Publication (2019)
Related Software: RidgeFusion; RSpectra; Rcpp; Rbgl; gRbase; sfsmisc; …
Main Fields: Statistics (62-XX); Operations research, mathematical programming (90-XX)

Kaskade

Software Authors:   Joana M. F. da Trindade, Konstantinos Karanasos, Carlo Curino, Samuel Madden, Julian Shun
Cited in: 0 Publications
Related Software: Ligra; GraphFrames; WebGraph; NetworkX; EmptyHeaded; GraphLab; …
Main Fields:

MFinder

Software Authors:   Nadav Kashtan, Shalev Itzkovitz, Ron Milo, Uri Alon
Cited in: 2 Publications (2010–2015)
Related Software: MultiPhyl; PathBLAST; Graemlin; MAVisto; MODA; Kavosh; …
Main Fields: Combinatorics (05-XX); Dynamical systems and ergodic theory (37-XX); Computer science (68-XX)