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

SEA-PHAGES Faculty Information

Welcome

Welcome to the Faculty Information page. This page is intended to be a one-stop hub for SEA-PHAGES faculty members to find what they need. If you don't see something here that you think should be here, use the Contact Us link below to let us know.

Some basics:

Timeline: 2022-2023 (for current schools)

Below is a timeline of important dates for the 2022-2023 academic year, with appropriate supporting links and documents.

PHAGES Cohort 15 members: please click here to show dates specific to you.

Members of the incoming cohort should click here to view important training and preparation dates for the 2023-2024 academic year.

Date Event/Item Add
Feb 1, 2022 Watch Recorded Welcome Webinar (Part 1) **
Add to calendar 02/01/2022 02/01/2022 America/New_York Watch Recorded Welcome Webinar (Part 1) SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_201
Feb 9, 2022 Attend Live Welcome Webinar (Part 2) **
Add to calendar 02/09/2022 02:30 PM 02/09/2022 America/New_York Attend Live Welcome Webinar (Part 2) SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_202
Mar 1, 2022 Procure Phage Discovery Lab Supplies **
Add to calendar 03/01/2022 03/01/2022 America/New_York Procure Phage Discovery Lab Supplies SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_204
Mar 1, 2022 Register Phage Discovery Cohort15 Trainees **
Add to calendar 03/01/2022 03/01/2022 America/New_York Register Phage Discovery Cohort15 Trainees SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_205
Apr 8 - Apr 10, 2022 SEA Symposium (Virtual) **
Add to calendar 04/08/2022 04/10/2022 America/New_York SEA Symposium (Virtual) SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_211
May 1 - Jul 1, 2022
Details
Phage Discovery Training (Remote) **
Add to calendar 05/01/2022 07/01/2022 America/New_York Phage Discovery Training (Remote) New SEA-PHAGES instructors are expected to attend HHMI-hosted webinars and perform ~3 hours of self-guided research at their home institutions, each week. Self-guided research for Phage Discovery will require lab access. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_207
Jun 3 - Jun 6, 2022
Details
Annual SEA Faculty Meeting (Hybrid) **
Add to calendar 06/03/2022 06/06/2022 America/New_York Annual SEA Faculty Meeting (Hybrid) This meeting is tentatively being planned as a hybrid meeting, with some participant attending in-person and others virtually. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_212
Jun 25 - Jul 1, 2022
Details
Phage Discovery Training (In-person; Option A) **
Add to calendar 06/25/2022 07/01/2022 America/New_York Phage Discovery Training (In-person; Option A) Given the uncertainty around in-person meetings due to COVID19, this in-person training will only be offered if it is safe to do so. Should in-person training be offered, HHMI will cover the cost of travel, food, and lodging. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_209
Jul 9 - Jul 15, 2022
Details
Phage Discovery Training (In-person; Option B) **
Add to calendar 07/09/2022 07/15/2022 America/New_York Phage Discovery Training (In-person; Option B) Given the uncertainty around in-person meetings due to COVID19, this in-person training will only be offered if it is safe to do so. Should in-person training be offered, HHMI will cover the cost of travel, food, and lodging. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_210
Sep 16, 2022 Deadline to Add Fall Section Data to seaphages.org
Add to calendar 09/16/2022 09/16/2022 America/New_York Deadline to Add Fall Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_222
Sep 16, 2022 Monthly Faculty Meeting Series
Add to calendar 09/16/2022 04:00 PM 09/16/2022 America/New_York Monthly Faculty Meeting Series SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_231
Oct 3 - Oct 31, 2022 Virtual Check-In with SEA Team **
Add to calendar 10/03/2022 10/31/2022 America/New_York Virtual Check-In with SEA Team SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_213
Oct 14, 2022 Monthly Faculty Meeting Series
Add to calendar 10/14/2022 04:00 PM 10/14/2022 America/New_York Monthly Faculty Meeting Series SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_232
Nov 1, 2022 Identify Phage Genomics Workshop Trainees **
