SEA-PHAGES | Faculty Information

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: 2020-2021 (for current schools)

Below is a timeline of important dates for the 2020-2021 academic year, with appropriate supporting links and documents.

Cohort 13 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 2021-2022 academic year.

* This item/event is for new applicants.

** This item/event is for newly accepted schools in their first year. Namely, Cohort 13 schools.

Timeline: 2021-2022 (for current and incoming schools)

Below is a timeline of important dates for the upcoming 2021-2022 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

Reagent Prep Guidelines

Course Guides

Other Course-related Materials

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 QuickStart Guide
- DNA Master Annotation Guide "Click Here" version
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 Webinar is for all faculty that are new to the Science Education Alliance. Program leadership, David Asai and Graham Hatfull, will introduce you to the educational and scientific goals of the program, and answer any questions you have about the program.
Prior to attending this webinar, please watch a brief (8 min) Introductory Video: https://seaphages.org/video/51/

A recording of the webinar is now available on the program website - click this link in the timeline to view the video.

Meeting Information for Cohort 13:

Symposium & Faculty Meeting (June 5 - 8, 2020)
Attendee: One faculty member from your institution is invited to attend the 2020 Symposium & Faculty Meeting. This meeting will be held at the National Conference Center in Ashburn, VA.

Phage Discovery Workshop (June 20 - June 26, or July 11 - July 17, 2020)
Attendee(s): Two faculty members from your institution, who will teach the Phage Discovery component of the SEA-PHAGES course, are invited to attend 1 of the 2 Phage Discovery workshop sessions in 2020. You may nominate and justify the attendance for a third person, typically a faculty member or support staff that will directly contribute towards the Phage Discovery component. If spaces are available, an invitation will be sent to the third person. Note that it is not essential for all participants from each school to attend the same workshop session, but it is recommended. These workshops will be held at the University of Maryland Baltimore County.

Note: HHMI is monitoring the SARS-CoV-2 outbreak, and is following CDC recommendations about travel. At the moment, we will continue making arrangements for our upcoming meetings as planned, and will share any changes to these plans with you. As part of the registration process, you will have the opportunity to share with us any comments or concerns you may have about traveling in relation to the current outbreak. Also note that HMI will cover the cost of travel to and from the meetings, as well as provide lodging and meals throughout. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the meetings).

Due to limited access to labs, including by SEA Staff at HHMI and at the University of Pittsburgh, shipment of biologicals to all Cohort 13 institutions are on hold. As soon as we regain access to our labs and are able to ship biologicals to you, we will check-in with you to determine if and when you are able to receive those biologicals.

If you happen to regain access to your lab before we are able to ship the biologicals to you, we recommend that you continue with the aspects of reagent prep that do not rely on these biologicals, as described in the "Reagent Prep Guide".

Due to the on-going restrictions on travel, gatherings, and regular access to labs, we write to share with you that the Phage Discovery training workshops scheduled for this June and July have now been cancelled.

As you are aware, each of the SEA-PHAGES training workshops are essential and a requirement for implementing each component of the PHAGES research project. As such, this cancellation has implications for your upcoming academic year. We are committed to working with each of you to develop a suitable plan for moving forward, and offer the two following options for you to consider:

1. Postpone your entire implementation of the PHAGES project to the 2021-2022 academic year. In this scenario, you will be included in the Phage Discovery and Phage Genomics training workshops scheduled for the summer and winter of 2021, respectively.

2. Offer a modified project in place of Phage Discovery this coming academic year, which we will work with you to develop based on your needs, preference, and access to labs. In this scenario, you will receive your Phage Genomics training in the winter of 2020, and Phage Discovery training in the summer 2021.

We would like to speak with each of you via video conference to discuss your situation and to develop a plan suited to your needs. Please use the link below to indicate dates and times you will be available to meet in April, or contact us directly at SEA@hhmi.org

