• Graphs

  • Referenced in 104 articles [sw12277]
  • Shortest-path queries in static networks. We consider the point-to-point (approximate) shortest-path ... query problem, which is the following generalization of the classical single-source (SSSP ... problems: we are first presented with a network (graph). A so-called preprocessing algorithm ... tradeoffs, query processing on spatial networks, and reachability queries; and theoretical computer scientists analyze distance...
  • Cytoscape

  • Referenced in 69 articles [sw09080]
  • source software project for integrating biomolecular interaction networks with high-throughput expression data and other ... provides basic functionality to layout and query the network; to visually integrate the network with...
  • Datalog

  • Referenced in 282 articles [sw20023]
  • Prolog. It is often used as a query language for deductive databases. In recent years ... application in data integration, information extraction, networking, program analysis, security, and cloud computing...
  • TAG

  • Referenced in 76 articles [sw20627]
  • tiny aggregation service for ad-hoc sensor networks. We present the Tiny AGgregation (TAG) service ... simple, declarative queries and have them distributed and executed efficiently in networks of low-power...
  • QPath

  • Referenced in 11 articles [sw35403]
  • method for querying pathways in a protein-protein interaction network. Results: We present ... comprehensive framework for protein network searches using pathway queries. Given a linear query pathway ... interest, our algorithm, QPath, efficiently searches the network for homologous pathways, allowing both insertions ... databases underscore the importance of our network querying framework for mining protein network data...
  • QNet

  • Referenced in 10 articles [sw13845]
  • QNet: A Tool for Querying Protein Interaction Networks. Molecular interaction databases can be used ... have been limited to simple queries (paths), or simple networks (forests). In this paper ... real network data. We show that QNet searches queries with up to 9 proteins ... complexes, by querying known yeast complexes against a fly protein interaction network. This comparison points...
  • BATON

  • Referenced in 23 articles [sw09436]
  • peer-to-peer network capable of supporting both exact queries and range queries efficiently ... network with N nodes, we guarantee that both exact queries and range queries ... that update operations (to both data and network) have an amortized cost...
  • ANQL

  • Referenced in 4 articles [sw02380]
  • ANQL -- an active networks query language. This paper discusses parallels between network communication packets, when ... application-specific language, ANQL (Active Networks Query Language), that exploits a database metaphor for packet ... processing. ANQL has been demonstrated in Active Network control and management plane activities, although...
  • InterViewer

  • Referenced in 28 articles [sw00443]
  • types of networks; and (3) it provides an integrated framework for querying protein interaction databases...
  • NeMa

  • Referenced in 4 articles [sw18899]
  • networks of labeled, heterogeneous entities. To query these networks, one often needs to identify ... matches of a given query graph in a (typically large) network modeled as a target ... graph querying tasks. In this paper, we propose NeMa (Network Match), a neighborhood ... based subgraph matching technique for querying real-life networks. (1) To measure the quality...
  • bnlearn

  • Referenced in 56 articles [sw08265]
  • learning algorithms for both discrete and Gaussian networks, along with many score functions and conditional ... likelihood and Bayesian) and inference, conditional probability queries and cross-validation. Development snapshots with...
  • RockIt

  • Referenced in 5 articles [sw35051]
  • also called probability queries), and learns the weights of Markov logic networks. Markov logic ... currently the fastest MAP query engine for Markov logic networks...
  • Flask

  • Referenced in 5 articles [sw09691]
  • node-level code to execute a network-wide query specified in a SQL-like language ... that can run effectively on existing sensor network hardware...
  • Frenetic

  • Referenced in 5 articles [sw16270]
  • programming distributed collections of network switches. Frenetic provides a declarative query language for classifying ... aggregating network traffic as well as a functional reactive combinator library for describing high-level ... details related to installing, uninstalling, and querying low-level packet-processing rules on physical switches ... languages for programming networks and identify the key limitations; (2) We present a language design...
  • DIASPORA

  • Referenced in 14 articles [sw02659]
  • implementation of DIASPORA, a highly distributed query processing system for the web. It is based ... opening up possibilities of significant reductions in network traffic and user response times. DIASPORA ... structural framework of a web site. Distributed queries on the model are expressed through ... site due to the same query arriving through different paths in the hyperlink framework...
  • Euk-PLoc

  • Referenced in 24 articles [sw22420]
  • they interact with each other in cellular networking. However, predicting subcellular location of eukaryotic proteins ... challenging problem, particularly when unknown query proteins do not have significant homology to proteins...
  • PathBLAST

  • Referenced in 7 articles [sw29737]
  • interaction pathways based on similarity to the network of another, well-characterized species. PathBLAST ... www.pathblast.org/ as a web-based query. In this implementation, the user specifies a short protein ... interaction path for query against a target protein–protein interaction network selected from a network...
  • Marabou

  • Referenced in 2 articles [sw31368]
  • based tool that can answer queries about a network’s properties by transforming these queries...
  • NatalieQ

  • Referenced in 1 article [sw34156]
  • server for protein-protein interaction network querying. Background: Molecular interactions need to be taken into ... captured by various types of biological networks, such as metabolic, gene-regulatory, signal transduction ... recently developed natalie, which computes high-quality network alignments via advanced methods from combinatorial optimization ... based alignment of a specified query protein-protein interaction network to a selected target network...
  • UniHI

  • Referenced in 2 articles [sw17425]
  • provides researchers with a comprehensive platform to query and access human protein–protein interaction ... researchers due to the complexity of interaction networks retrieved from the database. We therefore developed ... several new tools to query, analyze and visualize human PPI networks. Most importantly, UniHI allows ... construction of tissue-specific interaction networks and focused querying of canonical pathways. This will enable...