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Title: KBase: The United States Department of Energy Systems Biology Knowledgebase

Abstract

The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) is an open-source software and data platform designed to tackle the grand challenge of systems biology—predicting and designing biological function at scales ranging from the biomolecular to the ecological. KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large analyses on scalable computing infrastructure; and combine experimental evidence and conclusions to model plant and microbial physiology and community dynamics. The KBase platform has extensible analytical capabilities that currently include (meta)genome assembly, annotation, comparative genomics, transcriptomics, and metabolic modeling; a web-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; and a software development kit that enables the community to add functionality to the system.

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3]; ORCiD logo [4];  [5];  [6];  [4]; ORCiD logo [7]; ORCiD logo [8];  [9];  [4];  [4];  [4];  [3];  [4];  [4];  [7]; ORCiD logo [2];  [10];  [3] more »;  [4];  [11]; ORCiD logo [2];  [2];  [4];  [12];  [4];  [13];  [3];  [4];  [7];  [3];  [10];  [10]; ORCiD logo [2];  [14];  [3];  [10];  [4];  [15];  [16]; ORCiD logo [3];  [3];  [3]; ORCiD logo [17];  [9];  [7];  [2]; ORCiD logo [18];  [19];  [4];  [3];  [14];  [7]; ORCiD logo [2]; ORCiD logo [3];  [2];  [4]; ORCiD logo [20];  [21];  [3];  [3];  [7];  [4];  [11];  [4];  [22];  [23];  [19]; ORCiD logo [22];  [3];  [10];  [4];  [24];  [7];  [25]; ORCiD logo [26];  [10];  [10];  [27];  [28] « less
  1. Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  3. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  5. Univ. of Chicago, IL (United States). Computer Science Dept. and Computation Inst.; Argonne National Lab. (ANL), Argonne, IL (United States). Computing, Environment, and Life Sciences Directorate
  6. Brookhaven National Lab. (BNL), Upton, NY (United States). Biology Dept.; Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Bioengineering and Carl R. Woese Inst. for Genomic Biology
  7. Cold Spring Harbor Lab. (CSHL), Cold Spring Harbor, NY (United States)
  8. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division; Univ. of California, Berkeley, CA (United States). Berkeley Inst. for Data Science and Dept. of Statistics
  9. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
  10. Argonne National Lab. (ANL), Argonne, IL (United States). Computing, Environment, and Life Sciences Directorate
  11. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division
  12. Hope College, Holland, MI (United States). Dept. of Biology
  13. Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  14. Hope College, Holland, MI (United States). Dept. of Computer Science
  15. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division; Univ. of Chicago, IL (United States). Computation Inst.
  16. Yale Univ., New Haven, CT (United States). Program in Computational Biology and Bioinformatics; New York Univ. (NYU) Shanghai Campus, Shanghai (China)
  17. Yale Univ., New Haven, CT (United States). Program in Computational Biology and Bioinformatics
  18. Brookhaven National Lab. (BNL), Upton, NY (United States). Biology Dept.; Kansas State Univ., Manhattan, KS (United States). Dept. of Plant Pathology
  19. Univ. of California, Davis, CA (United States). Dept. of Plant Pathology and Genome Center; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst. (JBEI)
  20. Univ. of California, Davis, CA (United States). Dept. of Plant Pathology and Genome Center; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Inst. (JBEI); Insilicogen. Inc., Yongin (Korea, Republic of)
  21. Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Microbiology
  22. Cold Spring Harbor Lab. (CSHL), Cold Spring Harbor, NY (United States); Johns Hopkins Univ., Baltimore, MD (United States). Dept. of Computer Science
