KBase: The United States Department of Energy Systems Biology Knowledgebase

doi:10.1038/nbt.4163

. 2018 Jul 6;36(7):566-569.

doi: 10.1038/nbt.4163.

KBase: The United States Department of Energy Systems Biology Knowledgebase

Adam P Arkin^{1

2}, Robert W Cottingham³, Christopher S Henry⁴, Nomi L Harris², Rick L Stevens^{5

6}, Sergei Maslov^{7

8}, Paramvir Dehal², Doreen Ware⁹, Fernando Perez^{10

11

12

8}, Shane Canon¹³, Michael W Sneddon², Matthew L Henderson², William J Riehl², Dan Murphy-Olson⁴, Stephen Y Chan², Roy T Kamimura², Sunita Kumari⁹, Meghan M Drake³, Thomas S Brettin⁶, Elizabeth M Glass⁴, Dylan Chivian², Dan Gunter¹⁰, David J Weston³, Benjamin H Allen³, Jason Baumohl², Aaron A Best¹⁴, Ben Bowen², Steven E Brenner¹⁵, Christopher C Bun⁴, John-Marc Chandonia², Jer-Ming Chia⁹, Ric Colasanti⁴, Neal Conrad⁶, James J Davis⁶, Brian H Davison³, Matthew DeJongh¹⁶, Scott Devoid⁴, Emily Dietrich⁶, Inna Dubchak², Janaka N Edirisinghe^{4

17}, Gang Fang^{18

8}, José P Faria⁴, Paul M Frybarger⁴, Wolfgang Gerlach⁴, Mark Gerstein¹⁸, Annette Greiner¹³, James Gurtowski⁹, Holly L Haun³, Fei He^{7

8}, Rashmi Jain^{19

20}, Marcin P Joachimiak², Kevin P Keegan⁴, Shinnosuke Kondo¹⁶, Vivek Kumar⁹, Miriam L Land³, Folker Meyer⁴, Marissa Mills³, Pavel S Novichkov², Taeyun Oh^{19

20

8}, Gary J Olsen²¹, Robert Olson⁴, Bruce Parrello⁴, Shiran Pasternak⁹, Erik Pearson², Sarah S Poon¹⁰, Gavin A Price², Srividya Ramakrishnan^{9

8}, Priya Ranjan^{3

22}, Pamela C Ronald^{19

20}, Michael C Schatz^{9

8}, Samuel M D Seaver⁴, Maulik Shukla⁶, Roman A Sutormin², Mustafa H Syed^{3

8}, James Thomason⁹, Nathan L Tintle^{23

8}, Daifeng Wang^{18

8}, Fangfang Xia⁶, Hyunseung Yoo⁶, Shinjae Yoo²⁴, Dantong Yu^{24

8}

Affiliations

¹ Department of Bioengineering, University of California, Berkeley, California, USA.
² Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
³ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
⁴ Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
⁵ Computer Science Department and Computation Institute, University of Chicago, Chicago, Illinois, USA.
⁶ Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
⁷ Biology Department, Brookhaven National Laboratory, Upton, New York, USA.
⁸ Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.).
⁹ Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
¹⁰ Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
¹¹ Berkeley Institute for Data Science, University of California, Berkeley, California, USA.
¹² Department of Statistics, University of California, Berkeley, California, USA.
¹³ National Energy Research Scientific Computing Center, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
¹⁴ Department of Biology, Hope College, Holland, Michigan, USA.
¹⁵ Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.
¹⁶ Department of Computer Science, Hope College, Holland, Michigan, USA.
¹⁷ Computation Institute, University of Chicago, Chicago, Illinois, USA.
¹⁸ Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
¹⁹ Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.
²⁰ Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
²¹ Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
²² Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA.
²³ Department of Mathematics, Hope College, Holland, Michigan, USA.
²⁴ Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA.

PMID: 29979655
PMCID: PMC6870991
DOI: 10.1038/nbt.4163

KBase: The United States Department of Energy Systems Biology Knowledgebase

Adam P Arkin et al. Nat Biotechnol. 2018.

. 2018 Jul 6;36(7):566-569.

doi: 10.1038/nbt.4163.

