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  • GNA
  • Referenced in 26 articles [sw35974]
  • applied to the analysis of various regulatory systems, such as the networks controlling the initiation...

  • Siconos
  • Referenced in 12 articles [sw25724]
  • Digital converter. Sliding mode control systems. Biology (Gene regulatory network). Other applications are found...

  • Celldesigner
  • Referenced in 22 articles [sw09942]
  • structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based ... process diagram, with graphical notation system proposed by Kitano, and are stored using ... Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory...

  • SNOOPY
  • Referenced in 35 articles [sw04386]
  • natural systems, i.e. biochemcial networks as metabolic, signal transduction, gene regulatory networks, compare poster ”overview...

  • CALPUFF
  • Referenced in 10 articles [sw34665]
  • steady-state meteorological and air quality modeling system developed by scientists at Exponent ... details on CALPUFF’s Regulatory Status). The modeling system consists of three main components...

  • HPAM
  • Referenced in 3 articles [sw10931]
  • post-genomic era is identifying regulatory systems and integrating them into genetic networks. Gene expression ... determined by protein-protein interactions among regulatory proteins and with RNA polymerase(s), and protein...

  • REDfly
  • Referenced in 5 articles [sw29315]
  • identification and study of the cis-regulatory elements that control gene expression are important areas ... transcriptional regulation, represents the ideal system for regulatory bioinformatics. We have merged two existing Drosophila...

  • TRANSFAC
  • Referenced in 74 articles [sw17201]
  • TRANSFAC: an integrated system for gene expression regulation. TRANSFAC is a database on transcription factors ... provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt...

  • Cytoscape
  • Referenced in 81 articles [sw09080]
  • unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape ... interface to detailed stochastic/kinetic gene regulatory models...

  • LBS
  • Referenced in 15 articles [sw12372]
  • Biochemical Systems (CBS) which affords modular descriptions of metabolic, signalling and regulatory networks in terms...

  • SQUAD
  • Referenced in 5 articles [sw29353]
  • reconstruction of regulatory networks in diverse biological systems. This information, however, has proven ... about patterns of expression to infer the regulatory networks that generate such patterns...

  • ANDy
  • Referenced in 2 articles [sw16548]
  • natural modelling of time-dependent biological systems (i.e., regulatory pathways). Activities involve entities playing ... main results we show that ANDy systems have finite state representations even for potentially infinite...

  • CellPublisher
  • Referenced in 2 articles [sw35235]
  • sharing of metabolic, signalling and regulatory pathways. Systems biology relies increasingly on collaborations between several...

  • SW1PerS
  • Referenced in 10 articles [sw17206]
  • systems and the generation of hypotheses regarding the structure of gene regulatory networks...

  • IOTA
  • Referenced in 10 articles [sw19593]
  • Systems: Inner composition alignment (IOTA) is a permutation-based association measure to detect regulatory links...

  • Open TURNS
  • Referenced in 4 articles [sw12837]
  • robust performances for complex systems and to answer tighter regulatory processes (security, safety, environmental control...

  • PeTTSy
  • Referenced in 1 article [sw32750]
  • computational tool for perturbation analysis of complex systems biology models. Conclusions: PeTTSy is a comprehensive ... large and complex models of regulatory and signalling systems. It allows for simulation and analysis...

  • ComiRNet
  • Referenced in 2 articles [sw34289]
  • based system for the analysis of miRNA-gene regulatory networks. ComiRNet is a database...

  • REVEAL
  • Referenced in 29 articles [sw36999]
  • principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables ... enable in-depth analysis of complex dynamic systems in biology and other fields...

  • OKVAR-Boost
  • Referenced in 3 articles [sw24063]
  • engineering of gene regulatory networks remains a central challenge in computational systems biology, despite recent...