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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #337646

Research Project: Enhancing Plant Genome Function Maps Through Genomic, Genetic, Computational and Collaborative Research

Location: Plant, Soil and Nutrition Research

Title: KBase: the United States Department of Energy systems biology knowledgebase

Author
item ARKIN, ADAM - Lawrence Berkeley National Laboratory
item STEVENS, RICK - Argonne National Laboratory
item COTTINGHAM, ROBERT - Oak Ridge National Laboratory
item MASLOV, SERGEI - Brookhaven National Laboratory
item HENRY, CHRISTOPHER - Argonne National Laboratory
item DEHAL, PARAMVIR - Lawrence Berkeley National Laboratory
item Ware, Doreen
item PEREZ, FERNANDO - Lawrence Berkeley National Laboratory
item HARRIS, NAOMI - Lawrence Berkeley National Laboratory
item CANON, SHANE - Lawrence Berkeley National Laboratory
item SNEDDON, MICHAEL - Lawrence Berkeley National Laboratory
item HENDERSON, MATTHEW - Lawrence Berkeley National Laboratory
item RIEHL, WILLIAM - Lawrence Berkeley National Laboratory
item GUNTER, DAN - Lawrence Berkeley National Laboratory
item MURPHY-OLSON, DAN - Argonne National Laboratory
item CHEN, STEPHEN - Lawrence Berkeley National Laboratory
item KAMIMURA, ROY - Lawrence Berkeley National Laboratory
item BRETTIN, THOMAS - Argonne National Laboratory
item MEYER, FOLKER - Argonne National Laboratory
item CHIVIAN, DYLAN - Lawrence Berkeley National Laboratory
item WESTON, DAVID - Oak Ridge National Laboratory
item GLASS, ELIZABETH - Argonne National Laboratory
item DAVISON, BRIAN - Oak Ridge National Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item ALLEN, BENJAMIN - Oak Ridge National Laboratory
item BAUMOHL, JASON - Lawrence Berkeley National Laboratory
item BEST, AARON - Hope College
item BOWEN, BEN - Lawrence Berkeley National Laboratory
item BRENNER, STEVEN - Lawrence Berkeley National Laboratory
item BUN, CHRISTOPHER - Argonne National Laboratory
item CHANDONIA, JOHN-MARC - Lawrence Berkeley National Laboratory
item CHIA, JER-MING - Cold Spring Harbor Laboratory
item COLASANTI, RIC - Argonne National Laboratory
item CONRAD, NEAL - Argonne National Laboratory
item DAVID, JAMES - Argonne National Laboratory
item DEJONGH, MATTHEW - Hope College
item DEVOID, SCOTT - Argonne National Laboratory
item DIETRICH, EMILY - Argonne National Laboratory
item DRAKE, MEGHAN - Oak Ridge National Laboratory
item DUBCHAK, INNA - Lawrence Berkeley National Laboratory
item EDIRISINGHE, JANAKA - Argonne National Laboratory
item FANG, GANG - Yale University
item FARIA, JOSE - Argonne National Laboratory
item FRYBARGER, PAUL - Argonne National Laboratory
item GERLACH, WOLFGANG - Argonne National Laboratory
item GERSTEIN, MARK - Yale University
item GURTOWSKI, JAMES - Cold Spring Harbor Laboratory
item HAUN, HOLLY - Oak Ridge National Laboratory
item HE, FEI - Brookhaven National Laboratory
item JAIN, RASHMI - University Of California
item JOACHIMIAK, MARCIN - Lawrence Berkeley National Laboratory
item KEEGAN, KEVIN - Cold Spring Harbor Laboratory
item KONDO, SHINNOSUKE - Hope College
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item LAND, MIRIAM - Oak Ridge National Laboratory
item MILLS, MARISSA - Oak Ridge National Laboratory
item NOVICHKOV, PAVEL - Lawrence Berkeley National Laboratory
item OH, TAEYUN - University Of California
item OLSON, GARY - Argonne National Laboratory
item OLSON, BOB - Argonne National Laboratory
item PARRELLO, BRUCE - Argonne National Laboratory
item PASTERNAK, SHIRAN - Cold Spring Harbor Laboratory
item PEARSON, ERIK - Lawrence Berkeley National Laboratory
item POON, SARAH - Lawrence Berkeley National Laboratory
item PRICE, GAVIN - Lawrence Berkeley National Laboratory
item RAMAKRISHNAN, SRIVIDYA - Cold Spring Harbor Laboratory
item RANJAN, PRIYA - Oak Ridge National Laboratory
item RONALD, PAMELA - University Of California
item SCHATZ, MICHAEL - Cold Spring Harbor Laboratory
item SEAVER, SAMUEL - Argonne National Laboratory
item SHUKLA, MAULIK - Argonne National Laboratory
item SUTORMIN, ROMAN - Lawrence Berkeley National Laboratory
item SYED, MUSTAFA - Oak Ridge National Laboratory
item THOMASON, JAMES - Cold Spring Harbor Laboratory
item TINTLE, NATHAN - Hope College
item WANG, DAIFENG - Stoneybrook University
item XIA, FANGFANG - Argonne National Laboratory
item YOO, HYUNSEUNG - Argonne National Laboratory
item YOO, SHINJAE - Brookhaven National Laboratory

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/15/2018
Publication Date: 7/6/2018
Citation: Arkin, A., Stevens, R., Cottingham, R., Maslov, S., Henry, C., Dehal, P., Ware, D., Perez, F., Harris, N., Canon, S., Sneddon, M., Henderson, M., Riehl, W., Gunter, D., Murphy-Olson, D., Chen, S., Kamimura, R., Brettin, T., Meyer, F., Chivian, D., Weston, D., Glass, E., Davison, B., Kumari, S., Allen, B., Baumohl, J., Best, A., Bowen, B., Brenner, S., Bun, C., Chandonia, J., Chia, J., Colasanti, R., Conrad, N., David, J., Dejongh, M., Devoid, S., Dietrich, E., Drake, M., Dubchak, I., Edirisinghe, J., Fang, G., Faria, J., Frybarger, P., Gerlach, W., Gerstein, M., Gurtowski, J., Haun, H., He, F., Jain, R., Joachimiak, M., Keegan, K., Kondo, S., Kumar, V., Land, M., Mills, M., Novichkov, P., Oh, T., Olson, G., Olson, B., Parrello, B., Pasternak, S., Pearson, E., Poon, S., Price, G., Ramakrishnan, S., Ranjan, P., Ronald, P., Schatz, M., Seaver, S., Shukla, M., Sutormin, R., Syed, M., Thomason, J., Tintle, N., Wang, D., Xia, F., Yoo, H., Yoo, S. 2018. KBase: the United States Department of Energy systems biology knowledgebase. Nature Biotechnology. 36:566-569.

Interpretive Summary: KBase is an open science platform for comparative functional genomics and systems biology for microbes, plants and their communities, and for sharing results and methods with other scientists. KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase, an integrated environment, where knowledge and insights are created and multiplied.

Technical Abstract: 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 infrastructure; 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.