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Title: The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

Abstract

The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.

Authors:
 [1];  [2];  [3];  [1];  [4];  [4];  [5];  [1];  [6];  [1];  [7]; ORCiD logo [8];  [9];  [6];  [6];  [6];  [1];  [1];  [7];  [10] more »;  [1];  [1];  [11];  [1];  [5];  [1];  [12];  [5];  [5];  [6];  [1];  [6];  [1];  [1] « less
+ Show Author Affiliations
  1. Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
  2. Univ. of Virginia, Charlottesville, VA (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
  3. Cairo Univ., Cairo (Egypt)
  4. Argonne National Lab. (ANL), Argonne, IL (United States)
  5. Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
  6. Univ. of Virginia, Charlottesville, VA (United States)
  7. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
  8. Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
  9. Chicago State Univ., IL (United States)
  10. Univ. of Illinois at Urbana-Champaign, IL (United States)
  11. Univ. of Chicago, IL (United States)
  12. University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Institutes of Health (NIH) - National Institute of Allergy and Infectious Diseases (NIAID); U. S. Department of Health and Human Services; USDOE
OSTI Identifier:
1633068
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 48; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION

Citation Formats

Davis, James J., Wattam, Alice R., Aziz, Ramy K., Brettin, Thomas, Butler, Ralph, Butler, Rory M., Chlenski, Philippe, Conrad, Neal, Dickerman, Allan, Dietrich, Emily M., Gabbard, Joseph L., Gerdes, Svetlana, Guard, Andrew, Kenyon, Ronald W., Machi, Dustin, Mao, Chunhong, Murphy-Olson, Dan, Nguyen, Marcus, Nordberg, Eric K., Olsen, Gary J., Olson, Robert D., Overbeek, Jamie C., Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Shukla, Maulik, Thomas, Chris, VanOeffelen, Margo, Vonstein, Veronika, Warren, Andrew S., Xia, Fangfang, Xie, Dawen, Yoo, Hyunseung, and Stevens, Rick. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. United States: N. p., 2019. Web. doi:10.1093/nar/gkz943.
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Davis, James J., Wattam, Alice R., Aziz, Ramy K., Brettin, Thomas, Butler, Ralph, Butler, Rory M., Chlenski, Philippe, Conrad, Neal, Dickerman, Allan, Dietrich, Emily M., Gabbard, Joseph L., Gerdes, Svetlana, Guard, Andrew, Kenyon, Ronald W., Machi, Dustin, Mao, Chunhong, Murphy-Olson, Dan, Nguyen, Marcus, Nordberg, Eric K., Olsen, Gary J., Olson, Robert D., Overbeek, Jamie C., Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Shukla, Maulik, Thomas, Chris, VanOeffelen, Margo, Vonstein, Veronika, Warren, Andrew S., Xia, Fangfang, Xie, Dawen, Yoo, Hyunseung, & Stevens, Rick. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. United States. https://doi.org/10.1093/nar/gkz943
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Davis, James J., Wattam, Alice R., Aziz, Ramy K., Brettin, Thomas, Butler, Ralph, Butler, Rory M., Chlenski, Philippe, Conrad, Neal, Dickerman, Allan, Dietrich, Emily M., Gabbard, Joseph L., Gerdes, Svetlana, Guard, Andrew, Kenyon, Ronald W., Machi, Dustin, Mao, Chunhong, Murphy-Olson, Dan, Nguyen, Marcus, Nordberg, Eric K., Olsen, Gary J., Olson, Robert D., Overbeek, Jamie C., Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Shukla, Maulik, Thomas, Chris, VanOeffelen, Margo, Vonstein, Veronika, Warren, Andrew S., Xia, Fangfang, Xie, Dawen, Yoo, Hyunseung, and Stevens, Rick. Thu . "The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities". United States. https://doi.org/10.1093/nar/gkz943. https://www.osti.gov/servlets/purl/1633068.
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@article{osti_1633068,
title = {The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities},
author = {Davis, James J. and Wattam, Alice R. and Aziz, Ramy K. and Brettin, Thomas and Butler, Ralph and Butler, Rory M. and Chlenski, Philippe and Conrad, Neal and Dickerman, Allan and Dietrich, Emily M. and Gabbard, Joseph L. and Gerdes, Svetlana and Guard, Andrew and Kenyon, Ronald W. and Machi, Dustin and Mao, Chunhong and Murphy-Olson, Dan and Nguyen, Marcus and Nordberg, Eric K. and Olsen, Gary J. and Olson, Robert D. and Overbeek, Jamie C. and Overbeek, Ross and Parrello, Bruce and Pusch, Gordon D. and Shukla, Maulik and Thomas, Chris and VanOeffelen, Margo and Vonstein, Veronika and Warren, Andrew S. and Xia, Fangfang and Xie, Dawen and Yoo, Hyunseung and Stevens, Rick},
abstractNote = {The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.},
doi = {10.1093/nar/gkz943},
journal = {Nucleic Acids Research},
number = D1,
volume = 48,
place = {United States},
year = {Thu Oct 31 00:00:00 EDT 2019},
month = {Thu Oct 31 00:00:00 EDT 2019}
}
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https://doi.org/10.1093/nar/gkz943
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