2017 | Alice R. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, Terry Disz, Joseph L. Gabbard, Svetlana Gerdes, Christopher S. Henry, Ronald W. Kenyon, Dustin Machi, Chunhao Mao, Eric K. Nordberg, Gary J. Olsen, Daniel E. Murphy-Olson, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Andrew Warren, Fangfang Xia, Hyunseung Yoo and Rick L. Stevens
PATRIC is an all-bacterial bioinformatics database and analysis resource center. Recent improvements include a redesigned web interface, new services, and enhanced data analysis capabilities. The redesigned interface allows researchers direct access to tools and data, with a focus on user-created genome groups. Researchers can now analyze their private data and compare it with public data, using RASTtk for genome assembly and annotation. PATRIC provides services for RNA-Seq, variation, model reconstruction, and differential expression analysis, all delivered through an updated private workspace. Private data can be compared with public data via 'virtual integration'. The number of available genomes has expanded to over 80,000, with a focus on genomes with antimicrobial resistance data. PATRIC uses this data to improve subsystem annotation and k-mer classification, and to tag new genomes with antibiotic susceptibility or resistance signatures.
The PATRIC website has been redesigned to enhance user experience, with data indexed using SOLR and interfaced with the PATRIC Data API. This allows for searching, displaying, filtering, and downloading of genomes, genomic features, and experiment data. New services include genome assembly, annotation, RNA-Seq analysis, proteome comparison, expression import, and variation analysis. These services are available through a private workspace, enabling users to compare private data with public data. The number of jobs processed by PATRIC has increased significantly, with over 20,000 jobs submitted in 2016.
PATRIC has also enhanced its data and annotation capabilities, including improved genome annotation using RASTtk, and the integration of specialized databases for antibiotic resistance, virulence factors, and drug targets. PATRIC maintains an updated set of protein families for comparative analysis, including the new PATtyFams algorithm. The PATRIC FTP site has been reorganized to provide easier access to genome annotations and AMR metadata. Future directions include enhancing clinical research support, increasing focus on modeling, and improving therapeutic research. PATRIC is funded by the National Institute of Allergy and Infectious Diseases.PATRIC is an all-bacterial bioinformatics database and analysis resource center. Recent improvements include a redesigned web interface, new services, and enhanced data analysis capabilities. The redesigned interface allows researchers direct access to tools and data, with a focus on user-created genome groups. Researchers can now analyze their private data and compare it with public data, using RASTtk for genome assembly and annotation. PATRIC provides services for RNA-Seq, variation, model reconstruction, and differential expression analysis, all delivered through an updated private workspace. Private data can be compared with public data via 'virtual integration'. The number of available genomes has expanded to over 80,000, with a focus on genomes with antimicrobial resistance data. PATRIC uses this data to improve subsystem annotation and k-mer classification, and to tag new genomes with antibiotic susceptibility or resistance signatures.
The PATRIC website has been redesigned to enhance user experience, with data indexed using SOLR and interfaced with the PATRIC Data API. This allows for searching, displaying, filtering, and downloading of genomes, genomic features, and experiment data. New services include genome assembly, annotation, RNA-Seq analysis, proteome comparison, expression import, and variation analysis. These services are available through a private workspace, enabling users to compare private data with public data. The number of jobs processed by PATRIC has increased significantly, with over 20,000 jobs submitted in 2016.
PATRIC has also enhanced its data and annotation capabilities, including improved genome annotation using RASTtk, and the integration of specialized databases for antibiotic resistance, virulence factors, and drug targets. PATRIC maintains an updated set of protein families for comparative analysis, including the new PATtyFams algorithm. The PATRIC FTP site has been reorganized to provide easier access to genome annotations and AMR metadata. Future directions include enhancing clinical research support, increasing focus on modeling, and improving therapeutic research. PATRIC is funded by the National Institute of Allergy and Infectious Diseases.