SEA-PHAGES Logo

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

SEA SYMPOSIUM FAQ

As we gear up for the upcoming symposium, below are some guidelines to help you and your students prepare. Included are guidelines for the following:

REGISTRATION

Who should register?

All SEA faculty, and all SEA student-researchers from this academic year (Fall 2020 and/or Spring 2021), are invited to register and attend to 2021 SEA symposium.

How do I register?

All SEA faculty members will have received instructions to register for the symposium by email on March 1, 2021. If you are a SEA faculty member and need these instructions, please contact us at info@seaphages.org. If you are a SEA student from the 2020 – 2021 academic year and need these instructions, please contact your SEA instructor.

ABSTRACTS & POSTERS

Who should submit abstracts and posters?
SEA Faculty are responsible for submitting all abstracts and posters. Poster abstracts will be submitted via the seaphages.org program website, whereas the final posters will be uploaded to the symposium meeting website. Instructions for abstract and poster submissions are provided below.

How many posters should be submitted?
We encourage each SEA school to submit at least one poster that describes their SEA research from the 2020 – 2021 academic year. Since we are not limited by space this year, each school can submit as many posters as they have data to present. For example, if your school has multiple SEA sections, PHAGES or GENES, you may choose to submit one poster for each section or research project. Alternatively, you can choose to submit one poster that summarizes many projects. Faculty are also welcomed to submit posters describing SEA-related research that goes beyond their PHAGES and GENES courses.

What is the format for each poster?
This year, we are asking for posters to be submitted as short video recordings of ~ 5 minutes. This will allow attendees to view poster presentations asynchronously throughout the meeting. Minimally, the video must include a visual representation of your data and an accompanying narration. For example, your video poster can be prepared as a recorded PowerPoint presentation. We encourage you to be creative! Finally, please add closed captioning for your video. The University of Washington's recommendations for doing so using free online tools can be viewed here. Contact us at
info@seaphages.org if you need assistance.

What should I include in my abstract(s) and poster(s)?
Given that the symposium will happen early in your semester, we recognize that poster videos will likely feature a project that is a “work in progress”. This presents a new opportunity for the SEA, allowing faculty and student researchers to discuss their work with their SEA colleagues and get feedback to inform the ongoing research. Therefore, we encourage you to include the following items in your poster, adding or subtracting from this list as you see fit.
i. goal(s) of your project(s),
ii. methodology, especially if it includes techniques that are not core to the SEA projects,
iii. findings, whether they be complete data figures or early observations,
iv. research or questions that will be explored next, in the remainder of the semester or beyond,
v. questions related to your research that the SEA community (i.e., poster attendees) might be able to provide insight.
vi. and of course, the usual poster items such as your school logo, poster title, and author information.
Your abstract will represent a summary of what will be included in your poster and can primarily focus on items i, iii, iv from the list below. There is a 3,000 character-limit for abstracts.

What is the format for the poster session?
This year we will be introducing PosterPacks. Each PosterPack will consist of ~ 5 faculty members who have authored posters for the symposium. As a member of a PosterPack, faculty members and their students should plan to view and provide feedback for the posters of their PosterPack members. Of course, you should also plan to visit many other posters! Schools will be notified of PosterPack assignments by April 2. Since posters will also be uploaded by April 2, faculty members and their students will have the opportunity to view the video-posters of their PosterPack members ahead of time to discuss feedback that could be provided.

There will be two formal poster sessions, one on Saturday and another on Sunday, providing dedicated time for attendees to view poster videos. However, posters will also be available for viewing throughout the symposium. A chat feature will be available for each poster and will be the primary way attendees and poster authors interact with one another. We encourage faculty to assign at least one poster author to be present during the session to answer questions via the chat. Ideally, multiple authors for a given poster will take turns managing the poster chat.

On the second poster session (Sunday), we will ALSO host a series of concurrent Poster Discussion sessions. In each Poster Discussion session, the ~ 5 faculty members from each PosterPack will gather as a group, via Zoom, to discuss their posters / on-going research projects. Each faculty member should invite one student representative to join them for the poster discussion session. The goal of these poster discussion sessions is for SEA researchers to support each other, learn more about the exciting science done in the SEA, and move ongoing research projects forward. A discussion guide to facilitate these discussions is available for download here. Each discussion will be recorded and made available to the community at a later date.

The symposium agenda lists the dates and times for poster sessions.

How do I submit my abstract(s)?

