The DOE Systems Biology Knowledgebase (KBase) [article]

Adam P. Arkin, Rick L Stevens, Robert W Cottingham, Sergei Maslov, Christopher S Henry, Paramvir Dehal, Doreen Ware, Fernando Perez, Nomi L Harris, Shane Canon, Michael W Sneddon, Matthew L Henderson (+67 others)
2016 bioRxiv   pre-print
The U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology - predicting and designing biological function from the biomolecular (small scale) to the ecological (large scale). KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large-scale analyses on scalable computing
more » ... cture; and combine experimental evidence and conclusions that lead to accurate models of plant and microbial physiology and community dynamics. The KBase platform has (1) extensible analytical capabilities that currently include genome assembly, annotation, ontology assignment, comparative genomics, transcriptomics, and metabolic modeling; (2) a web-browser-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; (3) access to extensive computational resources; and (4) a software development kit allowing the community to add functionality to the system.
doi:10.1101/096354 fatcat:ojeek6qm4nca5c2wtapougjlm4