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) ** |
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) ** |
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 ** |
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 ** |
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) ** |
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)
**
|
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)
**
|
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)
**
|
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)
**
|
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 14, 2022 | Deadline to Add Fall Section Data to seaphages.org |
09/14/2022
09/14/2022
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
|
| Oct 3 - Oct 31, 2022 | Virtual Site-Visit with SEA Team ** |
10/03/2022
10/31/2022
America/New_York
Virtual Site-Visit with SEA Team
SEA-PHAGES Program
info@seaphages.org
false
MM/DD/YYYY
seaphages_event_213
|
| Nov 1, 2022 | Identify Phage Genomics Workshop Trainees ** |
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 ** |
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 |
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 16 - Dec 14, 2022 | Submit Lysates for Archiving |
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 29, 2022 | Submit DNA Samples [Semester schools] |
11/29/2022
11/29/2022
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 Spring Semester PITS Survey [Semester Schools] |
12/01/2022
12/09/2022
America/New_York
Students Complete Spring Semester PITS Survey [Semester Schools]
SEA-PHAGES Program
info@seaphages.org
false
MM/DD/YYYY
seaphages_event_219
|
| Dec 5 - Dec 16, 2022 | Phage Genomics Workshop ** |
12/05/2022
12/16/2022
America/New_York
Phage Genomics Workshop
SEA-PHAGES Program
info@seaphages.org
false
MM/DD/YYYY
seaphages_event_214
|
| Dec 5 - Dec 9, 2022 | Phage Genomics Workshop - In-Person, Tentative ** |
12/05/2022
12/09/2022
America/New_York
Phage Genomics Workshop - In-Person, Tentative
SEA-PHAGES Program
info@seaphages.org
false
MM/DD/YYYY
seaphages_event_230
|
| Dec 14, 2022 | Submit Genome Annotations for Quality Control [Fall Semester] |
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
|
| Jan 10, 2023 | Submit DNA Samples [Quarter Schools] |
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
|
| Feb 1, 2023 | Deadline to Add Spring Section Data to seaphages.org |
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
|
| Mar 1, 2023 | SEA Symposium Registration |
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
|
| Apr 14 - Apr 16, 2023 | SEA Symposium |
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] |
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 |
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
|
| Jun 2 - Jun 5, 2023 | Annual SEA Faculty Meeting (Hybrid) |
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 |
|---|
Phage Discovery Component
Supplies, Quotes, & Ordering Information
- Ordering Guide & Supplies List [updated February 2022]
- Fisher Scientific Quote - 2022 [updated June 2022]
Course Guides
Other Course-related Materials
- Phage Discovery Flowchart [pdf] [tif]
- Sample 15-week schedule
Phage Genomics (Bioinformatics) Component
Software Overview (Required and Add-ons)
Required Software to Install:
- DNA Master
Download DNA Master
DNA Master Installation Guide (includes computer requirements)
This program runs on Windows ONLY. If you have a Mac, you have two options:- Option 1 (preferred): Use Virtual Box to install a Windows virtual machine on your Mac, then install DNA Master on that Windows virtual machine.
Download Virtual Box (you may also use other emulation software)
Guide to Install Windows on a Mac - Option 2 (not recommended): Use WINE to install DNA Master directly on a Mac with no need for a Windows license. Installing DNA Master on a Mac using WINE*
- Option 1 (preferred): Use Virtual Box to install a Windows virtual machine on your Mac, then install DNA Master on that Windows virtual machine.
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
- SEA-PHAGES Bioinformatics Guide
- Video Tutorials
- Submit Annotated Genomes
- DNA Master
- Phamerator
- Starterator
* 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
- Suggestions to increase the diversity of the phages you're isolating*
- Restriction digest tips/tricks/modifications*
- Money-saving tips for a SEA-PHAGES course*
Advanced Experiments/Ideas
- Using DOGEMS to sequence all your genomes and find hidden gems*
- Doing RNA-Seq experiments in a SEA-PHAGES context*
- Exploring bacteriophage biology
Community Research Projects
Adding Sections at Your Institution
- What to Expect When You're Expanding: Tips from faculty who have grown their SEA-PHAGES implementations*
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!
Program Assessment
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.
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.
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.
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.
offered if it is safe to do so. Should in-person training be offered, HHMI will cover the cost of travel,
food, and lodging.