Authors

Affiliations

¹ Department of Bioengineering, University of California, Berkeley, California, USA.
² Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
³ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
⁴ Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
⁵ Computer Science Department and Computation Institute, University of Chicago, Chicago, Illinois, USA.
⁶ Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA.
⁷ Biology Department, Brookhaven National Laboratory, Upton, New York, USA.
⁸ Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.).
⁹ Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
¹⁰ Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
¹¹ Berkeley Institute for Data Science, University of California, Berkeley, California, USA.
¹² Department of Statistics, University of California, Berkeley, California, USA.
¹³ National Energy Research Scientific Computing Center, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
¹⁴ Department of Biology, Hope College, Holland, Michigan, USA.
¹⁵ Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.
¹⁶ Department of Computer Science, Hope College, Holland, Michigan, USA.
¹⁷ Computation Institute, University of Chicago, Chicago, Illinois, USA.
¹⁸ Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.
¹⁹ Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.
²⁰ Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
²¹ Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
²² Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA.
²³ Department of Mathematics, Hope College, Holland, Michigan, USA.
²⁴ Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA.

PMID: 29979655
PMCID: PMC6870991
DOI: 10.1038/nbt.4163

No abstract available

PubMed Disclaimer

Conflict of interest statement

F.P. declares competing interest related to his work for Plot.ly and research funding from Microsoft, Google, and Anaconda Inc. S.E.B. receives funding and has a research collaboration with Tata Consultancy Service that is unrelated to the KBase project.

Figures

**Figure 1. KBase Narratives.**
A Narrative is an interactive, dynamic, and persistent document created by users that promotes open, reproducible, and collaborative science.

**Figure 2. Major workflows and data types in KBase.**
The unboxed labels represent data types, while each colored box represents a single app. The box colors signify the category of functionality, and the numbers in parentheses indicate the number of alternative apps that implement each function. Apps that require a genome data type as input are marked with a green 'G' icon. For more information see http://kbase.us/apps/.

See this image and copyright information in PMC

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References

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1. Prlić, A. & Procter, J.B. PLoS Comput. Biol.8, e1002802 (2012). - PMC - PubMed
1. Millman, K.J. & Pérez, F. in Developing Open-Source Scientific Practice. Implementing reproducible research. (eds. F.L.V. Stodden & R.D. Peng) 149–183 (CRC Press, Boca Raton, FL; 2014).
1. Pruitt, K.D., Tatusova, T. & Maglott, D.R. Nucleic Acids Res.35, D61–D65 (2007). - PMC - PubMed
1. Goodstein, D.M. et al. Nucleic Acids Res.40, D1178–D1186 (2012). - PMC - PubMed

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[1] Stodden, V. et al. Science354, 1240–1241 (2016). - PubMed

[2] Stodden, V. et al. Science354, 1240–1241 (2016). - PubMed

[3] Prlić, A. & Procter, J.B. PLoS Comput. Biol.8, e1002802 (2012). - PMC - PubMed

[4] Prlić, A. & Procter, J.B. PLoS Comput. Biol.8, e1002802 (2012). - PMC - PubMed

[5] Millman, K.J. & Pérez, F. in Developing Open-Source Scientific Practice. Implementing reproducible research. (eds. F.L.V. Stodden & R.D. Peng) 149–183 (CRC Press, Boca Raton, FL; 2014).

[6] Millman, K.J. & Pérez, F. in Developing Open-Source Scientific Practice. Implementing reproducible research. (eds. F.L.V. Stodden & R.D. Peng) 149–183 (CRC Press, Boca Raton, FL; 2014).

[7] Pruitt, K.D., Tatusova, T. & Maglott, D.R. Nucleic Acids Res.35, D61–D65 (2007). - PMC - PubMed

[8] Pruitt, K.D., Tatusova, T. & Maglott, D.R. Nucleic Acids Res.35, D61–D65 (2007). - PMC - PubMed

[9] Goodstein, D.M. et al. Nucleic Acids Res.40, D1178–D1186 (2012). - PMC - PubMed

[10] Goodstein, D.M. et al. Nucleic Acids Res.40, D1178–D1186 (2012). - PMC - PubMed

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KBase: The United States Department of Energy Systems Biology Knowledgebase

Affiliations

KBase: The United States Department of Energy Systems Biology Knowledgebase

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Affiliations

Conflict of interest statement

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