There is almost no pathway in plants for which there is complete knowledge, especially with respect to signaling and other modes of regulation. A variety of tools exist to view biological data in the context of what is already known concerning metabolic/signaling pathways, and there is no shortage of databases that provide access to information regarding these pathways. However, what exists is static, cannot be modified by the user, is often out of date, and any linking between, and among, components that connect pathways is haphazard. Plant biologists are often left to generic graph drawing software that provides no standard representation of such pathways and offers no functionality beyond visualization. The Beacon system is designed to remedy such a deficit by providing biologists with a variety of tools: an interface to draw pathways using a standardized graphical language, an online repository to store pathways and (optionally) share them with a community of users, and a means to make inquiries of, modify, or amend, drawn pathways. It will be possible to populate Beacon images with data from “omics” experiments. Beacon will also have the capacity to run simulation, or “what-if”, in silico “experiments”.
The system supports the notion that the visual depiction of pathways is a powerful tool in the research stages of hypothesis generation and sense-making, in addition to serving as reference material and as a teaching tool. Beacon supports the use of biological pathways at all stages of research, the sharing of new ideas and pathway models, and the use of such models as a computational tool in targeting the most efficient experiments to confirm/reject novel hypotheses.