• expansion-network

  • Referenced in 1 article [sw34481]
  • distinct regulatory regions. Recent gene regulatory network models use binding measurements; but usually only ... define gene-to-gene interactions, ignoring regulatory module structure. Moreover, current huge amount of transcriptomic ... method to specify possible regulatory connections in a given Boolean network, based on transcription factor ... Boolean network model into a “cis-regulatoryBoolean network model. This expanded model explicitly defines...
  • REVEAL

  • Referenced in 28 articles [sw36999]
  • principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables ... models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series...
  • Jimena

  • Referenced in 1 article [sw29354]
  • system state identification for genetic regulatory networks. Background: Boolean networks capture switching behavior of many ... naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states ... high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such ... models, but suffers from scaling problems for networks which contain nodes with more than...
  • Aeon

  • Referenced in 2 articles [sw42182]
  • that verifies integrity of the Boolean network with its regulatory graph; (ii) state-space visualisation...
  • 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...
  • ATLANTIS

  • Referenced in 2 articles [sw42186]
  • cell fate discovery and reprogramming. Boolean modelling of biological networks is a well-established technique ... cells. Specifically, decoding linkages between salient regulatory network states and corresponding cell fate outcomes ... methodology which converts complex network behavior into a landscape of network states wherein each state ... occurrence. Towards undertaking attractor landscape analysis of Boolean networks, we propose an Attractor Landscape Analysis...
  • optPBN

  • Referenced in 2 articles [sw32145]
  • optPBN: An optimisation toolbox for probabilistic boolean networks. SUMMARY: The optPBN toolbox provides a simple ... studies such as the inference of gene regulatory networks or the identification of the interaction...
  • BooleSim

  • Referenced in 2 articles [sw20432]
  • tool for simulation and manipulation of Boolean networks. It was developed mainly during Google ... network visualization. It can be used specifically for the modeling of gene regulatory or signal...
  • 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...
  • BoolSi

  • Referenced in 1 article [sw36097]
  • tool for distributed simulations of synchronous Boolean networks. It uses MPI standard to support execution ... behavior of complex dynamic networks, such as gene regulatory networks. In particular, it allows...
  • multistatepdscontrol

  • Referenced in 2 articles [sw31987]
  • intracellular networks, such as gene regulatory networks or signaling networks, in order for cells ... phenotype, what happens in cancer. If the network is represented by a mathematical model ... some other model types, such as Boolean networks, where structure-based approaches have been developed...
  • BioLQM

  • Referenced in 2 articles [sw35162]
  • Logical Qualitative Models of biological regulatory networks. BioLQM provides core modeling operations as building blocks ... valued models with tools limited to the Boolean case. Finally, bioLQM provides a framework...
  • CoCoA

  • Referenced in 654 articles [sw00143]
  • CoCoA is a system for Computations in Commutative...
  • Macaulay2

  • Referenced in 1923 articles [sw00537]
  • Macaulay2 is a software system devoted to supporting...
  • Mathematica

  • Referenced in 6355 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 13544 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • PolyBoRi

  • Referenced in 48 articles [sw00723]
  • Polybori: A framework for Gröbner-basis computations with...
  • QEPCAD

  • Referenced in 283 articles [sw00752]
  • QEPCAD B: A program for computing with semi...
  • R

  • Referenced in 9969 articles [sw00771]
  • R is a language and environment for statistical...
  • SageMath

  • Referenced in 1994 articles [sw00825]
  • Sage (SageMath) is free, open-source math software...