SEA-PHAGES | Faculty Information

Faculty Information

Welcome
Timeline (current)
Timeline (next year)
Phage Discovery Component
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: 2018-2019 (for current schools)

Below is a timeline of important dates for the 2018-2019 academic year, with appropriate supporting links and documents.

Cohort 11 members: please click here to show dates specific to you.

Cohort 12 members should click here to view important training and preparation dates for the 2019-2020 academic year.

Date	Event/Item	Add
Sep 28, 2018	Deadline to Add Fall Section Data to seaphages.org	09/28/2018 09/28/2018 America/New_York Deadline to Add Fall Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_80
Oct 4, 2018	Details Identify Bioinformatics Workshop Trainees **	10/04/2018 10/04/2018 America/New_York Identify Bioinformatics Workshop Trainees Once activated, use this link to register for the 2018 Bioinformatics Workshop. HHMI Travel Services will use this information to contact the participants and begin arranging travel. Details of events: Date: Dec 10 - 14, 2018 Venue: HHMI HQ in Chevy Chase, MD Atendees: Two faculty members from your institution, who will teach the Bioinformatics component of the SEA PHAGES course, are invited to attend the Bioinformatics workshops in 2018. You may nominate and justify the attendance for a third person, typically a faculty member or support staff that will directly contribute towards the Bioinformatics component. If spaces are available, an invitation will be sent to the third person. Costs: HHMI will cover the cost of travel to and from the workshop, and provide lodging and meals throughout the workshop. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Bioinformatics Workshop). SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_81
Nov 1, 2018	Details Receive Archiving Materials from Program	11/01/2018 11/01/2018 America/New_York Receive Archiving Materials from Program Once you have entered information on phagesDB for all phage lysates to be archived, you should submit a request for archiving materials to the University of Pittsburgh. Instructions for doing so are provided in the link within the Timeline. You will then be sent the appropriate number of cryo-tubes for archiving. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_82
Nov 1 - Dec 1, 2018	Install software for Bioinformatics Workshop and Semester **	11/01/2018 12/01/2017 America/New_York Install software for Bioinformatics Workshop and Semester SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_83
Nov 15 - Dec 14, 2018	Details Submit Lysates for Archiving	11/15/2018 12/14/2018 America/New_York Submit Lysates for Archiving The University of Pittsburgh will house the archive of lysates for phages found through the SEA-PHAGES program, and to distribute samples when necessary. Please review the guidelines provided in Archiving Instructions before you begin the process to archive your institution’s phages. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_85
Nov 16, 2018	Details Submit DNA Samples [Semester Schools]	11/16/2018 11/16/2018 America/New_York Submit DNA Samples [Semester Schools] Schools should make an effort to send DNA samples to the University of Pittsburgh for sequencing by this date. This is a generalized date, and we understand that different circumstances exist (flipped semesters, quarter-system schools, contamination issues, etc.). If you cannot make this deadline, please email info@seaphages.org so that we know when to expect your DNA. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_84
