Padhoc: a computational pipeline for pathway reconstruction on the fly

Molecular pathway databases represent cellular processes in a structured and standardized way. These databases support the community-wide utilization of pathway information in biological research and the computational analysis of high-throughput biochemical data. Although pathway databases are critical in genomics research, the fast progress of biomedical sciences prevents databases from staying up-to-date. Moreover, the compartmentalization of cellular reactions into defined pathways reflects arbitrary choices that might not always be aligned with the needs of the researcher. Today, no tool exists that allow the easy creation of user-defined pathway representations.