Add to calendar 11/01/2022 11/01/2022 America/New_York Identify Phage Genomics Workshop Trainees SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_215
Nov 1 - Nov 30, 2022 Install software for Bioinformatics Workshop and Semester **
Add to calendar 11/01/2022 11/30/2022 America/New_York Install software for Bioinformatics Workshop and Semester SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_216
Nov 8, 2022 Receive Archiving Materials from Program
Add to calendar 11/08/2022 11/08/2022 America/New_York Receive Archiving Materials from Program SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_223
Nov 11, 2022 Monthly Faculty Meeting Series
Add to calendar 11/11/2022 04:00 PM 11/11/2022 America/New_York Monthly Faculty Meeting Series SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_233
Nov 16 - Dec 14, 2022 Submit Lysates for Archiving
Add to calendar 11/16/2022 12/14/2022 America/New_York Submit Lysates for Archiving SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_218
Nov 22, 2022 Submit DNA Samples [Semester schools]
Add to calendar 11/22/2022 11/22/2022 America/New_York Submit DNA Samples [Semester schools] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_217
Dec 1 - Dec 9, 2022 Students Complete Fall Semester PITS Survey [Semester Schools]
Add to calendar 12/01/2022 12/09/2022 America/New_York Students Complete Fall Semester PITS Survey [Semester Schools] SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_219
Dec 5 - Dec 9, 2022 Phage Genomics Workshop - In-Person **
Add to calendar 12/05/2022 12/09/2022 America/New_York Phage Genomics Workshop - In-Person SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_230
Dec 14, 2022 Submit Genome Annotations for Quality Control [Fall Semester]
Add to calendar 12/14/2022 12/14/2022 America/New_York Submit Genome Annotations for Quality Control [Fall Semester] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_220
Dec 16, 2022 Monthly Faculty Meeting Series
Add to calendar 12/16/2022 04:00 PM 12/16/2022 America/New_York Monthly Faculty Meeting Series SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_234
Jan 10, 2023 Submit DNA Samples [Quarter Schools]
Add to calendar 01/10/2023 01/10/2023 America/New_York Submit DNA Samples [Quarter Schools] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_221
Jan 13, 2023 Monthly Faculty Meeting Series
Add to calendar 01/13/2023 04:00 PM 01/13/2023 America/New_York Monthly Faculty Meeting Series SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_235
Feb 1, 2023 Deadline to Add Spring Section Data to seaphages.org
Add to calendar 02/01/2023 02/01/2023 America/New_York Deadline to Add Spring Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_224
Feb 10, 2023 Monthly Faculty Meeting Series
Add to calendar 02/10/2023 04:00 PM 02/10/2023 America/New_York Monthly Faculty Meeting Series SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_236
Mar 1, 2023 SEA Symposium Registration
Add to calendar 03/01/2023 03/01/2023 America/New_York SEA Symposium Registration SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_225
Mar 10, 2023 Monthly Faculty Meeting Series
Add to calendar 03/10/2023 04:00 PM 03/10/2023 America/New_York Monthly Faculty Meeting Series SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_237
Apr 14 - Apr 16, 2023 SEA Symposium
Add to calendar 04/14/2023 04/16/2023 America/New_York SEA Symposium SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_226
May 5, 2023 Students Complete Spring Semester PITS Survey [Semester Schools]
Add to calendar 05/05/2023 05/05/2023 America/New_York Students Complete Spring Semester PITS Survey [Semester Schools] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_228
May 12, 2023 Submit Genome Annotations for Quality Control
Add to calendar 05/12/2023 05/12/2023 America/New_York Submit Genome Annotations for Quality Control SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_227
May 12, 2023 Monthly Faculty Meeting Series
Add to calendar 05/12/2023 04:00 PM 05/12/2023 America/New_York Monthly Faculty Meeting Series SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_238
Jun 2 - Jun 5, 2023 Annual SEA Faculty Meeting (Hybrid)
Add to calendar 06/02/2023 06/05/2023 America/New_York Annual SEA Faculty Meeting (Hybrid) SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_229

Timeline: 2023-2024 (for current and incoming schools)

Below is a timeline of important dates for the upcoming 2023-2024 academic year, with appropriate supporting links and documents.

Dates for the current academic year are above.

Click here to hide/show events for new schools, useful for seeing program-wide dates only.

Date Event/Item Add
Oct 31, 2022 Cohort 16 Application Deadline *
Add to calendar 10/31/2022 10/31/2022 America/New_York Cohort 16 Application Deadline SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_239
Dec 19 - Jan 20, 2022 Cohort 16 Application Review Notification and Acceptance *
Add to calendar 12/19/2022 01/20/2023 America/New_York Cohort 16 Application Review Notification and Acceptance SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_240
Mar 1, 2023 Identify Phage Discovery Workshop Attendees **
Add to calendar 03/01/2023 03/01/2023 America/New_York Identify Phage Discovery Workshop Attendees SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_247
Apr 14 - Oct 16, 2023 SEA Symposium (Virtual) **
Add to calendar 04/14/2023 10/16/2022 America/New_York SEA Symposium (Virtual) SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_245
Jun 2 - Jun 5, 2023 SEA Faculty Meeting **
Add to calendar 06/02/2023 06/05/2023 America/New_York SEA Faculty Meeting SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_246
Jun 24 - Jun 30, 2023 Phage Discovery Workshop (Option A) **
Add to calendar 06/24/2023 06/30/2023 America/New_York Phage Discovery Workshop (Option A) SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_243
Jul 8 - Jul 14, 2023 Phage Discovery Workshop (Option B) **
Add to calendar 07/08/2023 07/14/2023 America/New_York Phage Discovery Workshop (Option B) SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_244
Sep 29, 2023 Deadline to Add Fall Section Data **
Add to calendar 09/29/2023 09/29/2023 America/New_York Deadline to Add Fall Section Data SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_252
Oct 2 - Oct 31, 2023 Virtual Check-In with SEA Team **
Add to calendar 10/02/2023 10/31/2023 America/New_York Virtual Check-In with SEA Team SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_241
Oct 2, 2023 Identify Phage Genomics Workshop Attendees **
Add to calendar 10/02/2023 10/02/2023 America/New_York Identify Phage Genomics Workshop Attendees SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_242
Nov 13 - Dec 15, 2023 Submit Lysates for Archiving **
Add to calendar 11/13/2023 12/15/2023 America/New_York Submit Lysates for Archiving SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_249
Nov 30, 2023 Submit DNA Samples [Semester schools] **
Add to calendar 11/30/2023 11/30/2023 America/New_York Submit DNA Samples [Semester schools] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_250
Dec 4 - Dec 8, 2023 Phage Genomics Workshop (Tentative Dates) **
Add to calendar 12/04/2023 12/08/2023 America/New_York Phage Genomics Workshop (Tentative Dates) SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_248

Phage Genomics (Bioinformatics) Component

Software Overview (Required and Add-ons)

Required Software to Install:

Optional software:

  • The SEA-PHAGES Virtual Machine
    • The SEA VM is an Ubuntu disc image with the programs Phamerator, Starterator, Newbler, AceUtil and Consed and associated databases pre-installed. The SEA-PHAGES Virtual Machine download is a ~4.6 Gb .zip file, so downloading it will take some time. Unpacked, the file is ~12 Gb.

Download SEA-PHAGES Virtual Machine

Setting up shared folders in Virtual Box

Course Material


* These documents were generated wholly or in part through work done at the 2016 SEA-PHAGES Faculty Retreat and Workshop.  Many thanks to the faculty members who helped craft them!

Modifying/Enhancing Your SEA-PHAGES Implementation

Potential Changes to Wet Lab Procedures

Advanced Experiments/Ideas

Community Research Projects

Adding Sections at Your Institution

Microbial Resource Announcements (used to be Genome Announcements)

  • We have created a resource on the SEA QUBES hub describing the process of writing an MRA. Click here to access it.

Other Helpful Tips

  • Using Inkscape—a free graphics tool—to import, edit, and produce high-quality Phamerator maps*
  • Using the Phage Enzyme Tools: A video tutorial that shows one way to interpret your restriction digest results

* These documents were generated wholly or in part through work done at the 2016 SEA-PHAGES Faculty Retreat and Workshop.  Many thanks to the faculty members who helped craft them!

Applying to Join

Applications are accepted yearly.  Each year, 12-20 new schools are added to the program as the latest cohort.  Generally, applications are due late Oct to mid Nov for the following academic year, but check the timeline above for precise dates.

Apply for 2019-2020 Now

All application materials are available at HHMI's Science Education Alliance website.

Onboarding

Note that PhagesDB.org and seaphages.org use the same user database, so if you've created an account on either site, it will work on the other as well.

Creating / updating an account at seaphages.org

New SEA-PHAGES instructors are expected to attend HHMI-hosted webinars and perform ~3 hours
of self-guided research at their home institutions, each week. Self-guided research for Phage
Discovery will require lab access.
This meeting is tentatively being planned as a hybrid meeting, with some participant attending in-person and others virtually.
Given the uncertainty around in-person meetings due to COVID19, this in-person training will only be
offered if it is safe to do so. Should in-person training be offered, HHMI will cover the cost of travel,
food, and lodging.
Given the uncertainty around in-person meetings due to COVID19, this in-person training will only be
offered if it is safe to do so. Should in-person training be offered, HHMI will cover the cost of travel,
food, and lodging.