Contents

• • Warning
  
  
• Introduction
• Network visualization and format conversion
  • Introduction
    • Network visualization
    • Graph formats
  • Visualisation of a co-expression network
    • Study case
    • Protocol for the web server
    • Protocol for the command-line tools
  
  
• Comparisons between networks
  • Introduction
  • Computing the intersection, union and differences between two graphs
    • Study case
    • Protocol for the web server
    • Protocol for the command-line tools
    • Interpretation of the results
  • Strengths and weaknesses of the approach
  • Exercises
  • Troubleshooting
  
  
• Node degree statistics
  • Introduction
  • Analysis of the node degree distribution of a biological network
    • Study case
    • Protocol for the web server
    • Protocol for the command-line tools
    • Interpretation of the results
  
  
• Study of the neighborhood of the nodes
  • Introduction
  • Analysis of the neighbours of orphan nodes in an interaction protein network
    • Study case
    • Protocol for the web server
    • Protocol for the command-line tools
    • Interpretation of the results
  
  
• Graph clustering
  • Introduction
  • Network clustering comparison
    • Study case
    • Protocol for the web server
    • Protocol for the command-line tools
    • Interpretation of the results
  
  
• Influence of graph alteration and randomization on clustering
  • Introduction
  • Quantitative assessment of a clustering algorithm
    • Study case
    • Protocol for the web server
    • Protocol for the command-line tools
    • Interpretation of the results
  
  
• Path finding
  • Introduction
  • Computing the k shortest paths in weighted networks
    • Study case
    • Protocol for the web server
    • Protocol for the command-line tools
    • Interpretation of the results
  • Summary
  • Strengths and Weaknesses of the approach
    • Strengths
    • Weaknesses
  • Troubleshooting
  
  
• Metabolic path finding
  • Introduction
  • Enumerating metabolic pathways between compounds, reactions or enzymes
    • Study case
    • Protocol for the web server
    • Protocol for the command-line tools
    • Interpretation of the results
  • Summary
  • Strengths and Weaknesses of the approach
    • Strengths
    • Weaknesses
  • Troubleshooting
  
  
• KEGG network provider
  • Introduction
  • Construction of yeast and E. coli metabolic networks
    • Study case
    • Protocol for the web server
    • Protocol for the command-line tools
    • Interpretation of the results
  • Summary
  • Troubleshooting
  
  
• Pathway inference
  • Introduction
  • Inferring a pathway for a set of co-expressed genes
    • Protocol for the web server
    • Protocol for the command-line tools
    • Interpretation of the results
  • Summary
  • Strengths and Weaknesses of the approach
    • Strengths
    • Weaknesses
  • Troubleshooting
  
  
• Bibliography

Warning

This tutorial is in construction. The current version only covers a very small fraction of the NeATtools. For the tools not covered yet by the tutorial, the DEMO buttons already give some hints about typical cases of utilization. We intend to develop further those tutorials very soon.