Overview

The Phage Discovery Workshop is designed to prepare a new cohort of SEA-PHAGES faculty to implement the Phage Discovery component of the course. The training includes

• an introduction to phage biology and the scientific goals of the program,
• an immersive, guided, and hands-on learning of the protocols and techniques for phage discovery,
• examples of best practices for preparation and instruction of the course, as well as
• detailing program and community-supported resources for course implementation.

As the first substantive introduction of new faculty to the program, the Phage Discovery workshop is also an opportunity to welcome faculty into the SEA community, and to familiarize faculty with the program, including program goals and deadlines, and faculty responsibilities.

If you teach the Phage Discovery component of the SEA-PHAGES course and are enthusiastic about helping train the next cohort of SEA faculty, we would love for you to be a facilitator.
 

Description of Role and Responsibilities

The role of facilitators is to support the delivery of the Phage Discovery Workshop, in partnership with the Course Director and SEA program staff. Ideally, the team of facilitators will include SEA faculty that represent the diversity of institution types in the program. The following are facilitator responsibilities prior to and during the workshops:

• Pre-workshop (Performed Remotely)
  January – May                   
  • Attend 1 - 3 virtual meetings to coordinate assignments and to provide feedback on workshop content
     
• During workshop (Performed On-site, at UMBC)
  9D/8N, either in June or July based on workshop schedule.
  • Arrive on-site 2 days prior to the workshop, to practice delivery of presentations and incorporate group feedback
  • Stay on-site throughout the workshop
  • Deliver assigned presentations, and lead assigned sessions
  • Participate in cohort-building activities with participants
  • Meet to debrief with facilitators and SEA program staff

Eligibility

All SEA faculty who have instructed the Phage Discovery semester at their institution in the year prior to applying to serve as a facilitator are eligible to apply.
 

Compensation

HHMI will provide an honorarium of $1,000.
 

Join the Team

The SEA Team will put out a call for facilitators between December – March, which will be sent by email to all SEA faculty. Interested parties will be asked to complete a brief application form, which can be viewed below. If you have any questions about the position or how to apply, please contact Vic Sivanathan at SEA@hhmi.org.

Overview

The Phage Genomics (Bioinformatics) Workshop is designed to prepare a new cohort of SEA-PHAGES faculty to implement the Bioinformatics component of the course. The training includes

• an introduction to phage biology and the scientific goals of the program,
• an immersive, guided, and hands-on learning of the protocols and techniques for bioinformatics,
• examples of best practices for preparation and instruction of the course, as well as
• detailing program and community-supported resources for course implementation.

As the second substantive introduction for new faculty to the program, the  workshop is also an opportunity to familiarize faculty with the SEA-PHAGES team, the SEA-PHAGES program—including program goals and deadlines—and faculty responsibilities.

Description of Role and Responsibilities

The role of facilitators is to support the delivery of the Phage Genomics (Bioinformatics) Workshop, in partnership with the SEA program staff. Facilitator responsibilities prior to and during the workshops:

Pre-workshop Functions (Performed Remotely)

November

• Attend virtual meetings to coordinate assignments and to provide feedback on workshop content

During workshops (Performed On-site, at HHMI)

5D/4N, in December based on the workshop schedule

• Arrive on-site by 2pm on the first day of the workshop
• Available to stay on-site (HHMI) throughout the entire workshop
• Deliver assigned presentations, and lead assigned sessions
• “Work the room”—this includes scaffolding the learning in the group setting and identifying and assisting faculty members that are struggling with material during large or group sessions
• Participate in cohort-building activities with participants
• Meet to debrief with facilitators and SEA program staff

Eligibility

Facilitator eligibility is limited to faculty members who serve on the SEA-PHAGES Annotation RevIew Team (SMART*) as well as those who are Expedited Sumitters. See how to become a member of SMART* at seaphages.org/faculty/information/

Compensation

HHMI will cover the costs of travel and lodging throughout the meeting, and provide an honorarium of $1,000.

To Apply

The SEA Team will put out a call for facilitators between September - December, which will be sent by email to all members of SMART*. Interested parties will be asked to complete a brief application form, which can be reviewed on the following page. If you have any questions about the position or how to apply, please contact Vic Sivanathan (SEA Program Officer) at SEA@hhmi.org.

Genome Announcement Reviewers
At present, the SEA team is seeking peer-reviewers of genome announcement:

Eligibility
All SEA faculty who have completed at least 2 years of instructing SEA research projects are eligible to apply. We are looking to establish a rotating team of ~5 reviewers to serve for a 2-year tenure. Each reviewer will commit to reviewing 10 genome announcements per calendar year. New reviewers will be provided guidance from the SEA team on how to review and provide feedback.
 

Recognition
In recognition of their contribution to the SEA community as a reviewer, HHMI will be reimburse each reviewer the cost of publishing one genome announcement (~$1,000) with their students for each year of service.

To Apply
Please complete the brief application form below. If you have any questions about the position or how to apply, please contact Vic Sivanathan at SEA@hhmi.org

Overview

More and more SEA schools are coming together to host regional SEA symposia. These meetings offer many benefits, including more opportunities for students and faculty to network, collaborate, and present their research.

HHMI Support

Typically, HHMI provides up to $1,000 to support a regional meeting. This amount, however, may be higher depending on the size of your meeting and the use of funds. Please contact Vic Sivanathan at sea@hhmi.org for additional information about the financial support.

When possible, the SEA Team would be delighted to join your meeting.

Considerations for Hosting

Below is a list of considerations and recommendations as you plan for your regional symposium.

