• Ginsim

  • Referenced in 29 articles [sw09090]
  • suite for the qualitative modelling, simulation and analysis of regulatory networks. This paper presents GINsim ... devoted to the qualitative modelling, analysis and simulation of genetic regulatory networks. Formally, our approach ... regulatory graph, as well as a simulation engine to compute the corresponding qualitative dynamical behaviour ... preliminary model analysis of the inter-cellular regulatory network activating Notch at the dorsal–ventral...
  • GNA

  • Referenced in 21 articles [sw35974]
  • constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination ... simulator of qualitative models of genetic regulatory networks in the form of piecewise-linear differential ... parameters, which are often not available for networks of biological interest, the user ... state transition graph that describes the qualitative dynamics of the network. The simulator has been...
  • SQUAD

  • Referenced in 5 articles [sw29353]
  • SQUAD Method for the Qualitative Modeling of Regulatory Networks. The wealth of molecular information provided ... efforts dedicated to the reconstruction of regulatory networks in diverse biological systems. This information, however ... insufficient for the construction of quantitative models due to the absence of sufficiently accurate measurements ... qualitative information about patterns of expression to infer the regulatory networks that generate such patterns...
  • BioLQM

  • Referenced in 1 article [sw35162]
  • Conversion of Logical Qualitative Models of Biological Networks. Here we introduce bioLQM, a new Java ... analysis of Logical Qualitative Models of biological regulatory networks. BioLQM provides core modeling operations ... tools. Model modifications enable the definition of various perturbations, as well as model reduction, easing ... large models. Another modification enables the study of multi-valued models with tools limited...
  • QSSPN

  • Referenced in 1 article [sw30010]
  • cell models is not yet possible. Simulation methods capable of using available qualitative data ... develop dynamic whole-cell models through an iterative process of modelling and experimental validation. Results ... predict the feasibility of qualitative dynamic behaviours in qualitative models of gene regulation, signalling ... dynamic simulations including regulatory mechanisms and a genome-scale metabolic network in human cell, using...
  • ANDy

  • Referenced in 2 articles [sw16548]
  • Activity Networks with Delays, is a discrete time framework aimed at the qualitative modelling ... easy and natural modelling of time-dependent biological systems (i.e., regulatory pathways). Activities involve entities ... activators, inhibitors or products of biochemical network operation. Activities may have given duration...
  • Mathematica

  • Referenced in 5883 articles [sw00554]
  • Almost any workflow involves computing results, and that...
  • Matlab

  • Referenced in 12074 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 8359 articles [sw00771]
  • R is a language and environment for statistical...
  • Sostools

  • Referenced in 270 articles [sw00891]
  • We are pleased to introduce SOSTOOLS, a free...
  • SUNDIALS

  • Referenced in 213 articles [sw00927]
  • SUNDIALS was implemented with the goal of providing...
  • Graphviz

  • Referenced in 81 articles [sw01283]
  • Graphviz is open source graph visualization software. Graph...
  • Design/CPN

  • Referenced in 37 articles [sw01952]
  • Modeling and verification of cryptographic protocols using coloured...
  • UCI-ml

  • Referenced in 3041 articles [sw04074]
  • UC Irvine Machine Learning Repository. We currently maintain...
  • Bioconductor

  • Referenced in 298 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • SNOOPY

  • Referenced in 31 articles [sw04386]
  • Snoopy is a software tool to design and...
  • gplots

  • Referenced in 6 articles [sw04555]
  • gplots: Various R Programming Tools for Plotting Data...
  • PLINK

  • Referenced in 61 articles [sw04581]
  • PLINK is a free, open-source whole genome...
  • YALMIP

  • Referenced in 913 articles [sw04595]
  • YALMIP Yet another LMI parser. YALMIP is a...