Once you are signed in at seaphages.org, links to add, modify, or view an abstract are provided at the top of your institution page. Abstracts should be submitted between March 1 – 16, 2021.

How do I submit my poster(s)?

Once you have submitted your abstracts, SEA staff will send you a unique link for each poster. With this unique link, you will be able to upload your video poster to the Symposium Meeting Website, either by submitting a hyperlink to the poster-video or by uploading the poster-video file. There are 4 steps to uploading your video-poster. A Step-by-Step guide can be downloaded here. Video-posters should be submitted by April 2, 2021.
 

TALKS  

Yes! If you would like your abstract to be considered for a talk, you can indicate so during abstract submission. If your abstract is selected for a talk, you will be notified by March 19.
We encourage you to submit a poster-video even if you are selected to give a talk, since the poster session is an additional and important opportunity for faculty and student co-authors, and other symposium attendees to interact and discuss research.

What are the formats for talks?

We have several slots set aside for SEA faculty and student researchers to present 12-minute talks (+3 minutes for Q&A). Talks will be presented live. Speakers will be invited to a practice session in the weeks prior to the meeting so that they are familiar with the technology.
There will also be two featured talks, one by our keynote speaker, Forest Rohwer, and another by our very own Graham Hatfull. The symposium agenda lists the dates and times for talks.

OTHER

How will symposium attendees be able to interact?

To provide many opportunities for you and your students to connect with the SEA community, there will be multiple ways for symposium attendees to interact, suited to particular sessions. We encourage all to participate in these interactions.

  • For talks, attendees will be able to ask questions via a Q&A and respond to polls.
  • For posters, presenters and visitors will be able to interact via a dedicated chat box at each poster.
  • We are particularly excited to feature a new gathering space, which allows every attendee to explore a common virtual space. In this space, you can see other attendees, wander up to each other to automatically launch a video-session, interact with games, watch HHMI shows, visit a photo booth, and more! We encourage attendees to use this space to meet between or after sessions to discuss science, or to simply catch up with old friends and to meet and make new friends.

What are important dates?
March 12, 2021:          Deadline to register for the Symposium.
March 16, 2021:          Deadline for abstract submission.
March 19, 2021:          Those selected to give talks will be notified.
April 2, 2021:               Schools notified of “Poster Group” assignments.
April 2, 2021:               Deadline to upload Poster-videos to the symposium website.
April 9 – 11, 2021:       Attend the symposium.

Archiving Information 2020-21

The procedure for sending archiving samples to the University of Pittsburgh is largely similar this year, with two important changes.

  1. Our shipping address has changed—see below for the new address.
  2. We are asking you to fill out a quick form to let us know what you're sending and help us track your package.

Contact Us/Questions

Please send any questions about the information below to Debbie (djs@pitt.edu) and Becky (rag4@pitt.edu).

Please read the latest Archiving Instructions at the link below.

https://phagesdb.org/protocols/96/

Archiving Sample Submission Form

Please submit the information about the samples you are sending using this Google Form. This will help us keep track of samples, correct any spelling errors, and make sure your samples are accounted for.

We are asking that you add a tracking number in the appropriate place on the form. We have rotating lab staff, and want to make sure all packages are accounted for.

https://forms.gle/pHq9LHyYiuSJPCHF7

Timeline

You should send archiving samples for phages found in 2020 for arrival no later than December 16.

Shipping

Please be sure to include an up-to-date Archiving Report in the package. You can print one from your institution's page on seaphages.org.

Shipping Address (NEW THIS YEAR)

Attn: Becky Garlena
University of Pittsburgh
Langley Garage 120F
Langley Hall
Fifth and Ruskin Avenues
Pittsburgh, PA 15260
(412) 624 6976

DNA Samples

Just a note that DNA samples should be sent to the same address as above, and so if it's convenient to you, you can send DNA samples and archiving samples together in a single box.

Sequencing Information 2020-21

Sequencing Information 2020-21

It's been a weird year, but through many trials and adjustments we have still arrived at phage DNA sequencing season! This post contains information about sending your SEA-PHAGES phage DNA samples to the University of Pittsburgh for sequencing. Because of the pandemic and other issues, several things have changed since previous years, so please read carefully.

Contact Us/Questions

Please send any questions about the information below to Dan (dar78@pitt.edu) and Becky (rag4@pitt.edu).

