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

The SEA-PHAGES Program

SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester, discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses, but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses.

The program aims to increase undergraduate interest and retention in the biological sciences through immediate immersion in authentic, valuable, yet accessible research. By finding and naming their own bacteriophages, students develop a sense of project ownership and have a ready-made personal research project at a fraction of the cost of traditional apprentice-based research programs. Some of the positive effects of the SEA-PHAGES program have been reported here.

SEA-PHAGES is jointly administered by Graham Hatfull's group at the University of Pittsburgh and the Howard Hughes Medical Institute's Science Education division.

SEA-PHAGES IN THE NEWS

Regional Symposia

We're delighted that more and more SEA institutions are coming together to host regional SEA symposia. In 2016-2017, 5 regional symposia were held, attended by students and faculty from 17 SEA institutions. Regional symposia offer many benefits, including more opportunities for students and faculty to network, collaborate, and present their research. HHMI is pleased to offer moderate contribution to help offset the costs of hosting these meetings.

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 hosting and/or participating in a regional symposium. A list of SEA institutions, sortable by location, is available at www.seaphages.org/institutions. The hosting institution should determine the number of participants that can be accommodated for the meeting, reserving 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.
  • Collaboration: Early symposium planning provides opportunities for regional schools to collaborate. For examples, participating schools may choose to work of different Actinobacterial hosts followed by a collaborative host-range project, or working collaboratively on a common Actinobacterial host and varying isolation strategies.
  • Costs: Meeting costs include travel expenses, poster printing, meals, and keynote honorarium.

Request for HHMI support

To request for moderate financial support from HHMI to offset some of the costs associated with a regional symposium, email SEA@hhmi.org with a brief Letter of Intent that includes:

  • the list of participating institutions and anticipated number of attendees
  • a draft agenda
  • a draft budget

Once a meeting date has been set, and an agenda finalzed, we will be happy to post this information on seaphages.org to promote your meeting.

2018 Membership and Responsibilities

Dear SEA-PHAGES Faculty,

We’re looking forward to the coming academic year, and its culmination in what will be the 10th Annual SEA-PHAGES Symposium at Janelia Research Campus on June 8-10, 2018. We are pleased that the program continues to be adopted by a variety of different institutions. This fall, seventeen new schools joined up as Cohort 10 of SEA-PHAGES, and applications for Cohort 11 are due in October.

The continued growth of the SEA is extremely gratifying, but we’ve now exceeded the capacity of Janelia Research Campus, which is the site of the annual Symposium. Because of this space limitation, we wanted to remind everyone that, in the future, we will need to limit the number of invitation slots per school for the Symposium, and some schools are likely to receive more slots than others. While we are still in the early planning and decision-making phase, there are some criteria which will likely help determine which schools are in good standing and merit the maximum number of invitation slots. Thus, before the academic year begins, we’re sharing these criteria.

Scientific Focus

  1. The scientific focus of the SEA-PHAGES program has been defined for several years as “Investigating the diversity and evolution of phages that infect Actinobacterial hosts.” Moving forward, only abstracts relevant to this topic will be accepted. Institutions and faculty with students that have been working on phages of different host bacteria who wish to attend the SEA Symposium should also adopt an Actinobacterial host.
  2. As we explore the biodiversity of bacteriophages by expanding systematically from mycobacteriophages to actinobacteriophages, we would like to encourage everyone to work with Actinobacterial hosts other than—or in addition to—M. smegmatis.

Science Education Focus

  1. The program was designed to provide an opportunity for large numbers of undergraduates to engage in research early in their academic tenure. We therefore encourage faculty and institutions to offer the SEA-PHAGES program in a manner that maximizes student numbers (primarily freshmen) in the course—for example, by substituting the traditional Introduction to Biology Lab series with SEA-PHAGES.
  2. Participation in the PITS survey allows us to measure the impact of SEA-PHAGES compared to traditional courses or other CREs, and provides defensible evidence for the value of this course. PITS can also be a formative assessment tool for valuable faculty feedback. We encourage everyone to participate in the PITS survey.

