• KEGG

  • Referenced in 250 articles [sw13866]
  • computer representation of the biological system, consisting of molecular building blocks of genes and proteins ... wiring diagrams of interaction, reaction and relation networks (systems information). It also contains disease ... information (health information) as perturbations to the biological system...
  • BiNGO

  • Referenced in 14 articles [sw13896]
  • overrepresentation of Gene Ontology categories in biological networks. Summary: The Biological Networks Gene Ontology tool ... text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant...
  • CFinder

  • Referenced in 21 articles [sw12379]
  • locating cliques and overlapping modules in biological networks. Summary: Most cellular tasks are performed...
  • GNA

  • Referenced in 21 articles [sw35974]
  • which are often not available for networks of biological interest, the user of GNA specifies ... that describes the qualitative dynamics of the network. The simulator has been implemented in Java...
  • DAVID

  • Referenced in 57 articles [sw17292]
  • number of biological modules for efficient interpretation of gene lists in a network context...
  • FANMOD

  • Referenced in 12 articles [sw26134]
  • than would be expected for a random network. They have recently gathered much attention ... uncover structural design principles of complex biological networks. FANMOD is a tool for fast network...
  • Kavosh

  • Referenced in 8 articles [sw29733]
  • particularly important to understand biological processes. Motifs in networks are small connected sub-graphs that ... algorithm (Kavosh), for finding k-size network motifs with less memory and CPU time ... undirected). We evaluated our algorithm on biological networks of E. coli and S. cereviciae ... also on non-biological networks: a social and an electronic network. Conclusion: The efficiency...
  • RAMAS

  • Referenced in 12 articles [sw10958]
  • find important applications in analysis of biological networks and robot control...
  • SA-cluster

  • Referenced in 8 articles [sw06867]
  • including social networks, road networks, sensor networks, biological networks, etc. Graph clustering has shown...
  • Spikenet

  • Referenced in 12 articles [sw08892]
  • large networks of spiking neurons. Many biological neural network models face the problem of scalability ... network simulation package. The type of model one can build is not only biologically compliant ... standard desktop computer. In addition, for large networks, we can set very small time steps...
  • Bio-PEPA

  • Referenced in 102 articles [sw01361]
  • modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined ... order to handle some features of biological models, suchas stoichiometry and the use of general...
  • KEGGgraph

  • Referenced in 8 articles [sw06934]
  • maps that represent current knowledge on biological networks in graph models. While valuable graph tools...
  • GGMselect

  • Referenced in 8 articles [sw10347]
  • with GGMselect. Applications on inference of biological networks have raised a strong interest...
  • MCINTYRE

  • Referenced in 8 articles [sw22925]
  • REcord, is evaluated on various problems: biological networks, artificial datasets and a hidden Markov model...
  • jHoles

  • Referenced in 6 articles [sw15020]
  • jHoles: A tool for understanding biological complex networks via clique weight rank persistent homology. Complex ... networks equipped with topological data analysis are one of the promising tools in the study ... biological systems (e.g., evolution dynamics, brain correlation, breast cancer diagnosis, etcdots). In this paper ... response to a tumor presence. The biological network has been derived from the proliferative, differentiated...
  • Polynome

  • Referenced in 6 articles [sw12584]
  • Parameter estimation for Boolean models of biological networks. Boolean networks have long been used ... molecular networks, and they play an increasingly important role in systems biology. This paper describes ... users construct Boolean network models based on experimental data and biological input. The key feature ... tool for reverse-engineering of Boolean network models from experimental time course data...
  • MoVisPP

  • Referenced in 3 articles [sw35665]
  • semi-automatic construction of large scale biological networks. For the implementation of the virtual cell ... model and simulate complex biological networks. During the last 15 years, Petri nets have attracted ... adequate method to model complex biological networks. Today, a Petri net model of biological networks ... essential step in constructing biological networks. We motivate the application of Petri nets for modeling...
  • Inc-cluster

  • Referenced in 4 articles [sw06866]
  • including social networks, road networks, sensor networks, biological networks, etc. Graph clustering has shown...
  • 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...
  • GADDI

  • Referenced in 5 articles [sw18895]
  • distance index based subgraph matching in biological networks. Currently, a huge amount of biological data ... graphs, e.g., protein interaction networks, gene regulatory networks, etc. The need for indexing large graphs ... very important task in many biological applications. This increases the complexity significantly. We propose...