RT Journal Article
SR Electronic
T1 The DOE Systems Biology Knowledgebase (KBase)
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 096354
DO 10.1101/096354
A1 Adam P Arkin
A1 Rick L Stevens
A1 Robert W Cottingham
A1 Sergei Maslov
A1 Christopher S Henry
A1 Paramvir Dehal
A1 Doreen Ware
A1 Fernando Perez
A1 Nomi L Harris
A1 Shane Canon
A1 Michael W Sneddon
A1 Matthew L Henderson
A1 William J Riehl
A1 Dan Gunter
A1 Dan Murphy-Olson
A1 Stephen Chan
A1 Roy T Kamimura
A1 Thomas S Brettin
A1 Folker Meyer
A1 Dylan Chivian
A1 David J Weston
A1 Elizabeth M Glass
A1 Brian H Davison
A1 Sunita Kumari
A1 Benjamin H Allen
A1 Jason Baumohl
A1 Aaron A Best
A1 Ben Bowen
A1 Steven E Brenner
A1 Christopher C Bun
A1 John-Marc Chandonia
A1 Jer-Ming Chia
A1 Ric Colasanti
A1 Neal Conrad
A1 James J Davis
A1 Matthew DeJongh
A1 Scott Devoid
A1 Emily Dietrich
A1 Meghan M Drake
A1 Inna Dubchak
A1 Janaka N Edirisinghe
A1 Gang Fang
A1 José P Faria
A1 Paul M Frybarger
A1 Wolfgang Gerlach
A1 Mark Gerstein
A1 James Gurtowski
A1 Holly L Haun
A1 Fei He
A1 Rashmi Jain
A1 Marcin P Joachimiak
A1 Kevin P Keegan
A1 Shinnosuke Kondo
A1 Vivek Kumar
A1 Miriam L Land
A1 Marissa Mills
A1 Pavel Novichkov
A1 Taeyun Oh
A1 Gary J Olsen
A1 Bob Olson
A1 Bruce Parrello
A1 Shiran Pasternak
A1 Erik Pearson
A1 Sarah S Poon
A1 Gavin A Price
A1 Srividya Ramakrishnan
A1 Priya Ranjan
A1 Pamela C Ronald
A1 Michael C Schatz
A1 Samuel M D Seaver
A1 Maulik Shukla
A1 Roman A Sutormin
A1 Mustafa H Syed
A1 James Thomason
A1 Nathan L Tintle
A1 Daifeng Wang
A1 Fangfang Xia
A1 Hyunseung Yoo
A1 Shinjae Yoo
YR 2016
UL http://biorxiv.org/content/early/2016/12/22/096354.abstract
AB 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.