SEA-PHAGES | SEA-PHAGES Faculty Information

SEA-PHAGES Faculty Information

Welcome
Timeline (current)
Timeline (next year)
Phage Discovery Component
Phage Genomics (Bioinformatics) Component
Modifying/Enhancing Your SEA-PHAGES Implementation
Program Assessment
Applying to Join
Onboarding
Faculty Meeting Notes

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.

Members of the incoming cohort should click here to view important training and preparation dates for the 2022-2023 academic year.

* This item/event is for new applicants.

** This item/event is for newly accepted schools in their first year. Namely, PHAGES Cohort 14 schools.

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.

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

* This item/event is for new applicants.

** This item/event is for newly accepted schools in their first year.

Phage Discovery Component

Supplies, Quotes, & Ordering Information

Course Guides

Other Course-related Materials

Phage Discovery Flowchart [pdf] [tif]
Sample 15-week schedule

MTA Instructions

Archiving Instructions

Sequencing Instructions

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*

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
- Annotation Cover Sheet and Checklist
- Approved List of Phage Gene Functions
DNA Master
- DNA Master Info and Installation Guide
Phamerator
- Server Address
Starterator
- Click Here for UPDATED Starterator Guide
- Create a link to Starterator reports on your desktop

* 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

The Host-Range Project | details* | forum
The Xeno Project | details* | forum

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)

Click here to access our DropBox Folder of materials to help you write an MRA. Start with "How to write a...."

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.

Creating / updating an account at seaphages.org

This 8-minute welcome video is for faculty members that are new to the SEA-PHAGES project.

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.

The webinar is scheduled for 2.30 - 3.10 pm. Feb 10, 2021.

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

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 symposium will be hosted virtually, and will be open to all SEA faculty and all SEA students from the 2021-2022 academic year.

This meeting is tentatively being planned as a hybrid meeting, with some participant attending in-person and others virtually.

