
Ginsim
 Referenced in 29 articles
[sw09090]
 genetic regulatory networks. Formally, our approach leans on discrete mathematical and graphtheoretical concepts. GINsim ... definition and the parameterisation of a regulatory graph, as well as a simulation engine ... preliminary model analysis of the intercellular regulatory network activating Notch at the dorsal–ventral...

GADDI
 Referenced in 6 articles
[sw18895]
 naturally represented by graphs, e.g., protein interaction networks, gene regulatory networks, etc. The need...

GNA
 Referenced in 23 articles
[sw35974]
 simulator of qualitative models of genetic regulatory networks in the form of piecewiselinear differential ... sufficient to generate a state transition graph that describes the qualitative dynamics of the network ... been applied to the analysis of various regulatory systems, such as the networks controlling...

SNOOPY
 Referenced in 32 articles
[sw04386]
 software tool to design and animate hierarchical graphs, among others Petri nets. The tool ... biochemcial networks as metabolic, signal transduction, gene regulatory networks, compare poster ”overview on the research...

MotifCut
 Referenced in 5 articles
[sw35400]
 MotifCut: regulatory motifs finding with maximum density subgraphs. Results: We present MotifCut, a graphtheoretic...

MotifClick
 Referenced in 2 articles
[sw29728]
 developed to find a set of cisregulatory binding sites called a motif ... graphbased polynomialtime algorithm, MotifClick, for the prediction of cisregulatory binding sites ... sites with length k, we construct a graph using some 2(k1)mers...

BNArray
 Referenced in 2 articles
[sw30810]
 using Bayesian network. Significant submodules of regulatory networks with high confidence are reconstructed using ... extended subnetwork mining algorithm for directed graphs...

INLOCANDA
 Referenced in 1 article
[sw34288]
 causality in gene network reconstruction based on graph embedding. Gene network reconstruction is a bioinformatics ... task that aims at modelling the complex regulatory activities that may occur among genes. This ... possible similar roles by means of graph embedding. Experiments performed along multiple dimensions of analysis...

GraphWeb
 Referenced in 2 articles
[sw20147]
 GraphWeb is a public web server for graphbased analysis of biological networks that: analyses ... modules using Gene Ontology, pathways, and cisregulatory motifs...

graphsim
 Referenced in 1 article
[sw33833]
 simulation of biological pathways from a graph structure based on a statistical model of gene ... methods to infer biological pathways and gene regulatory networks from gene expression data...

GENeVis
 Referenced in 1 article
[sw06743]
 expression time series data in a gene regulatory network context. This is a network ... target genes. The networks are represented as graphs, in which the nodes represent genes...

TRaCE+
 Referenced in 1 article
[sw29319]
 Closure Ensemble. Inferring the structure of gene regulatory networks (GRNs) from expression data ... upperbound and lowerbound directed graphs (digraphs) of the GRN ensemble. The difference between...

CoCoA
 Referenced in 631 articles
[sw00143]
 CoCoA is a system for Computations in Commutative...

Expokit
 Referenced in 179 articles
[sw00258]
 Expokit provides a set of routines aimed at...

Macaulay2
 Referenced in 1692 articles
[sw00537]
 Macaulay2 is a software system devoted to supporting...

MATCONT
 Referenced in 376 articles
[sw00551]
 MATCONT: Matlab software for bifurcation study of dynamical...

Mathematica
 Referenced in 5957 articles
[sw00554]
 Almost any workflow involves computing results, and that...

Matlab
 Referenced in 12309 articles
[sw00558]
 MATLAB® is a highlevel language and interactive...

Maxima
 Referenced in 154 articles
[sw00560]
 Maxima is a system for the manipulation of...

PolyBoRi
 Referenced in 45 articles
[sw00723]
 This work presents a new framework for Gröbner...