Contents

• Introduction
• Generalities and file formats
  • How to run GenRGenS
    • Downloading and installing GenRGenS
    • Command-line version
    • Graphical User Interface
  • Description files
    • Main structure
    • Common clauses
    • Simple example
  
  
• The MARKOV package : Markovian models
  • Some theoretical aspects
    • Main definition
    • What about heterogeneity ?
    • Hidden Markovian Models (HMMs)
  • Implementing a Markovian model
    • Main structure
    • Markovian generation specific clauses
  • Examples
    • A Bernoulli model
    • A model for a mRNA having order 1
    • An heterogenous model
    • Basic Hidden Markov Model
  • Command-line options and additional tools
    • Markov-specific option: Dead-Ends tolerance
    • BuildMarkov: Automatic construction of MARKOV description files
  
  
• The GRAMMAR package: Context-Free Grammars(CFG)
  • Minimal amount of language theory
    • Grammars and discrete models
  • Uniform random generation of words of context-free languages
    • Stochastic approach does not guarantee uniformity
    • A precomputation stage is needed
  • Weighted languages for controlled non-uniform random generation
  • Implementing a CFG-based model
    • Main structure
    • Grammar generation specific clauses
    • A complete example
  • Grammar-specific command line options
  
  
• The RATIONAL package : Regular Expressions and PROSITE patterns
  • Some theory
    • Regular expressions syntax
    • PROSITE Patterns
    • PROSITE patterns/Rational expressions relationship
    • Uniform random generation among the language denoted by a Regular Expression
  • Implementing a Rational/PROSITE model
    • Main structure
    • RATIONAL generation specific clauses
  • Examples
    • RATIONAL style example
    • PROSITE style example
  • Rational expressions-specific command line options
  
  
• The MASTER package : Hierarchical models
  • Hierarchical models: Principles
    • Saving time and space
    • Ambiguity and bias
  • Implementing a hierarchical model
    • Main structure
    • Master generation specific clauses
    • Capturing Dependencies between sequences size
  • A complete example
    • Source
    • Semantics
  
  
• Bibliography