A brief discussion of common practices and ground principles will aid the reader in digesting the data to come, and will illustrate the power of graph theoretic approaches to analyzing networks. This section will define graphs, and then introduce tools for visualizing graph structure, for probing the sub-structure of graphs, for describing large-scale attributes of graphs, and for finding and describing interesting nodes or collections of nodes within graphs. We ask for the reader’s patience in this somewhat abstract section. All concepts introduced will subsequently be applied to developmental data. It is our contention that these tools overcome many of the limitations of seed-based and component-based network analyses, and will enable us to reexamine some of the previously described developmental data in a clarifying light.
