Blog

PATRIC Workshop at GLBIO 2017 in Chicago, May 17, 2017

by patricwpadmin

PATRIC will be hosting a 1/2-day workshop entitled “Assemble, Annotate and Analyze Your Own Genome using PATRIC, the All Bacterial Bioinformatics Resource Center,” at the Great Lakes Bioinformatics (GLBIO) Conference at the University of Illinois at Chicago on May 17, 2017 in Chicago, Illinois.  The workshop will cover PATRIC’s analysis pipelines, which include genome assembly […]

PATRIC/RAST Tutorial Workshop December 12-14, 2016

by patricwpadmin

The PATRIC/RAST teams will be offering a tutorial on December 12-14, 2016 at Argonne National Laboratory in the suburbs of Chicago, IL. The workshop will run for three days with the third day optional and devoted solely to participants working on their own problems with help from the PATRIC/RAST team members. The tutorial will show […]

PATRIC / RAST Tutorial Workshop Agenda

by patricwpadmin

Dates: July 26 – 28, 2016 Location: Argonne National Laboratory, Argonne, IL Agenda: Tuesday, July 26 9am                PATRIC Introduction and registration 10am              Genome Assembly 11am              Genome Annotation and exploration 12pm              Lunch 1pm                SNP pipeline 2pm                Proteome Comparison 3pm                Questions and adjournment Wednesday, July 27 9am                Comparative Genomics 12pm              Lunch 1pm                RNA-Seq 2pm                Upload […]

Omics4TB TFOE Expression Experiments

by patricwpadmin

Mycobacterium tuberculosis senses and responds to the shifting and hostile landscape of the host. To characterize the underlying intertwined gene regulatory network governed by approximately 200 transcription factors of M. tuberculosis, we have assayed the global transcriptional consequences of overexpressing each transcription factor from an inducible promoter. We cloned and overexpressed 206 transcription factors in […]

GUNK Experiment 1

by patricwpadmin

Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii Publication: PMC4438207 Acinetobacter baumannii is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen’s success has been limited by the resources available for genome-scale experimental studies. This report describes the development […]

FLUTE Experiment 2

by patricwpadmin

Peptidoglycan synthesis in Mycobacterium tuberculosis is organized into networks with varying drug susceptibility Publication: PMCID: PMC4620856 Peptidoglycan (PG), a complex polymer composed of saccharide chains crosslinked by short peptides, is a critical component of the bacterial cell wall. PG synthesis has been extensively studied in model organisms but remains poorly understood in mycobacteria, a genus that […]

PATRIC Workshop – Chicago

by patricwpadmin

Tutorial workflows for the workshop: Chicago PATRIC Flyer – Dec. 2015 (1) Creating Genome Groups Exploring your annotated genome in PATRIC Fastq download from ENA Genome Annotation in PATRIC Genome Group Assignment Protein Family Analysis- Protein Family Sorter Protein Family Analysis- Proteome Comparison Protein Family Analysis-Comparative Pathway Viewer Submitting an assembly job to PATRIC Transcriptomics […]

PATRIC Workshop – San Diego State University

by patricwpadmin

AGENDA Monday, July 20, 2015 9:30am            Register for PATRIC Account 10:00am          Overview of PATRIC (www.patricbrc.org) – Tom Brettin 10:30am          Assemble a Genome in PATRIC – Bob Olson Uploading reads and read libraries Selecting assembly methods for comparison Queuing jobs and retrieving results Analyzing assembly output and comparisons http://enews.patricbrc.org/wp-content/uploads/2015/06/Genome-assembly-Workshop.pdf 11:00am          Break 11:15am          Annotate a Genome in PATRIC […]

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Assemble and Annotate Your Genome Sequences

by patricwpadmin

PATRIC now provides genome assembly and annotation services. Users can bring their sequence reads, upload them into the private workspace, assembly and annotate them, and download the fully annotated genome.