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The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Opportunities for SEA-PHAGES Faculty Members

This page describes opporunities for current SEA-PHAGES faculty members to get more deeply involved with the program. We need faculty members who can advocate for the program, help train new faculty members, assist with QC of genomes and annotations, host meetings, and more. Some of the opportunities below are open to all SEA-PHAGES faculty, and some have specific requirements. Read on for more information!

Phage Discovery Workshop Facilitator

Facilitators 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. All SEA faculty who have taught the Phage Discovery semester at their institution in the prior year may apply. If you are enthusiastic about helping train the next cohort of SEA faculty, we would love for you to be a facilitator.

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 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 (UMBC) 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 cover the costs of travel and lodging throughout the meeting, and provide an honorarium of $1,000.
 

Join the Team

The SEA Team will put out a call for facilitators between December – February, 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 (SEA Program Officer) at SEA@hhmi.org.

Phage Discovery Workshop Course Director

The role of the Course Director is to lead the delivery of the Phage Discovery Workshop, which prepares a new cohort of SEA-PHAGES faculty to implement the Phage Discovery component of the course. The Course Director appointment is for a full year, with roles and responsibilities for this period described in detail below. The Course Director will report to the HHMI UGP Senior Director, and work closely with the SEA Program Officer. Course Directors will have served as a Phage Discovery Workshop Facilitator at least once in the 3 years prior to serving as a Course Director.

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.

Description of Role and Responsibilities

The role of the Course Director is to lead the delivery of the Phage Discovery Workshop. The Course Director appointment is for a full-year, with roles and responsibilities for this period described in detail below. The Course Director will report to the HHMI UGP Senior Director, and work closely with the SEA Program Officer.

Pre-workshop Functions (October – May; Performed Remotely)

October

  • Discuss logistics of appointment: travel, accommodations, and compensation.
  • Finalize and accept appointment

January – May

  • Update workshop goals and schedule
  • Lead 3 virtual meetings with facilitators to establish expectations, coordinate assignments, and communicate the schedule for each workshop

During workshops (June & July; Performed On-site @ UMBC)

June & July

  • Commit to being on-site (UMBC) for June and July, and residing in the nearby area.
  • Attend annual SEA Symposium (June), and welcome new cohort of SEA faculty.
  • Stay on-site (UMBC) throughout each workshop.
  • Assist with pre-workshop preparation.
  • Host facilitators on-site 2 days prior to each workshop, overseeing facilitator preparation of presentations and assignments.
  • Lead overall delivery of workshops.
  • Establish leadership role for participants. This includes setting expectations for completing assignments, timeliness, and appropriate interactions with facilitators.
  • Establish leadership role for facilitators, including oversee facilitator presentation and responsibilities, and meeting with facilitators, daily, to plan/modify workshop delivery.
  • Participate in cohort-building activities with participants.
  • Meet to debrief with facilitators, SEA program staff, and Senior Director.

Eligibility

Course Directors will have served as a Phage Discovery Workshop Facilitator at least once in the 3 years prior to serving as a Course Director. See how to become a facilitator at the Phage Discovery Workshop Facilitator portion of this page.

Bioinformatics Workshop Facilitator

A Bioinformatics Workshop Facilitator attends the December Bioinformatics Workshop and assists in the training of new SEA-PHAGES faculty members in annotating phage genomes and using comparative genomics tools. This opportunity is available only to members of SMART, the annotation QC team.

Overview

The 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 Bioinformatics 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 Bioinformatics Workshop, in partnership with the SEA program staff. Bioinformatics 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

Bioinformatics Facilitator eligibility is limited to faculty members who serve on the SEA-PHAGES Annotation RevIew Team (SMART*). 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.

Host a Regional Meeting

With over 100 active SEA-PHAGES institutions in the US, many SEA schools have begun coming together with others in their region to host and attend local SEA-PHAGES symposia. These meetings offer many benefits, including more opportunities for students and faculty to network, collaborate, and present their research. If you're interested in hosting a regional SEA-PHAGES meeting, HHMI can help you get one together.

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.

Host a Faculty Hack-a-Thon

Hack-A-Thons are one-day meetings where SEA faculty brush up on annotation skills before teaching the spring Bioinformatics course. A Hack-a-Thon host works with SEA staff to identify dates and times, create a Forum page, set an agenda, identify/adopt a phage, and lead the meeting itself. Hack-a-Thons take place from October through December, and are typically held virtually, though we also welcome in-person meetings. Hosts of virtual Hack-a-Thons must be Expedited Submitters, whereas in-person meetings can be hosted by anyone but must include at least one Expedited Submitter as a co-host.

