New Results
The DOE Systems Biology Knowledgebase (KBase)
View ORCID ProfileAdam 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, William J Riehl, Dan Gunter, Dan Murphy-Olson, Stephen Chan, Roy T Kamimura, Thomas S Brettin, Folker Meyer, Dylan Chivian, David J Weston, Elizabeth M Glass, Brian H Davison, Sunita Kumari, Benjamin H Allen, Jason Baumohl, Aaron A Best, Ben Bowen, Steven E Brenner, Christopher C Bun, John-Marc Chandonia, Jer-Ming Chia, Ric Colasanti, Neal Conrad, James J Davis, Matthew DeJongh, Scott Devoid, Emily Dietrich, Meghan M Drake, Inna Dubchak, Janaka N Edirisinghe, Gang Fang, José P Faria, Paul M Frybarger, Wolfgang Gerlach, Mark Gerstein, James Gurtowski, Holly L Haun, Fei He, Rashmi Jain, Marcin P Joachimiak, Kevin P Keegan, Shinnosuke Kondo, Vivek Kumar, Miriam L Land, Marissa Mills, Pavel Novichkov, Taeyun Oh, Gary J Olsen, Bob Olson, Bruce Parrello, Shiran Pasternak, Erik Pearson, Sarah S Poon, Gavin A Price, Srividya Ramakrishnan, Priya Ranjan, Pamela C Ronald, Michael C Schatz, Samuel M D Seaver, Maulik Shukla, Roman A Sutormin, Mustafa H Syed, James Thomason, Nathan L Tintle, Daifeng Wang, Fangfang Xia, Hyunseung Yoo, Shinjae Yoo
doi: https://doi.org/10.1101/096354
Adam P Arkin
Department of Bioengineering, University of California, Berkeley, California, USA.Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Rick L Stevens
Computer Science Department and Computation Institute, University of Chicago, Chicago, Illinois, USA.Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Robert W Cottingham
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Sergei Maslov
Biology Department, Brookhaven National Laboratory, Upton, New York, USA.
Christopher S Henry
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Paramvir Dehal
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Doreen Ware
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Fernando Perez
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.Berkeley Institute for Data Science, University of California, Berkeley, California, USA.
Nomi L Harris
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Shane Canon
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Michael W Sneddon
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Matthew L Henderson
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
William J Riehl
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Dan Gunter
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Dan Murphy-Olson
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Stephen Chan
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Roy T Kamimura
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Thomas S Brettin
Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Folker Meyer
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Dylan Chivian
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
David J Weston
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Elizabeth M Glass
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Brian H Davison
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Sunita Kumari
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Benjamin H Allen
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Jason Baumohl
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Aaron A Best
Department of Biology, Hope College, Holland, Michigan, USA.
Ben Bowen
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Steven E Brenner
Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.
Christopher C Bun
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
John-Marc Chandonia
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Jer-Ming Chia
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Ric Colasanti
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Neal Conrad
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
James J Davis
Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Matthew DeJongh
Department of Computer Science, Hope College, Holland, Michigan, USA.
Scott Devoid
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Emily Dietrich
Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Meghan M Drake
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Inna Dubchak
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Janaka N Edirisinghe
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.Computation Institute, University of Chicago, Chicago, Illinois, USA.
Gang Fang
Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
José P Faria
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Paul M Frybarger
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Wolfgang Gerlach
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Mark Gerstein
Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
James Gurtowski
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Holly L Haun
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Fei He
Biology Department, Brookhaven National Laboratory, Upton, New York, USA.
Rashmi Jain
Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Marcin P Joachimiak
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Kevin P Keegan
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Shinnosuke Kondo
Department of Computer Science, Hope College, Holland, Michigan, USA.
Vivek Kumar
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Miriam L Land
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Marissa Mills
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Pavel Novichkov
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Taeyun Oh
Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Gary J Olsen
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.Department of Microbiology, University of Illinois at Urbana-Chamgain, Urbana, Illinois, USA.
