American Society for Microbiology

Description

10 a.m.–3 p.m. (includes a 1-hour break)
Get hands-on experience with NCBI pathogen detection and SARS-CoV-2 surveillance data in the cloud. No prior cloud experience necessary.

Summary

• Cloud computing allows researchers to flexibly use scalable computing for data exploration and analysis and provides a platform that can support FAIR (findable, accessible, interoperable and repeatable) data practices. As part of the NIH’s Science and Technology Research Infrastructure for Discovery, Experimentation and Sustainability (STRIDES) Initiative, NCBI has made sequence, metadata and analysis results available in the cloud for select high-value projects.

Workshop Objectives

• Learn about available NCBI Pathogen Detection and SARS-CoV-2 Surveillance data on the Google Cloud Platform (GCP). Cloud access will be provided to attendees.
• Gain practical experience using the GCP Console and BigQuery.
• Employ methods to search, retrieve and investigate metadata and sequence data and integrate these into your research.
• Explore SARS-CoV-2 genetic variation and sample metadata and find related sequence data.
• Learn to use the Pathogen Detection MicroBIGG-E Browser to investigate isolate metadata, genetic and genomic elements (including antimicrobial resistance genes) and find related sequence data.

Target Audience

• Genomic biologists and bioinformaticians who want to learn more about NCBI cloud-based tools and datasets.

Prerequisites

• A laptop with Wi-Fi access. 
• Familiarity with command-line. 

For queries or questions, please send an email to suggest@ncbi.nlm.nih.gov.

Description

3:15-4:45 p.m. 
Hackathon: Less Dependency Tracking and More Science Using Bioconda.

Registration

• This session is open to all conference attendees. 

Summary

• Bioconda is a valuable resource that allows the bioinformatics community to do more science and less debugging installs. Additionally, every tool in Bioconda has a Docker container made available from Biocontainers and a Singularity image from the Galaxy Project. 
• In this session, the hackathon leader will introduce attendees to Bioconda, its many services to the bioinformatics community and details on contributing to Bioconda, including submitting new recipes or reviewing changes. Attendees can expect to leave this session with a better understanding of how they can use Bioconda for their bioinformatic needs and how to make significant contributions to the bioinformatics community.
• The actual hackathon will be held virtually in fall 2022.

Leader

• ​Robert Petit, Ph.D., Senior Bioinformatics Scientist, Wyoming Public Health Laboratory

10 a.m.–3 p.m. 
NCBI Microbial Pathogen and SARS-CoV-2 Resources in the Cloud (Sold Out)

3:15-4:45 p.m. 
Hackathon Introductory and Planning Session: Less Dependency Tracking and More Science Using Bioconda

Leader

• ​Robert Petit, Ph.D., Senior Bioinformatics Scientist, Wyoming Public Health Laboratory

5–7 p.m.
Opening Session: COVID Origins and Reconstructing the Phylogeny of Those Early SARS-CoV-2 Lineages

Speakers

• Michael Worobey, Ph.D., Professor and Department Head of Ecology and Evolutionary Biology, University of Arizona.
• Jonathan Pekar, M.S., Ph.D. candidate, Department of Biomedical Informatics, University of California San Diego.

The Needle and The Haystack: Sequencing for Pandemic Preparedness and Global Health Equity

• Nahid Bhadelia, M.D., MALD, Senior Policy Advisor on Global COVID-19 Response, White House COVID-19 Response Team.

7–8:30 p.m.
Opening Reception

8:30 a.m.–12 p.m.
Scientific Session 1: Epidemiological Cues: NGS in Clinical and Public Health Microbiology

     8:30–9 a.m.
     Invited Speaker: Daria Van Tyn

     9–10 a.m.
     Epidemiological Cues Oral Abstract Presentations

     10–10:30 a.m.
     Morning Break                   

     12–1:30 p.m. (Lunch will be provided from 12–12:45 p.m.)
     Lunch & Learn: Evaluation of the bioMérieux EPISEQ Software for wgMLST-based Bacterial Strain Typing

     Speaker: Suzane Silbert, Ph.D., Director, Escoteric Testing/R&D and Microbiology Laboratories, Tampa General Hospital
1:30–5 p.m. 
Scientific Session 2: Bridging Silos: Exploring mechanisms for collecting and sharing microbial genomic data to foster interoperability

     1:30–2 p.m. 
     Invited Speaker: Emiley Eloe-Fadrosh 
     
     2–3 p.m. 
     Bridging Silos Oral Abstract Presentations

     3–3:30 p.m.
     Afternoon Break

     3:30-5 p.m.
     NCBI-NLM-NIH Joint Panel Discussion: An Institute at the Center of the Next Generation Sequencing Revolution

     Speakers

• William Klimke—Pathogen Detection: More Than One Million Genomes—Where Do We Go From Here?
• Ken Katz—SRA NGS Submission, Analysis, and Removing Unintended Human Contamination.
• J. Rodney Brister –​ SARS-CoV-2 Resources and Analyses, at NCBI Virus and in the Cloud.

5–7 p.m.
     Poster Session #1 - Poster Board Number Index
     Poster Session #1 Abstracts

8:30 a.m.–12 p.m.
Scientific Session 3: Secret Ingredient: NGS to Uncover the Role of Microbes in Agricultural and Food Systems

     8:30–9 a.m.
     Invited Speaker: Lawrence Goodridge

     9 a.m.–10 a.m.
     Secret Ingredient Oral Abstract Presentations

     10–10:30 a.m.
     Morning Break                   

     12–1:30 p.m.
     Lunch

1:30–5 p.m. 
Scientific Session 4: Microbial Chatter: Microbial Ecology in Health and Disease

     1:30–2 p.m. 
     Invited Speaker: Jamie Morton

     2–3 p.m. 
     Microbial Chatter Oral Abstract Presentations

     3–3:30 p.m.
     Afternoon Break

     4–5 p.m.
     Microbial Chatter-Wastewater Symposium
     Wastewater Symposium Abstract Oral Presentations 

5–7 p.m.
     Poster Session #2 - Poster Board Number Index
     Poster Session #2 Abstracts

8:30–12 p.m. 
Scientific Session 5: Pipe Dreams: Analytical Methods, Bioinformatic Tools and Pipelines

     8:30–9 a.m. 
     Invited Speaker: Yatish Turakia

     9–10 a.m. 
     Pipe Dreams Lightning Talk Presentations
     Pipe Dreams Oral Abstract Presentations

     10–10:30 a.m.
     Morning Break 

     10:30 a.m.–12 p.m.
     Scientific Session 5 continues

End of meeting