Sample Submission Form

Please submit the information about the samples you are sending using Google Form. This will help us keep track of samples, correct any spelling errors, and make sure your samples are accounted for. Please fill out a copy of this form for each sample you are submitting. The best time to fill it out is as you are getting your shipment packed, so that when your box arrives, we'll already have the information on your phages in our database.

NEW THIS YEAR: We are asking, if possible, that you add a tracking number in the appropriate place on the form. We have rotating lab staff, and want to make sure all packages are accounted for. Please note whether each sample is a "Priority" or "Backup" in the Notes field, along with any other info we should have.

https://docs.google.com/forms/d/e/1FAIpQLSfdhZpw1LHL42zxAotEVqhmrr8RBN9-kuPL_42ioYmuBU-4-Q/viewform

Quantity

Each SEA-PHAGES school may have two genomes sequenced per Bioinformatics section that it is teaching during the current academic year. Please indicate any order of preference, if you have one.

NEW THIS YEAR: Because many schools were not able to perform phage discovery as usual during the fall but still want to do bioinformatics in the spring, we will need some extra DNA samples to be donated to the Genome Exchange. If you have managed to extract more good quantity, high quality DNA samples than you need for your class, we would welcome those as well. Please indicate "Donate to Exchange" on the Notes field of the form. And thanks for helping out your fellow SEA-PHAGES institutions!

Deadlines

Semester Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, November 20.

Quarter Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, January 8.

If you will have trouble meeting these deadlines for any reason, please contact us.

Guidelines for DNA

Buffer

Samples that are resuspended in TE are problematic, since the EDTA may interfere with enzymatic shearing of the DNA. You can resuspend your DNA in Elution Buffer (Tris) or in purified water.

Amount

We need a minimum of 4 µg (micrograms) of genomic DNA. If you're in the ballpark of this number but not quite there, contact Dan and Becky to see if it's okay.

Concentration

At least 40 ng/µl. Ideal is 100-300 ng/µl. If you're above 300 ng/µl please consider diluting to a workable concentration and workable volume. Shipping volumes less than 20 µl is not recommended. Keep in mind that spec-based quantifications (like Nanodrop) count all absorbance at 260 nm, not just genomic DNA, so they often overestimate the real concentration. Err on the high side of the amount of DNA you send.

Gel Picture

Please submit—either via email or in the shipping box—an image of the gDNA being run on an agarose gel. We use these to look for sample integrity (not already sheared/degraded) and purity (no RNA).

Labeling

Please clearly label the tubes you are sending with the name of the phage as it appears on PhagesDB. Don't label tubes using student's initials only, or other ambiguous names like "Phage1" or "PittPhage". If possible, put a small circular sticker on the top of the tube and write the phage name only on it.

Shipping

Packaging

We prefer standard microcentrifuge tubes, and strongly recommend wrapping the caps with Parafilm to prevent spilling or evaporation. The tubes can be packed into a 50 ml conical tube with some KimWipes to stabilize them during shipment. If shipping overnight (preferred), you can actually just send the samples at room temperature, as the DNA should be fine for 24 hours in transit. If shipping on a slower schedule, you should use cold packs. Aim for delivery to Pittsburgh on Tuesday-Friday. If shipping near holidays, please check with us about when we'll be around to receive samples.

You can include a packing slip with any information you think we should have about the enclosed phages.

Address (NEW THIS YEAR)

Attn: Becky Garlena
University of Pittsburgh
Langley Garage 120F
Langley Hall
Fifth and Ruskin Avenues
Pittsburgh, PA 15260
(412) 624 6976

Additional Samples

For the past several years, the Genomics Sciences Laboratory at NC State has provided high-quality, for-cost sequencing services to schools in the SEA-PHAGES program who wish to sequence additional genomes beyond those allotted by the program. Contact Andy Baltzegar at dabaltze@ncsu.edu for pricing and details.

Archiving Samples

Just a note that archiving samples should be sent to the same address as above, and so if it's convenient to you, you can send DNA samples and archiving samples together in a single box.

Current Events

2021 SEA Symposium

April 9, 2021 to April 11, 2021

Upcoming Events

Recent Events

Cohort 13 Phage Genomics Workshop (Dec 2020)

December 7, 2020 to December 18, 2020

Cohort 13 Phage Genomics Workshop

June 15, 2020 to June 26, 2020

Forum Activity

Debbie Jacobs-Sera posted in A4 - no frameshift

smg366 posted in A4 - no frameshift

smg366 posted in A4 - no frameshift

FORUMS HOME PAGE