• COPASI

  • Referenced in 70 articles [sw12253]
  • application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand...
  • Nevada

  • Referenced in 7 articles [sw30918]
  • Nevada-system (Network Visualization and Analysis for Dynamic Networks) is an open-source system that ... hierarchic and orthogonal layout. Furthermore it supports analysis methods like visual mapping of centrality measures...
  • Radyban

  • Referenced in 7 articles [sw12543]
  • reliability analysis of dynamic fault trees through conversion into dynamic Bayesian networks. In this paper ... present Radyban (Reliability Analysis with DYnamic BAyesian Networks), a software tool which allows to analyze...
  • SNAP

  • Referenced in 171 articles [sw04184]
  • high performance system for analysis and manipulation of large networks. Graphs consists of nodes ... nodes. Networks are graphs with data on nodes and/or edges of the network. The core ... graph representation. It easily scales to massive networks with hundreds of millions of nodes ... graph or a network can be changed dynamically during the computation. SNAP was originally developed...
  • Ginsim

  • Referenced in 29 articles [sw09090]
  • qualitative modelling, analysis and simulation of genetic regulatory networks. Formally, our approach leans on discrete ... qualitative dynamical behaviour. Our computational approach is illustrated by a preliminary model analysis ... inter-cellular regulatory network activating Notch at the dorsal–ventral boundary in the wing imaginal...
  • RoVerGeNe

  • Referenced in 13 articles [sw10954]
  • analysis of genetic regulatory networks under parameter uncertainty. Genetic regulatory networks are described ... class of piecewise multiaffine differential equation models, dynamical properties are expressed in linear temporal logic ... intervals. The tool addresses two problems: robustness analysis: checking whether a dynamical property is satisfied ... analysis of the robustness of dynamical properties of gene networks with respect to parameter variations...
  • DynComm

  • Referenced in 2 articles [sw28442]
  • DynComm R Package -- Dynamic Community Detection for Evolving Networks. Nowadays, the analysis ... dynamics in networks represents a great deal in the Social Network Analysis research area ... used for community detection and analysis on dynamic networks. The package introduces interfaces to facilitate...
  • BioNetGen

  • Referenced in 60 articles [sw09072]
  • create a computational model that characterizes the dynamics of a signal transduction system, and that ... molecules. The output defines and parameterizes the network of molecular species that can arise during ... generated are relevant for rational drug discovery, analysis of proteomic data and mechanistic studies...
  • Gephi

  • Referenced in 62 articles [sw12110]
  • platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. Runs ... This is a software for Exploratory Data Analysis, a paradigm appeared in the Visual Analytics...
  • DyNetViewer

  • Referenced in 2 articles [sw24787]
  • DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization. SUMMARY: The molecular interactions ... environmental cues. The construction and analysis of dynamic molecular networks can elucidate dynamic cellular mechanisms ... construction, analysis and visualization of dynamic protein-protein interaction networks. The current version of DyNetViewer ... four different dynamic network construction methods, twelve topological variation analysis methods and four clustering algorithms...
  • REVEAL

  • Referenced in 28 articles [sw36999]
  • this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi ... problem may enable in-depth analysis of complex dynamic systems in biology and other fields...
  • GNA

  • Referenced in 26 articles [sw35974]
  • graph that describes the qualitative dynamics of the network. The simulator has been implemented ... Java and has been applied to the analysis of various regulatory systems, such...
  • LabelRankT

  • Referenced in 5 articles [sw20731]
  • Dynamic Networks via Label Propagation. An increasingly important challenge in network analysis is efficient detection...
  • BioGRID

  • Referenced in 48 articles [sw17422]
  • interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible ... visualization system called Osprey that is dynamically linked to the BioGRID...
  • IDTxl

  • Referenced in 5 articles [sw25603]
  • package for the efficient analysis of multivariate information dynamics in networks. The Information Dynamics Toolkit ... efficient inference of networks and their node dynamics from multivariate time series data using information ... estimate the following measures: 1) For network inference: multivariate transfer entropy (TE)/Granger causality ... TE/GC, bivariate MI; 2) For analysis of node dynamics: active information storage (AIS), partial information...
  • gNCA

  • Referenced in 4 articles [sw08821]
  • Component Analysis (NCA) is a network structure-driven framework for deducing regulatory signal dynamics ... classical approaches such as principal component analysis or independent ... component analysis, NCA makes use of the connectivity structure from transcriptional regulatory networks to restrict ... network topology such as information obtained from regulatory gene knockouts that constrain the dynamics...
  • XGobi

  • Referenced in 37 articles [sw11752]
  • with state-of-the-art interactive and dynamic methods for the manipulation of views ... been done for the data analysis language S, the geographic information system (GIS) Arc View ... ability to run across a network...
  • MuTE

  • Referenced in 7 articles [sw19722]
  • from the analysis of the recorded dynamics. The components of physiological networks often interact...
  • Bio3d

  • Referenced in 4 articles [sw15706]
  • read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches ... analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis ... data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various...
  • qLearn

  • Referenced in 20 articles [sw11117]
  • intervals for the parameters indexing the optimal dynamic regime. We propose an adaptive choice ... Comprehensive R-Archive Network (http://cran.r-project.org/). Analysis of the Sequenced Treatment Alternatives to Relieve Depression...