BV-BRC Workshop at the University of Virginia, April 25-27, 2023¶
Dear BV-BRC users, we have reached the limit for the maximum number of in-person participants for this workshop. The registration is now CLOSED. Please subscribe to the BV-BRC mailing list or follow us on social media to learn about upcoming workshops and webinars.
The BV-BRC (Bacterial and Viral Bioinformatics Resource Center) team will be offering a Bioinformatics Workshop on April 25-27, 2023, at the University of Virginia (UVA) in Charlottesville, VA. The workshop will be held at the UVA North Fork Discovery Park, approximately 10 miles north of UVA grounds. The workshop will show researchers how to analyze and explore antimicrobial resistance data using the BV-BRC website, which is a merger of the two long running bacterial and viral BRC resources, PATRIC and IRD/ViPR, respectively.
The workshop will consist of interactive hands-on training sessions. During the first two days, participants will learn how to search for public datasets of interest and perform genomic, comparative genomic, metagenomic, and transcriptomic analysis using various analysis services and tools at BV-BRC. The third day of the workshop will focus on using command-line interface for programmatic search and retrieval of the data and job submissions, as well as users working with their own data and analysis problems with the help from the BV-BRC team members.
To register for the workshop, send an email to firstname.lastname@example.org. Registration is limited to 50 people, and will be accepted based on the order the emails are received. You should receive a confirmation email within 2 business days. If you don’t receive one, you can also reach us at email@example.com. BV-BRC workshops tend to fill up very quickly, so please register soon if you would like to attend.
The workshop is free to attend, but participants must arrange and pay for their own travel, meals, and lodging. Light refreshments will be available. There is also a small coffee and snack bar in the building and a cafe and grill in the adjacent building.
Note: The following COVID-19 safety precautions are currently in place at the University of Virginia.
Wearing face masks is optional on UVA properties including the Biocomplexity Institute.
Full information can be found in UVA Policy SEC-045: COVID-19 Health & Safety Requirements.
There is plenty of free parking adjacent to the Biocomplexity Institute.
The Charlottesville Albemarle Airport is conveniently located 2 miles south of the Biocomplexity Institute. There are several hotels and dining options nearby.
Day 1 - Tuesday, April 25
9:00 am Information, registration, and overview * Welcome * BV-BRC registration * Overview (www.bv-brc.org) * Creating Genome Groups 10:15 am Taxonomic Classification Service * Description of Kraken2 * Uploading reads or contigs and submitting job * Saving classified or unclassified sequences * Viewing and interpreting the results 10:45 am Metagenomic Read Mapping Service * Description of CARD and VFDB * Uploading reads and submitting job * Viewing and interpreting the results 11:00 am Break 11:15 am FASTQ Utilities Service * Description of FASTQ files and service * Selecting pipeline (Trim, FastQC, Paired read, Align) * Uploading reads and submitting job * Viewing and interpreting results 12:00 pm Lunch 1:00 pm Metagenomic Binning Service * Description of algorithm * Uploading reads or contigs and submitting the job * Viewing and interpreting the results 1:00 pm Comprehensive Genome Analysis Service * Description of assembly and annotation algorithms * Uploading reads or contigs and submitting job * Viewing and interpreting results 3:15 pm Break 3:30 pm Similar Genome Finder Service * Description of MASH/MinHash * Uploading genome sequences, reads or contigs * Submitting job * Viewing and interpreting results 3:45 pm Phylogenetic Tree Building Service * Creating a genome group * Determining if selected genomes are â€œtreeableâ€ * Description of algorithm and submitting tree-building job * Viewing and interpreting results * Newick file download 4:45 pm Question and Answer Session and Hands on Work 5:00 pm Day 1 Adjourn
Day 2 - Wednesday, April 26
9:00 am Review of Day 1 9:15 am BLAST * Description of BLAST * Choosing BLAST database, parameters, and job submission * Viewing and interpreting the results 10:00 am Comparative Services (Protein Families, Pathways and Subsystems) * Description of protein families and job submission * Finding the pan, core, and accessory genomes * Visualizing and manipulating the heatmap viewer * Finding specific differences, downloading, and saving results into private workspace * Comparing pathways on pathway map and heatmap * Finding specific differences, downloading, and saving results into private workspace * Description of Subsystems * Exploring subsystems using the tabular and heatmap views * Finding specific differences, downloading, and saving results 11:00 am Break 11:15 am Proteome Comparison * Feature Overview * Description of calculations for gene neighborhoods * Adjusting the view * Seeing data of interest (genome and feature groups) 11:45 am Lunch 1:00 am Compare Region Viewer * Genome selection and job selection * Comparing pathways on pathway map and heatmap * Finding specific differences, downloading, and saving results into private workspace 1:30 pm SNP and MSA Variation Service * Description of SNP callers and aligners * Uploading reads * Discussion and selection of target genomes * Viewing and interpreting the results 2:00 pm Gene Tree * Description of algorithm * Selection of data and job submission * Viewing and interpreting the results 2:45 pm Break 3:00 pm Primer Design * Description of algorithm * Adjusting parameters and job submission * Viewing and interpreting the results 3:15 pm RNA-Seq Pipeline * Discussion of algorithm and choosing a strategy * Uploading RNA-seq data * Selecting genomes and job submission * Viewing and interpreting the results 4:15 pm Install Command line interface * Installing the Command Line Interface 4:15 pm Question and Answer Session and Hands on Work 5:00 pm Day 2 Adjourn
Day 3 - Thursday, April 27
9:00 am Variation Service * Uploading reads data * Description of aligners * Description of SNP callers * Discussion and selection of target genomes * Downloading and using the data in BV-BRC * Interpreting results 10:00 am Command Line Interface * Logging in * Searching for data * Creating groups from data selections * Downloading data 11:00 am Break 11:15 am Job submission via command line * Uploading private data (singular or batch) * Submitting assembly jobs (singular or batch) * Submitting annotation jobs (singular or batch) * Discussion of command line submission to other services 12:30 pm Lunch 1:30 pm Final demon on Job Submission via command line 2:15 pm Genome Alignment Service * Description of MAUVE * Selection of genomes and job submission * Viewing the results 2:30 pm Break 2:45 pm Working on specific use cases and participant data 4:00 pm Final questions 5:00 pm Workshop concludes