Link: https://doodle.com/poll/gtz2n6dmdtgqkhrx

Date	Event/Item	Add
Oct 31, 2019	Deadline for Cohort 13 Application *	10/31/2019 10/31/2019 America/New_York Deadline for Cohort 13 Application SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_127
Dec 13 - Jan 23, 2019	Cohort 13 Application Review Notification and Acceptance *	12/13/2019 01/23/2020 America/New_York Cohort 13 Application Review Notification and Acceptance SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_128
Feb 10, 2020	Details Welcome Webinar & Q&A (recording) **	02/10/2020 12:00 PM 02/10/2020 America/New_York Welcome Webinar & Q&A (recording) This Webinar is for all faculty that are new to the Science Education Alliance. Program leadership, David Asai and Graham Hatfull, will introduce you to the educational and scientific goals of the program, and answer any questions you have about the program. Prior to attending this webinar, please watch a brief (8 min) Introductory Video: https://seaphages.org/video/51/ A recording of the webinar is now available on the program website - click this link in the timeline to view the video. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_129
Mar 1 - May 1, 2020	Procure Phage Discovery Lab Supplies **	03/01/2020 05/01/2020 America/New_York Procure Phage Discovery Lab Supplies SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_130
Mar 16, 2020	Details Identify 2020 Symposium & Phage Discovery Cohort 13 Trainees **	03/16/2020 03/16/2020 America/New_York Identify 2020 Symposium & Phage Discovery Cohort 13 Trainees Meeting Information for Cohort 13: Symposium & Faculty Meeting (June 5 - 8, 2020) Attendee: One faculty member from your institution is invited to attend the 2020 Symposium & Faculty Meeting. This meeting will be held at the National Conference Center in Ashburn, VA. Phage Discovery Workshop (June 20 - June 26, or July 11 - July 17, 2020) Attendee(s): Two faculty members from your institution, who will teach the Phage Discovery component of the SEA-PHAGES course, are invited to attend 1 of the 2 Phage Discovery workshop sessions in 2020. You may nominate and justify the attendance for a third person, typically a faculty member or support staff that will directly contribute towards the Phage Discovery component. If spaces are available, an invitation will be sent to the third person. Note that it is not essential for all participants from each school to attend the same workshop session, but it is recommended. These workshops will be held at the University of Maryland Baltimore County. Note: HHMI is monitoring the SARS-CoV-2 outbreak, and is following CDC recommendations about travel. At the moment, we will continue making arrangements for our upcoming meetings as planned, and will share any changes to these plans with you. As part of the registration process, you will have the opportunity to share with us any comments or concerns you may have about traveling in relation to the current outbreak. Also note that HMI will cover the cost of travel to and from the meetings, as well as provide lodging and meals throughout. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the meetings). SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_131
Apr 1 - May 29, 2020	Details Receive, Prepare, and Test Biologicals for Phage Discovery: ON HOLD **	04/01/2020 05/29/2020 America/New_York Receive, Prepare, and Test Biologicals for Phage Discovery: ON HOLD Due to limited access to labs, including by SEA Staff at HHMI and at the University of Pittsburgh, shipment of biologicals to all Cohort 13 institutions are on hold. As soon as we regain access to our labs and are able to ship biologicals to you, we will check-in with you to determine if and when you are able to receive those biologicals. If you happen to regain access to your lab before we are able to ship the biologicals to you, we recommend that you continue with the aspects of reagent prep that do not rely on these biologicals, as described in the "Reagent Prep Guide". SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_132
Jun 5 - Jun 8, 2020	12th SEA Symposium & Faculty Meeting: CANCELLED **	06/05/2020 06/08/2020 America/New_York 12th SEA Symposium & Faculty Meeting: CANCELLED SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_152
Jun 20 - Jun 26, 2020	Details Phage Discovery Workshop Option A: CANCELLED **	06/20/2020 06/26/2020 America/New_York Phage Discovery Workshop Option A: CANCELLED Due to the on-going restrictions on travel, gatherings, and regular access to labs, we write to share with you that the Phage Discovery training workshops scheduled for this June and July have now been cancelled. As you are aware, each of the SEA-PHAGES training workshops are essential and a requirement for implementing each component of the PHAGES research project. As such, this cancellation has implications for your upcoming academic year. We are committed to working with each of you to develop a suitable plan for moving forward, and offer the two following options for you to consider: 1. Postpone your entire implementation of the PHAGES project to the 2021-2022 academic year. In this scenario, you will be included in the Phage Discovery and Phage Genomics training workshops scheduled for the summer and winter of 2021, respectively. 2. Offer a modified project in place of Phage Discovery this coming academic year, which we will work with you to develop based on your needs, preference, and access to labs. In this scenario, you will receive your Phage Genomics training in the winter of 2020, and Phage Discovery training in the summer 2021. We would like to speak with each of you via video conference to discuss your situation and to develop a plan suited to your needs. Please use the link below to indicate dates and times you will be available to meet in April, or contact us directly at SEA@hhmi.org Link: https://doodle.com/poll/gtz2n6dmdtgqkhrx SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_135