Dec 10 - Dec 14, 2018	Details Bioinformatics Workshop **	12/10/2018 12/14/2018 America/New_York Bioinformatics Workshop An intensive week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics. The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_86
Dec 10, 2018	Details Students Complete Fall Semester PITS Survey [Semester Schools]	12/10/2018 12/10/2018 America/New_York Students Complete Fall Semester PITS Survey [Semester Schools] The Persistence in the Sciences (PITS) Survey is one of the major assessment tools used SEA-PHAGES-wide. As with any survey, having more respondents is incredibly valuable, as is the institution-specific output data when making the case to administrators or colleagues that this class is worthwhile. Please have as many of your students as possible complete the survey! SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_87
Jan 8, 2019	Details Submit DNA Samples [Quarter Schools]	01/08/2019 01/08/2019 America/New_York Submit DNA Samples [Quarter Schools] Schools should make an effort to send DNA samples to the University of Pittsburgh for sequencing by this date. This is a generalized date, and we understand that different circumstances exist (flipped semesters, quarter-system schools, contamination issues, etc.). If you cannot make this deadline, please email info@seaphages.org so that we know when to expect your DNA. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_88
Jan 30, 2019	Deadline to Add Spring Section Data to seaphages.org	01/30/2019 01/30/2019 America/New_York Deadline to Add Spring Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_89
Mar 15, 2019	Details Identify 2019 Symposium attendees	03/15/2019 03/15/2019 America/New_York Identify 2019 Symposium attendees Symposium (June 7 - 9, 2019) Attendee: One faculty member and one student from your institution is invited to attend the 2019 Symposium. The symposium is scheduled for June 7 - 9 at HHMI’s Janelia Research Campus in Ashburn, VA. Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the meeting. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the meetings). International members will be expected to contribute towards the costs of travel, as described in the Acceptance Letter. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_90
Apr 24, 2019	Submit Student Abstract for 2019 Symposium	04/24/2019 04/24/2019 America/New_York Submit Student Abstract for 2019 Symposium SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_91
May 10, 2019	Details Students Complete Spring Semester PITS Survey [Semester Schools]	05/10/2019 05/10/2019 America/New_York Students Complete Spring Semester PITS Survey [Semester Schools] On the 16th of April you will receive a link to the PITS survey that needs to be distributed to your students. The survey takes 15 minutes to do and allows us to assess the outcomes of the SEA-PHAGES course as a research experience. The survey should be done during the last two weeks of class. If you do not find the link in your inbox on the 16th of April please check your spam or junk mail folder. If you still cannot find it please contact David Hanauer at hanauer@pitt.edu and he will work with you to find a solution. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_92
May 15, 2019	Details Submit Genome Annotations for Quality Control	05/15/2019 05/15/2019 America/New_York Submit Genome Annotations for Quality Control Please submit your final DNA Master files, Author List, and Cover Sheet for phages sequenced and annotated during the 2018-19 school year by this date. More information on submitting annotations can be found in Bioinformatics Guide SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_93

