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: 2021-2022 (for current schools)
Below is a timeline of important dates for the 2021-2022 academic year, with appropriate supporting links and documents.
PHAGES Cohort 14 members: please click here to show dates specific to you.
PHAGES Cohort 15 members should click here to view important training and preparation dates for the 2022-2023 academic year.
Date | Event/Item | Add |
---|---|---|
Oct 31, 2020 | Deadline for Cohort 14 Application * |
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Dec 18 - Jan 21, 2020 | Cohort 14 Application Review Notification and Acceptance * |
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Feb 1, 2021 |
Details
Watch Recorded Welcome Webinar (Part I)
**
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Feb 10 - Feb 10, 2021 |
Details
Attend Live Welcome Webinar (2.30 - 3.10pm): see Details for Zoom password -->
**
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Mar 1, 2021 | Register Phage Discovery Cohort 13 & 14 Trainees ** |
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Mar 1 - Mar 31, 2021 | Procure Phage Discovery Lab Supplies ** |
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Apr 1 - Jun 30, 2021 |
Details
Phage Discovery Training (Remote)
**
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Apr 9 - Apr 11, 2021 | Attend 13th SEA Symposium (Virtual) ** |
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Jun 7 - Jun 9, 2021 | Attend SEA Faculty Meeting (Virtual) ** |
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Sep 1 - Oct 29, 2021 | Virtual Site-Visit with SEA Team ** |
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Sep 10, 2021 | Monthly Virtual Faculty Meeting |
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Sep 17, 2021 | Deadline to Add Fall Section Data to seaphages.org |
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Oct 8, 2021 | Monthly Virtual Faculty Meeting |
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Nov 1, 2021 | Identify Phage Genomics (Bioinformatics) Workshop Trainees ** |
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Nov 1 - Nov 30, 2021 | Install software for Bioinformatics Workshop and Semester ** |
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Nov 3, 2021 | Receive Archiving Materials from Program |
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Nov 12, 2021 | Monthly Virtual Faculty Meeting |
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Nov 16 - Dec 16, 2021 | Submit Lysates for Archiving |
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Dec 1 - Dec 10, 2021 | Students Complete Spring Semester PITS Survey [Semester Schools] |
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Dec 2, 2021 | Submit DNA Samples [Semester Schools] |
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Dec 6 - Dec 17, 2021 | Phage Genomics (Bioinformatics) Workshop ** |
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Dec 10, 2021 | Monthly Virtual Faculty Meeting |
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Dec 17, 2021 | Submit Genome Annotations for Quality Control [Fall Semester] |
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Jan 11, 2022 | Submit DNA Samples [Quarter Schools] |
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Jan 14, 2022 | Monthly Virtual Faculty Meeting |
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Jan 28, 2022 | Deadline to Add Spring Section Data to seaphages.org |
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Feb 11, 2022 | Monthly Virtual Faculty Meeting |
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Mar 1, 2022 | SEA Symposium Registration |
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Mar 11, 2022 | Monthly Virtual Faculty Meeting |
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Mar 15, 2022 | Submit Student Abstract for 2022 Symposium |
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Apr 8 - Apr 10, 2022 |
Details
SEA Symposium
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May 3, 2022 | Submit Genome Annotations for Quality Control |
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May 6, 2022 | Students Complete Spring Semester PITS Survey [Semester Schools] |
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May 13, 2022 | Monthly Virtual Faculty Meeting |
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Jun 3 - Jun 6, 2022 |
Details
Annual SEA Faculty Meeting (Hybrid)
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Timeline: 2022-2023 (for current and incoming schools)
Below is a timeline of important dates for the upcoming 2022-2023 academic year, with appropriate supporting links and documents.
Members of PHAGES Cohort 15 should pay particular attention to the double-asterisk (**) items.
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 |
---|---|---|
Feb 1, 2022 | Watch Recorded Welcome Webinar (Part 1) ** |
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Feb 9, 2022 | Attend Live Welcome Webinar (Part 2) ** |
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Mar 1, 2022 | Procure Phage Discovery Lab Supplies ** |
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Mar 1, 2022 | Register Phage Discovery Cohort15 Trainees ** |
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Apr 8 - Apr 10, 2022 | SEA Symposium (Virtual) ** |
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May 1 - Jul 1, 2022 |
Details
Phage Discovery Training (Remote)
**
|
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Jun 3 - Jun 6, 2022 |
Details
Annual SEA Faculty Meeting (Hybrid)
**
|
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Jun 25 - Jul 1, 2022 |
Details
Phage Discovery Training (In-person; Option A)
**
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Jul 9 - Jul 15, 2022 |
Details
Phage Discovery Training (In-person; Option B)
**
|
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Sep 14, 2022 | Deadline to Add Fall Section Data to seaphages.org |
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Oct 3 - Oct 31, 2022 | Virtual Site-Visit with SEA Team ** |
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Nov 1, 2022 | Identify Phage Genomics Workshop Trainees ** |
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Nov 1 - Nov 30, 2022 | Install software for Bioinformatics Workshop and Semester ** |
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Nov 8, 2022 | Receive Archiving Materials from Program |
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Nov 16 - Dec 14, 2022 | Submit Lysates for Archiving |
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Nov 29, 2022 | Submit DNA Samples [Semester schools] |
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Dec 1 - Dec 9, 2022 | Students Complete Spring Semester PITS Survey [Semester Schools] |
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Dec 5 - Dec 16, 2022 | Phage Genomics Workshop ** |
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Dec 5 - Dec 9, 2022 | Phage Genomics Workshop - In-Person, Tentative ** |
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Dec 14, 2022 | Submit Genome Annotations for Quality Control [Fall Semester] |
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Jan 10, 2023 | Submit DNA Samples [Quarter Schools] |
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Feb 1, 2023 | Deadline to Add Spring Section Data to seaphages.org |
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Mar 1, 2023 | SEA Symposium Registration |
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Apr 14 - Apr 16, 2023 | SEA Symposium |
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May 5, 2023 | Students Complete Spring Semester PITS Survey [Semester Schools] |
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May 12, 2023 | Submit Genome Annotations for Quality Control |
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Jun 2 - Jun 5, 2023 | Annual SEA Faculty Meeting (Hybrid) |
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Phage Discovery Component
Supplies, Quotes, & Ordering Information
- Ordering Guide & Supplies List [updated February 2022]
- Fisher Scientific Quote - 2022 [updated February 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.
Please note that specific times and dates mentioned in the welcome video are for illustration purposes only. Please always refer to the main timeline on this page for up-to-date information.
1. From your desktop or cell: https://hhmi.zoom.us/j/95342461213?pwd=QVoyVDZDd2RxK0NZZUZIMGozYi9RUT09
Password: 1111
2. From a cell phone (if you are not able to use the link above):
US: +13017158592,,95342461213# or +19294362866,,95342461213#
3. From a standard telephone (for higher quality, dial a number based on your current location):
US: +1 301 715 8592 or +1 929 436 2866 or +1 312 626 6799 or +1 669 900 6833 or +1 253 215 8782 or +1 346 248 7799 or 888 475 4499 (Toll Free) or 833 548 0276 (Toll Free) or 833 548 0282 (Toll Free) or 877 853 5257 (Toll Free)
Meeting ID: 953 4246 1213
Password: 1111
International numbers available: https://hhmi.zoom.us/u/apOB98tBR
of self-guided research at their home institutions, each week. Self-guided research for Phage
Discovery will require lab access.
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.