Jul 11 - Jul 17, 2020	Details Phage Discovery Workshop Option B: CANCELLED **	07/11/2020 07/17/2020 America/New_York Phage Discovery Workshop Option B: CANCELLED Due to the on-going restrictions on travel, gatherings, and regular access to labs, we write to share with you that the Phage Discovery training workshops scheduled for this June and July have now been cancelled. As you are aware, each of the SEA-PHAGES training workshops are essential and a requirement for implementing each component of the PHAGES research project. As such, this cancellation has implications for your upcoming academic year. We are committed to working with each of you to develop a suitable plan for moving forward, and offer the two following options for you to consider: 1. Postpone your entire implementation of the PHAGES project to the 2021-2022 academic year. In this scenario, you will be included in the Phage Discovery and Phage Genomics training workshops scheduled for the summer and winter of 2021, respectively. 2. Offer a modified project in place of Phage Discovery this coming academic year, which we will work with you to develop based on your needs, preference, and access to labs. In this scenario, you will receive your Phage Genomics training in the winter of 2020, and Phage Discovery training in the summer 2021. We would like to speak with each of you via video conference to discuss your situation and to develop a plan suited to your needs. Please use the link below to indicate dates and times you will be available to meet in April, or contact us directly at SEA@hhmi.org Link: https://doodle.com/poll/gtz2n6dmdtgqkhrx SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_136
Aug 1 - Aug 31, 2020	Phage Discovery Test-Run & Report-Out **	08/01/2020 08/31/2020 America/New_York Phage Discovery Test-Run & Report-Out SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_154
Sep 1 - Oct 31, 2020	Virtual Site-Visit with SEA Team **	09/01/2020 10/31/2020 America/New_York Virtual Site-Visit with SEA Team SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_137
Sep 17, 2020	Deadline to Add Fall Section Data to seaphages.org	09/17/2020 09/17/2020 America/New_York Deadline to Add Fall Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_138
Oct 1, 2020	Identify Phage Genomics (Bioinformatics) Workshop Trainees **	10/01/2020 10/01/2020 America/New_York Identify Phage Genomics (Bioinformatics) Workshop Trainees SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_139
Nov 1 - Nov 30, 2020	Install software for Bioinformatics Workshop and Semester **	11/01/2020 11/30/2020 America/New_York Install software for Bioinformatics Workshop and Semester SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_140
Nov 3, 2020	Receive Archiving Materials from Program	11/03/2020 11/03/2020 America/New_York Receive Archiving Materials from Program SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_141
Nov 16 - Dec 15, 2020	Submit Lysates for Archiving	11/16/2020 12/15/2020 America/New_York Submit Lysates for Archiving SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_142
Nov 16, 2020	Submit DNA Samples [Semester Schools]	11/16/2020 11/16/2020 America/New_York Submit DNA Samples [Semester Schools] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_143
Dec 1 - Dec 11, 2020	Students Complete Fall Semester PITS Survey [Semester Schools]	12/01/2020 12/11/2020 America/New_York Students Complete Fall Semester PITS Survey [Semester Schools] SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_145
Dec 7 - Dec 11, 2020	Phage Genomics (Bioinformatics) Workshop **	12/07/2020 12/11/2020 America/New_York Phage Genomics (Bioinformatics) Workshop SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_144
Dec 18, 2020	Submit Genome Annotations for Quality Control [Fall Semester]	12/18/2020 12/18/2020 America/New_York Submit Genome Annotations for Quality Control [Fall Semester] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_155
Jan 11, 2021	Submit DNA Samples [Quarter Schools]	01/11/2021 01/11/2021 America/New_York Submit DNA Samples [Quarter Schools] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_146
Jan 28, 2021	Deadline to Add Spring Section Data to seaphages.org	01/28/2021 01/28/2021 America/New_York Deadline to Add Spring Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_147
Mar 16, 2021	Identify 2021 Symposium attendees	03/16/2021 03/16/2021 America/New_York Identify 2021 Symposium attendees SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_148
Apr 26, 2021	Submit Student Abstract for 2021 Symposium	04/26/2021 04/26/2021 America/New_York Submit Student Abstract for 2021 Symposium SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_149
May 3, 2021	Submit Genome Annotations for Quality Control	05/03/2021 05/03/2021 America/New_York Submit Genome Annotations for Quality Control SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_151
May 7, 2021	Students Complete Spring Semester PITS Survey [Semester Schools]	05/07/2021 05/07/2021 America/New_York Students Complete Spring Semester PITS Survey [Semester Schools] SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_150