Overview

Hack-A-Thons are one-day meetings where SEA faculty meet to brush up on annotation skills before teaching the spring Bioinformatics course. These meetings take place from October through December, and are typically held virtually, though we also welcome in-person meetings. Virtual Hack-A-Thons are hosted by Expedited Submitters, whereas in-person meetings can be hosted by other SEA-PHAGES faculty but must include at least one Expedited Submitter as a co-host.

HHMI Support

HHMI will provide each host $500 to run a Hack-A-Thon, and up to a total of $1,000 to host more than one Hack-A-Thon.
Note: If multiple Expedited Submitters jointly facilitate a meeting, HHMI will provide up to $1,000, to be distributed evenly to all facilitators for a given meeting.
HHMI will also reimburse, up to $500, the cost of an in-person meeting.

Steps for Hosting a Hack-A-Thon

Please note that SEA Staff will support you in this process.

Identify an Expedited Submitter Co-Host

Contact an Expedited Submitter. If you are already an Expedited Submitter, and you are comfortable hosting a hack-a-thon solo, we are delighted to have you do so.

Identify Dates and Times

Identify several dates from October through the end of December that work best for you and the Expedited Submitter to host a meeting. Email these dates to SEA staff at info@seaphages.org. SEA staff will then compile a list of Hack-A-Thons such that they all fall on different days. We will then confirm those dates with the hosts before posting it on seaphages.org for faculty to sign-up.

Note: We will send out a request for these dates. We put together a master list of all Hack-A-Thons early in the fall, so please respond promptly.

Finalize Dates and Times

Once a list of Hack-A-Thons have been posted online, SEA faculty that wish to attend a Hack-A-Thon will be asked to identify three hack-a-thon dates that fit their schedules. SEA staff will then make the final participant assignments based on interest, annotation ability, and geographic location, such that the hack-athons have approximately equal groups of attendees. Based on faculty sign-up, some hack-a-thons may be consolidated, canceled, or rescheduled due to participant availability and interest. SEA staff will confirm these dates with the hosts.

Hack-A-Thon Forum

Once a Hack-A-Thon participant list has been confirmed, a Forum will be created for each Hack-A-Thon, and will include the meeting dates and time, participant lists, and how to attend (for virtual meetings). Hosts and participants can then begin communicating and planning for the meeting together. Here is a link to the 2018 Hack-a-thon forums for examples.

Other Considerations

Agenda: The goal of a Hack-A-Thon is to help faculty get ready for the spring Bioinformatics semester. Your participants are likely to have a wide range of abilities, some may be ready for Expedited Submission while others may not know how to access their institution page on seaphages.org. So while your project is phage annotation, remember to include a review of the basics like the location and use of the Online Bioinformatics Guide, finding important information on phagesdb.org, using online Phamerator, final file formatting, and annotation submission.

Identify/Adopt a Phage: If you plan to annotate an entire phage, identify a phage or phages to work with. Past hack-a-thon hosts have selected phages isolated from their own institutions, from participant institutions, and/or adopted phages from the Genome Exchange. It is possible to work on multiple phages at one Hack-A-Thon, in fact, using related phages is a great way to illustrate some of the comparative tools we use.

Skills: If your Hack-a-thon will focus on annotation skills, identify those skills and what your goals will be, and identify phage(s) that will help you meet those goals.

Assessment: After the Hack-A-Thon, send us an email to let us know how it went! Did all the participants attend? What topics did you cover? What do most faculty still struggle with? Do you have any ideas about how to improve the format?

Become an Expedited Submitter

Expedited Submitters are SEA faculty members whose genome annotations have consistently demonstrated very high quality work, and who can therefore bypass the typical annotation QC process and proceed more directly to GenBank. Expedited submitters have more leeway regarding annotation deadlines, generate a different set of submission files, and are eligible for other faculty opportunities.

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.

Become a SMART Member

SMART is a team of experienced SEA-PHAGES staff and faculty members that is responsible for reviewing annotations produced by SEA-PHAGES schools to ensure high-quality data makes its way into GenBank. SMART—the SEA-PHAGES Actinobacteriophage Annotation Review Team—members review annotations each summer and are provided an honorarium for their work. Expedited Submitters are eligible to apply to become SMART members.

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.

Become a SEA Ambassador

A SEA Ambassador is a SEA faculty member that collaborates with SEA staff to disseminate information about the SEA-PHAGES program. Any active faculty member with at least a year of SEA-PHAGES experience can serve as a SEA Ambassador. If you are interested in being called upon when such opportunities arise, please contact us.

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.