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
1Department of Bioengineering, University of California, Berkeley, California, USA.
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Rick L Stevens
3Computer Science Department and Computation Institute, University of Chicago, Chicago, Illinois, USA.
4Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Robert W Cottingham
5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Sergei Maslov
6Biology Department, Brookhaven National Laboratory, Upton, New York, USA.
Christopher S Henry
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Paramvir Dehal
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Doreen Ware
8Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Fernando Perez
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
9Berkeley Institute for Data Science, University of California, Berkeley, California, USA.
Nomi L Harris
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Shane Canon
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Michael W Sneddon
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Matthew L Henderson
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
William J Riehl
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Dan Gunter
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Dan Murphy-Olson
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Stephen Chan
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Roy T Kamimura
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Thomas S Brettin
4Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Folker Meyer
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Dylan Chivian
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
David J Weston
5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Elizabeth M Glass
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Brian H Davison
5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Sunita Kumari
8Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Benjamin H Allen
5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Jason Baumohl
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Aaron A Best
10Department of Biology, Hope College, Holland, Michigan, USA.
Ben Bowen
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Steven E Brenner
11Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.
Christopher C Bun
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
John-Marc Chandonia
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Jer-Ming Chia
8Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Ric Colasanti
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Neal Conrad
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
James J Davis
4Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Matthew DeJongh
12Department of Computer Science, Hope College, Holland, Michigan, USA.
Scott Devoid
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Emily Dietrich
4Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Meghan M Drake
5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Inna Dubchak
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Janaka N Edirisinghe
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
13Computation Institute, University of Chicago, Chicago, Illinois, USA.
Gang Fang
14Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
José P Faria
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Paul M Frybarger
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Wolfgang Gerlach
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Mark Gerstein
14Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
James Gurtowski
8Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Holly L Haun
5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Fei He
6Biology Department, Brookhaven National Laboratory, Upton, New York, USA.
Rashmi Jain
16Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Marcin P Joachimiak
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Kevin P Keegan
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Shinnosuke Kondo
12Department of Computer Science, Hope College, Holland, Michigan, USA.
Vivek Kumar
8Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Miriam L Land
5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Marissa Mills
5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Pavel Novichkov
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Taeyun Oh
16Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Gary J Olsen
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
17Department of Microbiology, University of Illinois at Urbana-Chamgain, Urbana, Illinois, USA.
Bob Olson
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Bruce Parrello
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Shiran Pasternak
8Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Erik Pearson
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Sarah S Poon
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Gavin A Price
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Srividya Ramakrishnan
8Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Priya Ranjan
5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
18Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA.
Pamela C Ronald
16Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Michael C Schatz
8Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Samuel M D Seaver
7Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Maulik Shukla
4Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Roman A Sutormin
2Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Mustafa H Syed
5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
James Thomason
8Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Nathan L Tintle
19Department of Mathematics, Hope College, Holland, Michigan, USA.
Daifeng Wang
14Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
Fangfang Xia
4Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Hyunseung Yoo
4Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
Shinjae Yoo
6Biology 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
Subject Area
Subject Areas
- Biochemistry (6741)
- Bioengineering (4869)
- Bioinformatics (18980)
- Biophysics (9228)
- Cancer Biology (7082)
- Cell Biology (10338)
- Clinical Trials (138)
- Developmental Biology (5962)
- Ecology (9296)
- Epidemiology (2063)
- Evolutionary Biology (12600)
- Genetics (8939)
- Genomics (11916)
- Immunology (6978)
- Microbiology (17621)
- Molecular Biology (6880)
- Neuroscience (38161)
- Paleontology (275)
- Pathology (1138)
- Pharmacology and Toxicology (1965)
- Physiology (2916)
- Plant Biology (6357)
- Synthetic Biology (1774)
- Systems Biology (5022)
- Zoology (1002)