5th ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines (#ASMNGS)
- Important Information
- Schedule & Presentations
- Code of Conduct
- Live Notes
- NCBI Preconference Workshop - TBD
- ASMNGS Hackathon
- About ASMNGS
Welcome to ASMNGS 2022! We are back with an in-person meeting this year.
As in years past, we're trying to make this conference as open, accessible, and user-friendly as possible in the interest of open science. This repo will store slides, posters, and notes from the conference from those participants who are up for sharing their material, and it will also serve as another mechanism to receive realtime feedback in the form of issues (check this out if you're unsure how to create an issue).
The conference website contains all sorts of useful information, and if you're tweeting, gramming, tiktoking, or whatever, please use the hashtag #ASMNGS. You can tag @ASMicrobiology too.
Hotel: Sheraton Inner Harbor Hotel, Baltimore MD
The ASMNGS abstract submisison window will be open between June 2nd -> July 20th, 2022.
- Abstract submission site: https://asm.org/Events/ASM-NGS/Home
- Early abstract submission deadline: June 23, 2022 at 12pm EST.
- Final abstract submission deadline: extended to July 28th at 12pm EST.
If you need to get in touch with the organizers at any time, you have multiple options. You can tweet at or email this year's meeting chairs – Ruth Timme (twitter | email) and Elodie Ghedin (twitter | email). You can also open a new issue in this repo, or you can contact the wonderful ASM Conferences team through the meeting website.
- Bridging Silos: Exploring mechanisms for collecting and sharing microbial genomic data to foster interoperability
ASM and the ASMNGS team is committed to providing an environment that encourages the free expression and exchange of scientific ideas and promotes equal opportunities and respectful treatment for all participants. All participants are expected to treat others with respect and consideration, follow venue rules, and alert ASM staff or security of any dangerous situations or anyone in distress.
ASM prohibits and will not tolerate any form of harassment or bullying at its events. Harassment is unwanted and unwelcome attention or other conduct that creates an environment where a reasonable person would feel unwelcome, intimidated, excluded, or abused. Harassment based on gender, race, religion, national origin, age, marital status, personal appearance, sexual orientation, gender identity or expression, family responsibilities, genetic information, disability, matriculation, political affiliation, and any other personal characteristic is strictly prohibited.
ASM will investigate all complaints of harassment, and investigations will be conducted in an unbiased manner. Violation of this code of conduct may result in the participant being asked to leave the event at which the incident occurred, without warning or refund; being barred from attending ASM events in the future; and, if relevant, being barred from or revocation of membership in the ASM. Event security and local police may be contacted in the event violators pose an imminent threat to others or are disrupting the event. If an ASM Staff member is found to be in violation, the ASM Headquarters Employment Policy (Prohibition against Sexual and Other Harassment and Discrimination) will be followed. Action regarding an ASM staff member may result in termination of employment.
This policy applies to all attendees, speakers, exhibitors, contractors, volunteers, and guests at ASM events. If a participant experiences or witnesses harassment, he/she should contact ASM staff (ASM staff are identifiable by their ASM Staff name badge) as soon as possible or contact security if they feel unsafe. All complaints will be responded to promptly and treated seriously and, to the extent possible, confidentially. Complaints that require broader investigation will be handled by ASM’s Ethics Committee. ASM expressly forbids any retaliation against individuals for reporting harassment.
In the event that an individual knowingly provides false information regarding a harassment situation, ASM may take similar disciplinary action.
If a participant experiences or witnesses harassment as described in ASM’s Events Code of Conduct, they should contact ASM staff (identifiable by ASM staff badge) to report the incident. If at any time a participant feels unsafe, they should contact meeting venue security immediately. If the participant is unsure that the incident was in violation of the ASM’s Events Code of Conduct, they may inquire first from an ASM staff member before filing a formal complaint.
The following information should be provided when reporting a harassment incident:
- Name and contact information of participant
- Name and contact information of any witnesses
- Identifying information (e.g. name, badge number, physical appearance) of the individual(s) who are accused of the harassment
- The specific action or behavior that was in violation of the ASM Events Code of Conduct
- The date and approximate time of the incident
- The location and circumstances surrounding the incident
ASM will accept and investigate all complaints of harassment and investigations will be conducted in an unbiased manner. All complaints will be responded to promptly and treated seriously and, to the extent possible, confidentially.
Thank you for helping to make this a welcoming, friendly space for all!
We will continue the tradition of collecting live notes during the meeting. Past meeting notes included below:
ASMNGS will once again be hosting a pre-meeting hackathon, this time with a focus on Bioconda. Bioconda allows members of the scientific community to easily start using thousands of bioinformatic tools. Additionally, every tool in Bioconda has a Docker container made available from Biocontainers and a Singularity image from the Galaxy Project. In this hackathon, participants will be introduced to the submission and review process for Bioconda recipes, with the goal of contributing new recipes, reviewing open pull requests, and/or fixing recipes that are failing CI tests.
ASMNGS began in 2015 (if you're feeling nostalgic, the program is available here), organized by Dag Harmsen (University of Muenster), Marc Allard (FDA), and Eric Brown (FDA). In 2017, the program committee was co-chaired by Dag and Jennifer Gardy (BCCDC), and also included Marc, Eric, and new committee members Elodie Ghedin (NYU), Paul Keim (TGen), Duncan MacCannell (CDC), Adam Phillippy (NHGRI). In order to both coincide with the GenomeTrakr annual meeting and to not conflict with ABPHM, the committee decided to move the meeting to even years beginning in 2018. Also in 2018, Ruth Timme (FDA) replaced Eric Brown on the organizing committee and the 2020 planning committee grew to include George Gthinji, Torsten Seemann, and Sofonias Tessema.
Keynote speakers were selected by soliciting ideas from the organizing committee, who then arrived at our top choices through an email discussion. Submitted abstracts were reviewed by the planning committee - ## were accepted, and ## were declined. Reasons for declining abstracts included a topic not consistent with the conference's scope, or inadequate/inappropriate/insufficient methods/results/conclusions. All accepted abstracts were reviewed by the organizing committee, and six committee members cast votes for that they felt merited oral presentation. Votes were tallied, and abstracts selected for oral presentation accordingly. We also looked for diversity in our presenters, to ensure that ASMNGS continues to represent the full breadth, brightness and potential of our field.
We are grateful to all of our corporate sponsors this year, and look forward to a great conference.
Ruth Timme - Chair, U.S. Food and Drug Administration, College Park, MD
Elodie Ghedin - Co-chair, National Institute of Allergy and Infectious Diseases, Bethesda, MD
Duncan MacCannell - Centers for Disease Control and Prevention, Atlanta, GA
George Gthinji - KEMRI/Wellcome Trust, Nairobi, Kenya
Torsten Seemann - University of Melbourne, Melbourne, Australia
Sofonias Tessema - Africa CDC, Addis Ababa, Ethiopia
Jasna Kovac - Penn State University, State College, PA
Julie Dunning Hotopp - IGS, University of Maryland, School of Medicine, Baltimore, MD
Todd Treangen - Rice University Houston, TX
Arjun Prasad - NCBI, Bethesda, MD