• Participants: Identify SEA faculty from nearby SEA institutions that may be interested in co-hosting and/or participating in a regional symposium. Remember, especially for our colleagues out West, a regional meeting can be as small as 2 SEA institutions coming together. A list of SEA institutions, sortable by location, is available at seaphages.org. The hosting institution should determine the number of participants that can be accommodated for the meeting and reserve appropriate space for talks, posters, meals, and other planned activities.
• Date and Time: Begin planning early. Set a date for the meeting, taking into consideration when students will have gathered sufficient data to present or to work on collaboratively, as well as end of year events, including final exams, the Annual SEA Symposium, and the summer break. Start and end times for the symposium should accommodate travel time to and from the meeting.
• Agenda: Past regional meetings have included a keynote presentation by an invited speaker, talks by SEA faculty, talks and posters by individual and/or teams of students, poster sessions, and activities such as a Genome Annotation Hackathon. Poster sessions and breaks are great opportunities for students to interact and network. A list of previous regional meetings are listed on the SEA-PHAGES website.

To Apply

As you begin planning, please contact us (Vic Sivanathan & Billy Biederman) at sea@hhmi.org for additional information about the financial support, and to post your meeting on seaphages.org.

Overview & Benefits

As faculty members increase their understanding of phage biology and their annotation skills, the quality of their genome annotations increases as well—to the point that some no longer routinely have their annotations reviewed by SMART prior to GenBank submission. These “Expedited Submitters”—so called because their annotations bypass the review process—have distinguished themselves by consistently submitting high quality annotations that adhere to the formatting guidelines laid out in the Bioinformatics Guide.

Once a faculty member has been identified as an Expedited Submitter, that faculty member

• has additional leeway regarding annotation deadlines (as no one else will be reviewing the work, except upon request), as well as more control over when annotations are submitted to GenBank. Since their annotations will not be reviewed by SMART, Expedited Submitters also generate a different set of submission files, NOT including a complete “Notes” DNA Master file.

See notes on workflow below*.

• are eligible to serve on SMART, and SMART members/alumni are eligible to serve as Bioinformatics Workshop Facilitators. SMART members and Facilitators are provided honoraria by HHMI as compensation for their time.

*Workflow: All genome annotations finished by the SEA-PHAGES program are submitted to phagesdb.org (whether through SMART or through Expedited Submission) and subjected to a final, computer-based quality control process to ensure the integrity of the underlying genome sequence and the file formatting. Annotation files that pass this final test are submitted to GenBank en masse approximately once a week directly from the University of Pittsburgh.

Becoming an Expedited Submitter

Nomination

Expedited submitters may be identified and nominated by SMART members through review of multiple genome annotations, or self-nominated by following the guidelines in the “Review to Improve” section of the Bioinformatics Guide. See additional notes below.

In general, a faculty member must submit high quality annotations for phages from three different clusters prior to becoming an Expedited Submitter.

Training

Once identified, Expedited Submitters go through additional training in file formatting and use of quality control programs before they are officially added to the Expedited Submitter list with all of the privileges that entails.

Note: If you believe you are submitting high quality annotations and have not been contacted about Expedited Submitter status, follow the Review to Improve guidelines in the Bioinformatics Guide using your submitted annotation files (these should be your initial submissions, not files that were resubmitted after preliminary QC. Remember, Expedited Submitters no longer go through Preliminary QC, so if your files were returned during the intial screen you may not be ready yet). If your file comparisons show three or fewer changes were made between your files and the final versions, please contact welkin@pitt.edu to discuss becoming an Expedited Submitter.

Overview

In order to maintain the quality of annotations produced by SEA-PHAGES program, all actinobacteriophage genome annotations produced by SEA institutions undergo a review. The review team, known as the SEA-PHAGES Actinobacteriophage Annotation Review Team (SMART)*, is comprised of SEA faculty who are Expedited Submitters as well as SEA program staff.

Responsibilities

• Review at least ten genome annotations from May through September 1 from SEA institutions in addition to the genomes from their own institution. (Part-time arrangements can be made upon request.)
• Attend weekly virtual meetings during June/July/August and/or review minutes/video for meetings you missed.
• Post/Answer annotation queries on the SEA-PHAGES annotation forums.
• Identify faculty members who are ready to be Expedited Submitters.
• Provide feedback to faculty on annotation revisions when faculty ask specific questions.
• Attend a final summary meeting to identify best annotation practices, address new infrastructure needs, identify programmatically weak annotation areas.

Note: Additionally, SMART members may also serve as Bioinformatics Workshop Faciliators or host fall Hack-A-Thons.

Compensation

HHMI will provide an honorarium of up to $1,000 each year, depending on the number of annotations reviewed.

Eligibility

SEA faculty that are currently Expedited Submitters are eligible to apply. See how to become an Expedited Submitter here.

To Apply

Openings on SMART are based on the number of returning members and the number of new annotations due in the following year. A general call may be made to all Expedited Submitters in the Fall if current SMART membership will be unable to meet the demand. Please email welkin@pitt.edu for more information.

*Back in the day, we only had mycobacteriophage annotations to review, and so this acronym made more sense, with "Mycobacteriophage" replacing "Actinobacteriophage". But “SAART” looks silly and is hard to pronounce, so we stuck with the original.

Overview

From time to time, SEA faculty members have disseminated information about the SEA on behalf of, and in partnership with, HHMI. For example, HHMI has called upon a number of SEA faculty members to present about the SEA-PHAGES program at local and national meetings that are focussed on advancing undergraduate science education (e.g. NABT, ASM-CUE, ABLE, NC3ABI, Bio-Link).

If you would like to be called upon when such opportunities arise, please let us know by filling in the form below and sending it to SEA@hhmi.org. For more information, contact Vic Sivanathan (Program Officer) at SEA@hhmi.org.