title: Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.
abstract: The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by 'virtual integration' to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.
authors.affiliation: Biocomplexity Institute, Virginia Tech University, Blacksburg, VA 24060, USA rwattam@vbi.vt.edu.
authors.forename: Alice R
authors.initials: AR
authors.lastname: Wattam
authors.affiliation: Computation Institute, University of Chicago, Chicago, IL 60637, USA.|Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: James J
authors.initials: JJ
authors.lastname: Davis
authors.affiliation: Department of Computer Science, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Rida
authors.initials: R
authors.lastname: Assaf
authors.affiliation: Gydle Inc. 101-1332 Chanoine Morel Quebec, QC G1S, 4B4, Canada.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Boisvert
authors.affiliation: Computation Institute, University of Chicago, Chicago, IL 60637, USA.|Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Brettin
authors.affiliation: Department of Computer Science, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Bun
authors.affiliation: Computation Institute, University of Chicago, Chicago, IL 60637, USA.|Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA.
authors.forename: Neal
authors.initials: N
authors.lastname: Conrad
authors.affiliation: Computation Institute, University of Chicago, Chicago, IL 60637, USA.|Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Emily M
authors.initials: EM
authors.lastname: Dietrich
authors.affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA.
authors.forename: Terry
authors.initials: T
authors.lastname: Disz
authors.affiliation: Grado Department of Industrial & Systems Engineering, Virginia Tech, Blacksburg, VA 24060, USA.
authors.forename: Joseph L
authors.initials: JL
authors.lastname: Gabbard
authors.affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA.
authors.forename: Svetlana
authors.initials: S
authors.lastname: Gerdes
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Henry
authors.affiliation: Biocomplexity Institute, Virginia Tech University, Blacksburg, VA 24060, USA.
authors.forename: Ronald W
authors.initials: RW
authors.lastname: Kenyon
authors.affiliation: Biocomplexity Institute, Virginia Tech University, Blacksburg, VA 24060, USA.
authors.forename: Dustin
authors.initials: D
authors.lastname: Machi
authors.affiliation: Biocomplexity Institute, Virginia Tech University, Blacksburg, VA 24060, USA.
authors.forename: Chunhong
authors.initials: C
authors.lastname: Mao
authors.affiliation: Biocomplexity Institute, Virginia Tech University, Blacksburg, VA 24060, USA.
authors.forename: Eric K
authors.initials: EK
authors.lastname: Nordberg
authors.affiliation: Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Olsen
authors.affiliation: Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Murphy-Olson
authors.affiliation: Computation Institute, University of Chicago, Chicago, IL 60637, USA.|Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Olson
authors.affiliation: Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.|Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA.
authors.forename: Ross
authors.initials: R
authors.lastname: Overbeek
authors.affiliation: Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.|Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA.
authors.forename: Bruce
authors.initials: B
authors.lastname: Parrello
authors.affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA.
authors.forename: Gordon D
authors.initials: GD
authors.lastname: Pusch
authors.affiliation: Computation Institute, University of Chicago, Chicago, IL 60637, USA.|Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Maulik
authors.initials: M
authors.lastname: Shukla
authors.affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA.
authors.forename: Veronika
authors.initials: V
authors.lastname: Vonstein
authors.affiliation: Biocomplexity Institute, Virginia Tech University, Blacksburg, VA 24060, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Warren
authors.affiliation: Computation Institute, University of Chicago, Chicago, IL 60637, USA.|Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA.
authors.forename: Fangfang
authors.initials: F
authors.lastname: Xia
authors.affiliation: Computation Institute, University of Chicago, Chicago, IL 60637, USA.|Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Hyunseung
authors.initials: H
authors.lastname: Yoo
authors.affiliation: Computation Institute, University of Chicago, Chicago, IL 60637, USA.|Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA.|Department of Computer Science, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Rick L
authors.initials: RL
authors.lastname: Stevens
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001419:Bacteria / Q000187:drug effects / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D024881:Drug Resistance, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation; D020543:Proteome; D040901:Proteomics / Q000379:methods; D012984:Software; D064878:Web Browser
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D020543:Proteome