Program Deadlines

  1. The timely archiving of phage lysates is an essential scientific responsibility for SEA-PHAGES members. Archive samples are to be sent each calendar year (not each semester) and received by December 15. Be sure the lysates match complete entries in PhagesDB. Previous years’ samples are due immediately.
  2. Annotated genomes are reviewed for completeness by a team of SEA faculty before the genomes can be submitted to GenBank. In order for all genomes to be reviewed in a timely fashion, it is important that all sequenced genomes are annotated and submitted for quality control (QC) by May 15th, 2018. Previous years’ annotations are due immediately.
  3. Entering section information and faculty contact information allows us to track how the program is being implemented, as well as giving access to the PITS survey. Please keep all course section information up to date and accurate on seaphages.org in accordance with the deadlines.

Deadlines and more information can be found on the Faculty Information page. https://seaphages.org/faculty/information/

If you have any questions, please contact us at info@seaphages.org.

Thank you, The SEA-PHAGES Team

Annotation Forum Reorganization

An Inherent Problem with Annotation

With the constant influx of new software tools, new genomes, and new publications, the way we annotate genomes is always changing. We always know a bit more than we did last year, and often a lot more than we did 5 years ago.

This leads to an inherent problem, however, in that we only officially train SEA-PHAGES faculty once, and obviously Cohorts 1-8 were trained more than one year ago. In addition, the genome you worked on at the Bioinformatics Workshop may be nothing like the genome you're currently annotating, and you'll inevitably come across new and puzzling regions.

Before? No...After? No...During!

The question is, how can we share what we've learned with the whole SEA in a manner that helps you do the most up-to-date annotations possible? We can put out "What's New?" documents before you begin annotating, which we do, but these often only cover broad strokes rather than details. Or we can provide feedback after you've submitted your final annotation, which we also do, but these details can be easily forgotten over the summer before you tuck into your next genome, and may not apply if you have a different cluster phage anyway.

Therefore, to our mind, the best time to get feedback is while you're actively annotating your genomes. And while we love answering questions about the cool and interesting things you're finding, we'd like that answer to be shared with everyone who might be coming across something similar so we don't end up have to answer it many times over!

Which obviously brings us to the seaphages.org Annotation Forum, where we can give specific, real-time feedback in a manner that's visible to others who might have similar questions. Therefore, we strongly encourage you to use the forum for questions you've come across while annotating.

Reorganization of the Forum

Which brings me to the point: I've slightly rearranged the Annotation Forum and renamed/clarified/broken up some of the existing threads to try to make everything more transparent and useful. Within the main annotation forum, there are now specific sub-forums for questions about calling start sites, calling functions, getting the notes right, and more. Please go ahead and ask questions in any of these. Here are a few quick pointers...

  • Post specific titles to your questions, like "Large gap in a Cluster F1 phage" or "Write NKF or leave blank in minimal notes?" This will help others find answers more than titles like "Question about two genes".
  • On each thread, try to keep the discussion specific to that topic. So if someone asks a question about the difference between a hydrolase and an esterase, don't use that same thread to ask about the HHPred cutoff for a hydrolase. Instead, create a new topic.
  • The Annotation Forums are public, which means students can use them as well. And their PhagesDB logins will also work on seaphages.org.

Happy annotating!

Current Events

Virtual Site Visit with SEA Team

September 18, 2017 to October 31, 2017

Upcoming Events

Submit Fall Section Data to seaphages.org

September 29, 2017

Identify Bioinformatics Workshop Trainees

October 3, 2017

Receive Archival Materials from Program

November 1, 2017

Recent Events

Prepare & Test Reagents for Phage Discovery

July 17, 2017 to August 31, 2017

Receive Shipment of Biologicals from Program

July 17, 2017 to August 31, 2017