Workshop, Northern Arizona Unviersity, Spring 2011

Workshop Learning Objectives

Participants will be able to ...

  • Describe the features of a generic network model and explain the advantages and disadvantages of this model type
  • Characterize the three general aims of network science and explain why they are relevant for biologists
  • Calculate and apply common structural properties of networks
  • Calculate and apply common throughflow propertier of flow network models



Presentation Slides

Activity 1: Using Matlab
  (10 min break)  
Network Statics: Structural Analysis
  Network Properties Activity 2
  Pathway Enumeration Activity 3
  Centrality Concepts & Degree Distributions Activity 4
  (10 min break)  
Network Dynamics (on): Throughflow Analysis
  Throughflow Properties Activity 5
  Throughflow Dynamcs Activity 6

I expect this workshop to take 3-4 hours, depending on participant preparation and engagement.



Proloux et al. 2005. Network thinking in ecology and evolution. TREE

Fath and Patten 1999. Review of the Foundations of network environ analysis. Ecosystems

GYAGTOM: Yet Another Guide TO Matlab (Dunham & Murphy)


ENA - This is a collection of matlab functions for Ecological Network Analysis. The NEA.m function is documented in Fath & Borrett 2006 doi:10.1016/j.envsoft.2004.11.007)


Graph - Graph theory toolbox. All functions written by Kevin Murphy (1998) unless otherwise noted. The latest version is available from http://www.cs.ubc.ca/~murphyk/Software/index.html)

You will need to download theses zipped files and put the unzipped folders somewhere on your MATLAB search path.

I have selected to use MATLAB for this workshop, but I should point out that there are a number of useful tools for network analysis now in R. These include the 'network', 'sna', and 'statnet' packages. J.S. Choi ported the NEA.m function into R codes at one point as well, but I am not sure of its availability.

Other useful software inlcudes Pajek, UCINET, NETWRK4, WAND.