Computational representation of developmental genetic regulatory networks

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2005.04.023 Byline: William J.R. Longabaugh (a), Eric H. Davidson (b), Hamid Bolouri (a)(b) Abstract: Developmental genetic regulatory networks (GRNs) have unique architectural characteristics. They are typically large-scale, multi-layered, and organized in a nested, modular hierarchy of regulatory network kernels, function-specific building blocks, and structural gene batteries. They are also inherently multicellular and involve changing topological relationships among a growing number of cells. Reconstruction of developmental GRNs requires unique computational tools that support the above representational requirements. In addition, we argue that DNA-centered network modeling, separate descriptions of network organization and network behavior, and support for network documentation and annotation are essential requirements for computational modeling of developmental GRNs. Based on these observations, we have developed a freely available, platform-independent, open source software package (BioTapestry) which supports both the process of model construction and also model visualization, analysis, documentation, and dissemination. We provide an overview of the main features of BioTapestry. The BioTapestry software and additional documents are available from http://www.biotapestry.org. We recommend BioTapestry as the substrate for further co-development for and by the developmental biology community. Author Affiliation: (a) Institute for Systems Biology, Seattle, WA 98103-8904, USA (b) Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA