Animal development is controlled by highly complex transcriptional regulatory circuits. The enormous complexity of these networks, however, makes it difficult to determine how regulatory proteins act within the embryo to generate complex 3D patterns of gene expression. To overcome this difficulty, we have initiated an interdisciplinary collaboration to develop new system wide methods to decode these networks. This large project, The Berkeley Drosophila Transcription Network Project, includes Bioinformaticists, Biochemists, Geneticists, Engineers, and Image Analysis Physicists. One of our goals is to learn how to read the cis regulatory information in animal genome sequences, which contain much of the genetic information specifying animal form. For more information see http://bdtnp.lbl.gov/Fly-Net/.