Bob Olson
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Bruce Parrello
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Shiran Pasternak
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Erik Pearson
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Sarah S Poon
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Gavin A Price
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Srividya Ramakrishnan
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Priya Ranjan
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA.
Pamela C Ronald
Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Michael C Schatz
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Samuel M D Seaver
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Maulik Shukla
Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Roman A Sutormin
Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Mustafa H Syed
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
James Thomason
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Nathan L Tintle
Department of Mathematics, Hope College, Holland, Michigan, USA.
Daifeng Wang
Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
Fangfang Xia
Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Hyunseung Yoo
Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Shinjae Yoo
Biology Department, Brookhaven National Laboratory, Upton, New York, USA.
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.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Posted December 22, 2016.
The DOE Systems Biology Knowledgebase (KBase)
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, William J Riehl, Dan Gunter, Dan Murphy-Olson, Stephen Chan, Roy T Kamimura, Thomas S Brettin, Folker Meyer, Dylan Chivian, David J Weston, Elizabeth M Glass, Brian H Davison, Sunita Kumari, Benjamin H Allen, Jason Baumohl, Aaron A Best, Ben Bowen, Steven E Brenner, Christopher C Bun, John-Marc Chandonia, Jer-Ming Chia, Ric Colasanti, Neal Conrad, James J Davis, Matthew DeJongh, Scott Devoid, Emily Dietrich, Meghan M Drake, Inna Dubchak, Janaka N Edirisinghe, Gang Fang, José P Faria, Paul M Frybarger, Wolfgang Gerlach, Mark Gerstein, James Gurtowski, Holly L Haun, Fei He, Rashmi Jain, Marcin P Joachimiak, Kevin P Keegan, Shinnosuke Kondo, Vivek Kumar, Miriam L Land, Marissa Mills, Pavel Novichkov, Taeyun Oh, Gary J Olsen, Bob Olson, Bruce Parrello, Shiran Pasternak, Erik Pearson, Sarah S Poon, Gavin A Price, Srividya Ramakrishnan, Priya Ranjan, Pamela C Ronald, Michael C Schatz, Samuel M D Seaver, Maulik Shukla, Roman A Sutormin, Mustafa H Syed, James Thomason, Nathan L Tintle, Daifeng Wang, Fangfang Xia, Hyunseung Yoo, Shinjae Yoo
bioRxiv 096354; doi: https://doi.org/10.1101/096354
The DOE Systems Biology Knowledgebase (KBase)
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, William J Riehl, Dan Gunter, Dan Murphy-Olson, Stephen Chan, Roy T Kamimura, Thomas S Brettin, Folker Meyer, Dylan Chivian, David J Weston, Elizabeth M Glass, Brian H Davison, Sunita Kumari, Benjamin H Allen, Jason Baumohl, Aaron A Best, Ben Bowen, Steven E Brenner, Christopher C Bun, John-Marc Chandonia, Jer-Ming Chia, Ric Colasanti, Neal Conrad, James J Davis, Matthew DeJongh, Scott Devoid, Emily Dietrich, Meghan M Drake, Inna Dubchak, Janaka N Edirisinghe, Gang Fang, José P Faria, Paul M Frybarger, Wolfgang Gerlach, Mark Gerstein, James Gurtowski, Holly L Haun, Fei He, Rashmi Jain, Marcin P Joachimiak, Kevin P Keegan, Shinnosuke Kondo, Vivek Kumar, Miriam L Land, Marissa Mills, Pavel Novichkov, Taeyun Oh, Gary J Olsen, Bob Olson, Bruce Parrello, Shiran Pasternak, Erik Pearson, Sarah S Poon, Gavin A Price, Srividya Ramakrishnan, Priya Ranjan, Pamela C Ronald, Michael C Schatz, Samuel M D Seaver, Maulik Shukla, Roman A Sutormin, Mustafa H Syed, James Thomason, Nathan L Tintle, Daifeng Wang, Fangfang Xia, Hyunseung Yoo, Shinjae Yoo
bioRxiv 096354; doi: https://doi.org/10.1101/096354
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