• Celldesigner

  • Referenced in 21 articles [sw09942]
  • drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with ... Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks ... Networks are able to link with simulation and other analysis packages through Systems Biology Workbench...
  • BiNoM

  • Referenced in 3 articles [sw13481]
  • Cytoscape plugin for manipulating and analyzing biological networks. BiNoM (Biological Network Manager ... usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX ... addition, BiNoM allows the analysis of networks created with CellDesigner software and their conversion into...
  • BioNet

  • Referenced in 5 articles [sw13828]
  • package provides an extensive framework for integrated network analysis using R and BioConductor. It includes ... transcriptomic and functional data with biological networks, the methods for scoring of nodes, methods...
  • C-GRAAL

  • Referenced in 3 articles [sw08317]
  • neighbors-based global GRAph ALignment of biological networks. Networks are an invaluable framework for modeling ... biological systems. Analyzing protein–protein interaction (PPI) networks can provide insight into underlying cellular processes ... expected that comparison and alignment of biological networks will have a similar impact ... understanding of evolution, biological function, and disease as did sequence comparison and alignment. Here...
  • SING

  • Referenced in 5 articles [sw18904]
  • Conclusions Extensive tests on chemical compounds, biological networks and synthetic graphs show that the proposed...
  • SABRE

  • Referenced in 6 articles [sw12884]
  • analysis of biochemical reaction networks. The importance of stochasticity within biological systems has been shown ... tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization ... biochemical reaction networks. Biochemical reactions networks represent biological systems studied at a molecular level...
  • NeMoFinder

  • Referenced in 4 articles [sw29732]
  • existence of network motifs in biological networks such as the protein-protein interaction (PPI) networks...
  • MODA

  • Referenced in 4 articles [sw29734]
  • algorithm for network motif discovery in biological networks. In recent years, interest has been growing...
  • MMG

  • Referenced in 4 articles [sw29328]
  • distributed; however, biological quantities are usually related through a complex (weighted) network of interactions ... identify differentially expressed submodules of biological networks and pathways. The method can easily incorporate information ... easily generalized to directed networks. We propose an efficient sampling strategy to infer posterior probabilities ... proteomic data leads to the identification of biologically significant subnetworks, as well as the prediction...
  • NETWORKINFERENCE

  • Referenced in 6 articles [sw06744]
  • applying them to biologically realistic simulations with known network topology. Here, we seek to determine ... possibilities and limitations of network inference based on biological data...
  • GEDEVO

  • Referenced in 2 articles [sw08298]
  • evolutionary graph edit distance algorithm for biological network alignment. With the so-called OMICS technology ... sequence alignment, the comparison of biological networks has proven great potential to infer the biological ... comparison dedicated to real-world size biological networks. Underlying our approach is the so-called ... exploding number and size of available biological networks. The software as well as all used...
  • Siconos

  • Referenced in 10 articles [sw25724]
  • converter. Sliding mode control systems. Biology (Gene regulatory network). Other applications are found in Systems...
  • GHOST

  • Referenced in 4 articles [sw08322]
  • software package for global biological network alignment. It computes alignments based on a novel spectral...
  • MI-GRAAL

  • Referenced in 3 articles [sw08318]
  • network alignment reveals large regions of global network similarity in yeast and human. Motivation: High ... interactions have produced large sets of biological network data with much more yet to come ... improve our understanding of biological systems. Unlike sequence alignment, network alignment is computationally intractable. Hence ... foremost challenge in computational biology. Results: We introduce a novel network alignment algorithm, called Matching...
  • CytoNCA

  • Referenced in 2 articles [sw25624]
  • method for identifying essential proteins in biological networks. Here we present CytoNCA, a Cytoscape plugin ... applied to both weighted and unweighted biological networks. (ii) It allows users to upload biological ... nodes and edges in the network, to integrate biological data with topological data to detect ... calculating centrality, evaluating and visualizing biological networks. AVAILABILITY: http://apps.cytoscape.org/apps/cytonca....
  • MFinder

  • Referenced in 2 articles [sw08095]
  • network motifs detection. To understand biological networks, our lab has defined network motifs: basic interaction ... patterns that recur throughout biological networks, much more often than in random networks. The same ... networks and other biological and non-biological networks...
  • multi2boolean

  • Referenced in 4 articles [sw25069]
  • Boolean dynamics. Many discrete models of biological networks rely exclusively on Boolean variables and many...
  • ADAM

  • Referenced in 8 articles [sw21957]
  • Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical ... discrete models arising in systems biology and randomly generated networks, we found that the algebraic ... systems with the structure maintained by most biological systems, namely sparseness and robustness...
  • SynBioSS

  • Referenced in 3 articles [sw20854]
  • retrieval and quantitative simulation of synthetic biological networks. SynBioSS facilitates computational synthetic biology and consists...
  • BicNET

  • Referenced in 2 articles [sw29989]
  • Flexible module discovery in large-scale biological networks using biclustering. Methods: This work proposes Biclustering ... trivial yet coherent modules in weighted biological networks with heightened efficiency. Three major contributions ... interaction networks from yeast, E. coli and Human reveals new modules with heightened biological significance ... efficient unsupervised analysis of large-scale network data for the discovery of coherent modules with...