  23. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Plant Sciences
  24. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Memorial Sloan Kettering Cancer Center (MSKCC), New York City, NY (United States)
  25. Hope College, Holland, MI (United States). Dept. of Mathematics; Dordt College, Sioux Center, IA (United States)
  26. Yale Univ., New Haven, CT (United States). Program in Computational Biology and Bioinformatics; Stony Brook Univ., NY (United States). Dept. of Biomedical Informatics
  27. Brookhaven National Lab. (BNL), Upton, NY (United States). Computer Science and Mathematics and Computational Science Initiative (CSI)
  28. Brookhaven National Lab. (BNL), Upton, NY (United States). Computer Science and Mathematics and Computational Science Initiative (CSI); New Jersey Inst. of Technology, Newark, NJ (United States). Martin Tuchman School of Management
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1471834
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231; AC02-06CH11357; AC02-98CH10886
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Biotechnology
Additional Journal Information:
Journal Volume: 36; Journal Issue: 7; Journal ID: ISSN 1087-0156
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Arkin, Adam P., Cottingham, Robert W., Henry, Christopher S., Harris, Nomi L., Stevens, Rick L., Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W., Henderson, Matthew L., Riehl, William J., Murphy-Olson, Dan, Chan, Stephen Y., Kamimura, Roy T., Kumari, Sunita, Drake, Meghan M., Brettin, Thomas S., Glass, Elizabeth M., Chivian, Dylan, Gunter, Dan, Weston, David J., Allen, Benjamin H., Baumohl, Jason, Best, Aaron A., Bowen, Ben, Brenner, Steven E., Bun, Christopher C., Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J., Davison, Brian H., DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N., Fang, Gang, Faria, José P., Frybarger, Paul M., Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L., He, Fei, Jain, Rashmi, Joachimiak, Marcin P., Keegan, Kevin P., Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L., Meyer, Folker, Mills, Marissa, Novichkov, Pavel S., Oh, Taeyun, Olsen, Gary J., Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S., Price, Gavin A., Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C., Schatz, Michael C., Seaver, Samuel M. D., Shukla, Maulik, Sutormin, Roman A., Syed, Mustafa H., Thomason, James, Tintle, Nathan L., Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, and Yu, Dantong. KBase: The United States Department of Energy Systems Biology Knowledgebase. United States: N. p., 2018. Web. doi:10.1038/nbt.4163.
Arkin, Adam P., Cottingham, Robert W., Henry, Christopher S., Harris, Nomi L., Stevens, Rick L., Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W., Henderson, Matthew L., Riehl, William J., Murphy-Olson, Dan, Chan, Stephen Y., Kamimura, Roy T., Kumari, Sunita, Drake, Meghan M., Brettin, Thomas S., Glass, Elizabeth M., Chivian, Dylan, Gunter, Dan, Weston, David J., Allen, Benjamin H., Baumohl, Jason, Best, Aaron A., Bowen, Ben, Brenner, Steven E., Bun, Christopher C., Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J., Davison, Brian H., DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N., Fang, Gang, Faria, José P., Frybarger, Paul M., Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L., He, Fei, Jain, Rashmi, Joachimiak, Marcin P., Keegan, Kevin P., Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L., Meyer, Folker, Mills, Marissa, Novichkov, Pavel S., Oh, Taeyun, Olsen, Gary J., Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S., Price, Gavin A., Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C., Schatz, Michael C., Seaver, Samuel M. D., Shukla, Maulik, Sutormin, Roman A., Syed, Mustafa H., Thomason, James, Tintle, Nathan L., Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, & Yu, Dantong. KBase: The United States Department of Energy Systems Biology Knowledgebase. United States. doi:10.1038/nbt.4163.
