Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

作者：Peter D. Karp, Suzanne Paley, Markus Krummenacker, Mario Latendresse, J. M. Dale, T. J. Lee, P. Kaipa, Fred Gilham, Aaron Spaulding, Liviu Popescu, Tomer Altman, Ian T. Paulsen, Ingrid M. Keseler, Ron Caspi · 发表于：Briefings in Bioinformatics · 年份：2009 · DOI：10.1093/bib/bbp043 · 被引用次数：711 · 研究领域：Microbial Metabolic Engineering and Bioproduction、Metabolomics and Mass Spectrometry Studies、Bioinformatics and Genomic Networks

MOTIVATION: Biological systems function through dynamic interactions among genes and their products, regulatory circuits and metabolic networks. Our development of the Pathway Tools software was motivated by the need to construct biological knowledge resources that combine these many types of data, and that enable users to find and comprehend data of interest as quickly as possible through query and visualization tools. Further, we sought to support the development of metabolic flux models from pathway databases, and to use pathway information to leverage the interpretation of high-throughput data sets. RESULTS: In the past 4 years we have enhanced the already extensive Pathway Tools software in several respects. It can now support metabolic-model execution through the Web, it provides a more accurate gap filler for metabolic models; it supports development of models for organism communities distributed across a spatial grid; and model results may be visualized graphically. Pathway Tools supports several new omics-data analysis tools including the Omics Dashboard, multi-pathway diagrams called pathway collages, a pathway-covering algorithm for metabolomics data analysis and an algorithm for generating mechanistic explanations of multi-omics data. We have also improved the core pathway/genome databases management capabilities of the software, providing new multi-organism search tools for organism communities, improved graphics rendering, faster performance and re-designed gene...