• Ginsim

  • Referenced in 29 articles [sw09090]
  • genetic regulatory networks. Formally, our approach leans on discrete mathematical and graph-theoretical concepts. GINsim ... definition and the parameterisation of a regulatory graph, as well as a simulation engine ... preliminary model analysis of the inter-cellular 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 piecewise-linear 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 graph-theoretic...
  • MotifClick

  • Referenced in 2 articles [sw29728]
  • developed to find a set of cis-regulatory binding sites called a motif ... graph-based polynomial-time algorithm, MotifClick, for the prediction of cis-regulatory binding sites ... sites with length k, we construct a graph using some 2(k-1)-mers...
  • BNArray

  • Referenced in 2 articles [sw30810]
  • using Bayesian network. Significant submodules of regulatory networks with high confidence are reconstructed using ... extended sub-network 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 graph-based analysis of biological networks that: analyses ... modules using Gene Ontology, pathways, and cis-regulatory 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 ... upper-bound and lower-bound 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 high-level 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...