Arkin, Adam P., Cottingham, Robert W., Henry, Christopher S., Harris, Nomi L., Stevens, Rick L., Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W., Henderson, Matthew L., Riehl, William J., Murphy-Olson, Dan, Chan, Stephen Y., Kamimura, Roy T., Kumari, Sunita, Drake, Meghan M., Brettin, Thomas S., Glass, Elizabeth M., Chivian, Dylan, Gunter, Dan, Weston, David J., Allen, Benjamin H., Baumohl, Jason, Best, Aaron A., Bowen, Ben, Brenner, Steven E., Bun, Christopher C., Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J., Davison, Brian H., DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N., Fang, Gang, Faria, José P., Frybarger, Paul M., Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L., He, Fei, Jain, Rashmi, Joachimiak, Marcin P., Keegan, Kevin P., Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L., Meyer, Folker, Mills, Marissa, Novichkov, Pavel S., Oh, Taeyun, Olsen, Gary J., Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S., Price, Gavin A., Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C., Schatz, Michael C., Seaver, Samuel M. D., Shukla, Maulik, Sutormin, Roman A., Syed, Mustafa H., Thomason, James, Tintle, Nathan L., Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, and Yu, Dantong. Fri . "KBase: The United States Department of Energy Systems Biology Knowledgebase". United States. doi:10.1038/nbt.4163. https://www.osti.gov/servlets/purl/1471834.
@article{osti_1471834,
title = {KBase: The United States Department of Energy Systems Biology Knowledgebase},
author = {Arkin, Adam P. and Cottingham, Robert W. and Henry, Christopher S. and Harris, Nomi L. and Stevens, Rick L. and Maslov, Sergei and Dehal, Paramvir and Ware, Doreen and Perez, Fernando and Canon, Shane and Sneddon, Michael W. and Henderson, Matthew L. and Riehl, William J. and Murphy-Olson, Dan and Chan, Stephen Y. and Kamimura, Roy T. and Kumari, Sunita and Drake, Meghan M. and Brettin, Thomas S. and Glass, Elizabeth M. and Chivian, Dylan and Gunter, Dan and Weston, David J. and Allen, Benjamin H. and Baumohl, Jason and Best, Aaron A. and Bowen, Ben and Brenner, Steven E. and Bun, Christopher C. and Chandonia, John-Marc and Chia, Jer-Ming and Colasanti, Ric and Conrad, Neal and Davis, James J. and Davison, Brian H. and DeJongh, Matthew and Devoid, Scott and Dietrich, Emily and Dubchak, Inna and Edirisinghe, Janaka N. and Fang, Gang and Faria, José P. and Frybarger, Paul M. and Gerlach, Wolfgang and Gerstein, Mark and Greiner, Annette and Gurtowski, James and Haun, Holly L. and He, Fei and Jain, Rashmi and Joachimiak, Marcin P. and Keegan, Kevin P. and Kondo, Shinnosuke and Kumar, Vivek and Land, Miriam L. and Meyer, Folker and Mills, Marissa and Novichkov, Pavel S. and Oh, Taeyun and Olsen, Gary J. and Olson, Robert and Parrello, Bruce and Pasternak, Shiran and Pearson, Erik and Poon, Sarah S. and Price, Gavin A. and Ramakrishnan, Srividya and Ranjan, Priya and Ronald, Pamela C. and Schatz, Michael C. and Seaver, Samuel M. D. and Shukla, Maulik and Sutormin, Roman A. and Syed, Mustafa H. and Thomason, James and Tintle, Nathan L. and Wang, Daifeng and Xia, Fangfang and Yoo, Hyunseung and Yoo, Shinjae and Yu, Dantong},
abstractNote = {The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) is an open-source software and data platform designed to tackle the grand challenge of systems biology—predicting and designing biological function at scales ranging from the biomolecular to the ecological. KBase is available for anyone to use, and enables researchers to collaboratively generate, test, compare, and share hypotheses about biological functions; perform large analyses on scalable computing infrastructure; and combine experimental evidence and conclusions to model plant and microbial physiology and community dynamics. The KBase platform has extensible analytical capabilities that currently include (meta)genome assembly, annotation, comparative genomics, transcriptomics, and metabolic modeling; a web-based user interface that supports building, sharing, and publishing reproducible and well-annotated analyses with integrated data; and a software development kit that enables the community to add functionality to the system.},
doi = {10.1038/nbt.4163},
journal = {Nature Biotechnology},
number = 7,
volume = 36,
place = {United States},
year = {Fri Jul 06 00:00:00 EDT 2018},
month = {Fri Jul 06 00:00:00 EDT 2018}
}

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