* This item/event is for new applicants.

** This item/event is for newly accepted schools in their first year. Namely, Cohort 11 schools.

Timeline: 2019-2020 (for current and incoming schools)

Below is a timeline of important dates for the upcoming 2019-2020 academic year, with appropriate supporting links and documents.

Members of Cohort 12 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
Oct 31, 2018	Details Deadline for Cohort 12 Applications *	10/31/2018 10/31/2018 America/New_York Deadline for Cohort 12 Applications We are welcoming applications for Cohort 12 to join the SEA-PHAGES program during the 2019-20 academic year. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_113
Jan 29, 2019	Details Orientation Webinar PartII, Option A **	01/29/2019 04:00 PM 01/29/2019 America/New_York Orientation Webinar PartII, Option A A live webinar will be led by program leadership, and will cover the goals and expectations for the upcoming year, as well as offer some time for you to ask questions. The webinars are scheduled for: January 29, 2019 at 4 pm US Eastern Standard Time February 1, 2019 at 11 am US Eastern Standard Time You may attend either session. You may access the live webinars by using the following links: Join Zoom Meeting https://zoom.us/j/400423828 Dial by your location +1 646 558 8656 US (New York) +1 669 900 6833 US (San Jose) +1 647 558 0588 Canada +55 11 4680 6788 Brazil +55 21 3958 7888 Brazil Meeting ID: 400 423 828 Find your local number: https://zoom.us/u/acShQS1cuV SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_120
Feb 1, 2019	Details Orientation Webinar PartII, Option B **	02/01/2019 11:00 AM 02/01/2019 America/New_York Orientation Webinar PartII, Option B A live webinar will be led by program leadership, and will cover the goals and expectations for the upcoming year, as well as offer some time for you to ask questions. The webinars are scheduled for: January 29, 2019 at 4 pm US Eastern Standard Time February 1, 2019 at 11 am US Eastern Standard Time You may attend either session. You may access the live webinars by using the following links: Join Zoom Meeting https://zoom.us/j/400423828 Dial by your location +1 646 558 8656 US (New York) +1 669 900 6833 US (San Jose) +1 647 558 0588 Canada +55 11 4680 6788 Brazil +55 21 3958 7888 Brazil Meeting ID: 400 423 828 Find your local number: https://zoom.us/u/acShQS1cuV SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_121
Mar 1 - Mar 31, 2019	Details Order Phage Discovery Lab Supplies **	03/01/2019 03/31/2019 America/New_York Order Phage Discovery Lab Supplies To ensure that you are able to obtain all the supplies you need for the course, we encourage you to begin the ordering process as early as possible. While you will not need many of these supplies until after you have attended the summer workshops, a limited quantity for a subset of supplies (as indicated in the Supplies List; see Order by April 2019) will be needed prior to you receiving the biologicals for the program, which will be sent to you between April and May, 2019. As such, you should plan to begin purchasing supplies as soon as possible. Please carefully review the Ordering Guide before purchasing supplies, and contact info@seaphages.org if you have any questions. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_114
Mar 15, 2019	Details Submit Completed PITS Assessment IRB Approval Letter **	03/15/2019 03/15/2019 America/New_York Submit Completed PITS Assessment IRB Approval Letter Implementing the SEA-PHAGES program assessment survey (PITS Survey) at your university requires appropriate IRB approval. We currently have in place an IRB approval from the Indiana University of Pennsylvania Institutional Review Board stating that compliance by your institution can be satisfied by a simple letter from you and co-signed by your Department Head (or Dean, Vice Dean or Provost) stating that you are aware of this data collection process in the SEA-PHAGES course. To download this IRB Approval Letter, go to the Program Assessment section of the Faculty Info Page, below. You will need to print the attached letter with your institution’s letterhead, have it signed by yourself and your Department Head, then scanned and emailed back to us at info@seaphages.org, by March 15, 2019. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_115
Mar 15, 2019	Details Identify 2019 Symposium & Phage Discovery Workshop Trainees **	03/15/2019 03/15/2019 America/New_York Identify 2019 Symposium & Phage Discovery Workshop Trainees Below is information for upcoming meetings, and we encourage you to begin identifying attendees for all 3 meetings. Symposium (June 7 - 9, 2019) Attendee: One faculty member from your institution is invited to attend the 2019 Symposium. The symposium is scheduled for June 7 - 9 at HHMI’s Janelia Research Campus in Ashburn, VA. Phage Discovery Workshop (June 22 - June 28, or July 7 - July 13, 2019) 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 2019. 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. Costs: HHMI will cover the cost of travel to and from the meetings, and provide lodging and meals throughout the workshop. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Phage Discovery Workshop). International members will be expected to contribute towards the costs of travel, as described in the Acceptance Letter. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_116
Mar 15, 2019	Complete Materials Transfer Agreement **	03/15/2019 03/15/2019 America/New_York Complete Materials Transfer Agreement SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_118