Date	Event/Item	Add
Oct 31, 2020	Deadline for Cohort 14 Application *	10/31/2020 10/31/2020 America/New_York Deadline for Cohort 14 Application SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_168
Dec 18 - Jan 21, 2020	Cohort 14 Application Review Notification and Acceptance *	12/18/2020 01/21/2021 America/New_York Cohort 14 Application Review Notification and Acceptance SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_169
Feb 1, 2021	Details Watch Recorded Welcome Webinar (Part I) **	02/01/2021 02/01/2021 America/New_York Watch Recorded Welcome Webinar (Part I) This 8-minute welcome video is for faculty members that are new to the SEA-PHAGES project. 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. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_187
Feb 10 - Feb 10, 2021	Details Attend Live Welcome Webinar (2.30 - 3.10pm): see Details for Zoom password --> **	02/10/2021 02:30 PM 02/10/2021 03:10 PM America/New_York Attend Live Welcome Webinar (2.30 - 3.10pm): see Details for Zoom password --> The webinar is scheduled for 2.30 - 3.10 pm. Feb 10, 2021. 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 SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_170
Mar 1, 2021	Register Phage Discovery Cohort 13 & 14 Trainees **	03/01/2021 03/01/2021 America/New_York Register Phage Discovery Cohort 13 & 14 Trainees SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_148
Mar 1 - Mar 31, 2021	Procure Phage Discovery Lab Supplies **	03/01/2021 03/31/2021 America/New_York Procure Phage Discovery Lab Supplies SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_171
Apr 1 - Jun 30, 2021	Details Phage Discovery Training (Remote) **	04/01/2021 06/30/2021 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_173
Apr 9 - Apr 11, 2021	Attend 13th SEA Symposium (Virtual) **	04/09/2021 04/11/2021 America/New_York Attend 13th SEA Symposium (Virtual) SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_186
Jun 7 - Jun 9, 2021	Attend SEA Faculty Meeting (Virtual) **	06/07/2021 06/09/2021 America/New_York Attend SEA Faculty Meeting (Virtual) SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_185
Sep 1 - Oct 29, 2021	Virtual Site-Visit with SEA Team **	09/01/2021 10/29/2021 America/New_York Virtual Site-Visit with SEA Team SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_176
Sep 10, 2021	Monthly Virtual Faculty Meeting	09/10/2021 04:00 PM 09/10/2021 America/New_York Monthly Virtual Faculty Meeting SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_191
Sep 17, 2021	Deadline to Add Fall Section Data to seaphages.org	09/17/2021 09/17/2021 America/New_York Deadline to Add Fall Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_157
Oct 8, 2021	Monthly Virtual Faculty Meeting	10/08/2021 04:00 PM 10/08/2021 America/New_York Monthly Virtual Faculty Meeting SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_192
Nov 1, 2021	Identify Phage Genomics (Bioinformatics) Workshop Trainees **	11/01/2021 11/01/2021 America/New_York Identify Phage Genomics (Bioinformatics) Workshop Trainees SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_177
Nov 1 - Nov 30, 2021	Install software for Bioinformatics Workshop and Semester **	11/01/2021 11/30/2021 America/New_York Install software for Bioinformatics Workshop and Semester SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_178
Nov 3, 2021	Receive Archiving Materials from Program	11/03/2021 11/03/2021 America/New_York Receive Archiving Materials from Program SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_179
Nov 12, 2021	Monthly Virtual Faculty Meeting Time TBD	11/12/2021 12:00 PM 11/12/2021 America/New_York Monthly Virtual Faculty Meeting Time TBD SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_200
Nov 16 - Dec 15, 2021	Submit Lysates for Archiving	11/16/2021 12/15/2021 America/New_York Submit Lysates for Archiving SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_158
Nov 16, 2021	Submit DNA Samples [Semester Schools]	11/16/2021 11/16/2021 America/New_York Submit DNA Samples [Semester Schools] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_159
Dec 1 - Dec 10, 2021	Students Complete Spring Semester PITS Survey [Semester Schools]	12/01/2021 12/10/2021 America/New_York Students Complete Spring Semester PITS Survey [Semester Schools] SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_160
Dec 6 - Dec 17, 2021	Phage Genomics (Bioinformatics) Workshop **	12/06/2021 12/17/2021 America/New_York Phage Genomics (Bioinformatics) Workshop SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_180
Dec 10, 2021	Monthly Virtual Faculty Meeting	12/10/2021 04:00 PM 12/10/2021 America/New_York Monthly Virtual Faculty Meeting SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_193
Dec 17, 2021	Submit Genome Annotations for Quality Control [Fall Semester]	12/17/2021 12/17/2021 America/New_York Submit Genome Annotations for Quality Control [Fall Semester] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_161
Jan 11, 2022	Submit DNA Samples [Quarter Schools]	01/11/2022 01/11/2022 America/New_York Submit DNA Samples [Quarter Schools] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_162
Jan 14, 2022	Monthly Virtual Faculty Meeting	01/14/2022 04:00 PM 01/14/2022 America/New_York Monthly Virtual Faculty Meeting SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_194
Jan 28, 2022	Deadline to Add Spring Section Data to seaphages.org	01/28/2022 01/28/2022 America/New_York Deadline to Add Spring Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_163
Feb 11, 2022	Monthly Virtual Faculty Meeting	02/11/2022 04:00 PM 02/11/2022 America/New_York Monthly Virtual Faculty Meeting SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_195
Mar 11, 2022	Monthly Virtual Faculty Meeting	03/11/2022 04:00 PM 03/11/2022 America/New_York Monthly Virtual Faculty Meeting SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_196
Mar 15, 2022	Submit Student Abstract for 2022 Symposium	03/15/2022 03/15/2022 America/New_York Submit Student Abstract for 2022 Symposium SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_165
Apr 8 - Apr 10, 2022	Details SEA Symposium	04/08/2022 04/10/2022 America/New_York SEA Symposium This symposium will be hosted virtually, and will be open to all SEA faculty and all SEA students from the 2021-2022 academic year. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_198
May 3, 2022	Submit Genome Annotations for Quality Control	05/03/2022 05/03/2022 America/New_York Submit Genome Annotations for Quality Control SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_166
May 6, 2022	Students Complete Spring Semester PITS Survey [Semester Schools]	05/06/2022 05/06/2022 America/New_York Students Complete Spring Semester PITS Survey [Semester Schools] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_167
May 13, 2022	Monthly Virtual Faculty Meeting	05/13/2022 04:00 PM 05/13/2022 America/New_York Monthly Virtual Faculty Meeting SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_197
Jun 3 - Jun 5, 2022	Details Annual SEA Faculty Meeting	06/03/2022 06/05/2022 America/New_York Annual SEA Faculty Meeting 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_199