• REVEAL

  • Referenced in 28 articles [sw36999]
  • models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series ... controlling each element or gene in the network. This process is unequivocal and exact ... this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi...
  • BoolNet

  • Referenced in 18 articles [sw07365]
  • analysis of synchronous, asynchronous, and probabilistic Boolean networks Provides methods to reconstruct and generate synchronous ... asynchronous, and probabilistic Boolean networks, and to analyze and visualize attractors in Boolean networks...
  • booleannet

  • Referenced in 8 articles [sw22019]
  • Boolean network simulations for life scientists. Modern life sciences research increasingly relies on computational solutions ... theoretical modeling. Within the theoretical models Boolean networks occupy an increasing role as they ... mathematical formalism. The conceptual underpinnings of Boolean modeling are very accessible even without a background...
  • Polynome

  • Referenced in 6 articles [sw12584]
  • estimation for Boolean models of biological networks. Boolean networks have long been used as models ... molecular networks, and they play an increasingly important role in systems biology. This paper describes ... service, that helps users construct Boolean network models based on experimental data and biological input ... tool for reverse-engineering of Boolean network models from experimental time course data...
  • ToulBar2

  • Referenced in 22 articles [sw07289]
  • Weighted Max-SAT, Quadratic Pseudo-Boolean Optimization, and Bayesian Networks...
  • ADAM

  • Referenced in 8 articles [sw21957]
  • with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based...
  • TCPDUMP

  • Referenced in 22 articles [sw04165]
  • packets on a network interface that match the boolean expression. It can also ... rather than to read packets from a network interface. In all cases, only packets that...
  • SQUAD

  • Referenced in 5 articles [sw29353]
  • patterns of expression to infer the regulatory networks that generate such patterns. One of these ... SQUAD method, which approximates a Boolean network with the use of a set of ordinary ... benefit of the SQUAD method over purely Boolean approaches is the possibility of evaluating...
  • PyBoolNet

  • Referenced in 3 articles [sw35161]
  • generation, analysis and visualization of boolean networks. Results: PYBOOLNET is a Python package for working ... with Boolean networks that supports simple access to model checking via NUSMV, standard graph algorithms...
  • ASSA-PBN

  • Referenced in 3 articles [sw32146]
  • approximate steady-state analyser of probabilistic Boolean networks. We present ASSA-PBN, a tool ... steady-state analysis of large probabilistic Boolean networks (PBNs). ASSA-PBN contains a constructor...
  • MaBoSS

  • Referenced in 4 articles [sw34208]
  • time Markov processes, applied on a Boolean network. MaBoSS uses a specific language for associating...
  • BooleSim

  • Referenced in 2 articles [sw20432]
  • BooleSim: an interactive Boolean network simulator. SUMMARY: BooleSim (Boolean network simulator) is an open-source ... tool for simulation and manipulation of Boolean networks. It was developed mainly during Google...
  • Aeon

  • Referenced in 2 articles [sw42182]
  • Aeon 2021: bifurcation decision trees in Boolean networks. Aeon is a recent tool which enables ... long-term behaviour of asynchronous Boolean networks with unknown parameters. In this tool paper ... functionality that verifies integrity of the Boolean network with its regulatory graph; (ii) state-space...
  • CANA

  • Referenced in 2 articles [sw25679]
  • quantifying control and canalization in Boolean Networks. Logical models offer a simple but powerful means ... simplifies these models, making even very large networks amenable to analysis. Moreover, canalization plays ... control, robustness, modularity and criticality of Boolean network dynamics, especially those used to model biochemical ... visualize canalizing redundancy present in Boolean network models. It extracts the pathways most effective...
  • SimBoolNet

  • Referenced in 2 articles [sw35190]
  • dynamics of signaling transduction using Boolean networks. In a Boolean network, every node is assigned...
  • ATLANTIS

  • Referenced in 2 articles [sw42186]
  • cell fate discovery and reprogramming. Boolean modelling of biological networks is a well-established technique ... complex network behavior into a landscape of network states wherein each state is represented ... Towards undertaking attractor landscape analysis of Boolean networks, we propose an Attractor Landscape Analysis Toolbox...
  • expansion-network

  • Referenced in 1 article [sw34481]
  • distinct regulatory regions. Recent gene regulatory network models use binding measurements; but usually only ... possible regulatory connections in a given Boolean network, based on transcription factor binding evidence. This ... algorithm which expands a regular Boolean network model into a “cis-regulatory” Boolean network model...
  • optPBN

  • Referenced in 2 articles [sw32145]
  • optPBN: An optimisation toolbox for probabilistic boolean networks. SUMMARY: The optPBN toolbox provides a simple...
  • Anteater

  • Referenced in 4 articles [sw32373]
  • devices. Anteater translates high-level network invariants into boolean satisfiability problems (SAT), checks them against...
  • ASP-G

  • Referenced in 2 articles [sw34356]
  • method for finding attractors in genetic regulatory networks. To allow for a more flexible simulation ... correctness of ASP-G in simulating Boolean network models and obtaining attractors under different assumptions...