Apr 1 - May 31, 2019	Details Receive, Prepare, and Test Biologicals for Phage Discovery	04/01/2019 05/31/2019 America/New_York Receive, Prepare, and Test Biologicals for Phage Discovery ** Instructions for receiving and reviving biologicals from the program will be sent to Cohort 12 primary faculty by email. You will be informed of a short window of time when you can expect to receive your biologicals from the program. Upon receiving these biologicals (bacteria and phage), you will propagate, test, and store them. Instructions on how to handle these biologicals are included in "Reagent Prep Guide". SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_119
Jun 7 - Jun 9, 2019	11th SEA Symposium **	06/07/2019 06/09/2019 America/New_York 11th SEA Symposium SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_94
Jun 22 - Jun 28, 2019	Details Phage Discovery Workshop Option A **	06/22/2019 06/28/2019 America/New_York Phage Discovery Workshop Option A 2019 Phage Discovery Workshop (June 22 - 28, or July 7 - 13) Attendee: 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 workshops in 2019. 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. Costs: HHMI will cover the cost of travel to and from the workshop, and provide lodging and meals throughout the workshop. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Phage Discovery Workshop). SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_97
Jul 7 - Jul 13, 2019	Details Phage Discovery Workshop Option B **	07/07/2019 07/13/2019 America/New_York Phage Discovery Workshop Option B 2019 Phage Discovery Workshop (June 22 - 28, or July 7 - 13) Attendee: 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 workshops in 2019. 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. Costs: HHMI will cover the cost of travel to and from the workshop, and provide lodging and meals throughout the workshop. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Phage Discovery Workshop). SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_98
Sep 1 - Oct 31, 2019	Details Virtual Site-Visit with SEA Team **	09/01/2019 10/31/2019 America/New_York Virtual Site-Visit with SEA Team "The SEA Team will arrange for a time early in your first implementation of the Phage Discovery component of the course to check-in with you, via video-conferencing. This meeting is intended to provided you with an opportunity to share your successes and challenges, and for us to learn how to best assist you. Instructions to connect will be provided by email" SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_99
Sep 28, 2019	Deadline to Add Fall Section Data to seaphages.org	09/28/2019 09/28/2019 America/New_York Deadline to Add Fall Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_100
Oct 2, 2019	Details Identify Bioinformatics Workshop Trainees **	10/02/2019 10/02/2019 America/New_York Identify Bioinformatics Workshop Trainees "Once activated, use this link to register for the 2019 Bioinformatics Workshop. HHMI Travel Services will use this information to contact the participants and begin arranging travel. Details of events: Date: Dec 9 - 13, 2019 Venue: HHMI HQ in Chevy Chase, MD Atendees: Two faculty members from your institution, who will teach the Bioinformatics component of the SEA PHAGES course, are invited to attend the Bioinformatics workshops 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 Bioinformatics component. If spaces are available, an invitation will be sent to the third person. Costs: HHMI will cover the cost of travel to and from the workshop, and provide lodging and meals throughout the workshop. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Bioinformatics Workshop)." SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_101
Nov 1 - Dec 1, 2019	Install software for Bioinformatics Workshop and Semester **	11/01/2019 12/01/2019 America/New_York Install software for Bioinformatics Workshop and Semester SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_102
Nov 1, 2019	Details Receive Archiving Materials from Program	11/01/2019 11/01/2019 America/New_York Receive Archiving Materials from Program Once you have entered information on phagesDB for all phage lysates to be archived, you should submit a request for archiving materials to the University of Pittsburgh. Instructions for doing so are provided in the link within the Timeline. You will then be sent the appropriate number of cryo-tubes for archiving. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_103
Nov 15 - Dec 14, 2019	Details Submit Lysates for Archiving	11/15/2019 12/14/2019 America/New_York Submit Lysates for Archiving The University of Pittsburgh will house the archive of lysates for phages found through the SEA-PHAGES program, and to distribute samples when necessary. Please review the guidelines provided in Archiving Instructions before you begin the process to archive your institution’s phages. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_104
Nov 15, 2019	Details Submit DNA Samples [Semester Schools]	11/15/2019 11/15/2019 America/New_York Submit DNA Samples [Semester Schools] Schools should make an effort to send DNA samples to the University of Pittsburgh for sequencing by this date. This is a generalized date, and we understand that different circumstances exist (flipped semesters, quarter-system schools, contamination issues, etc.). If you cannot make this deadline, please email info@seaphages.org so that we know when to expect your DNA. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_105
Dec 9 - Dec 13, 2019	Details Bioinformatics Workshop **	12/09/2019 12/13/2019 America/New_York Bioinformatics Workshop "An intensive week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics. The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop." SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_106
Dec 10, 2019	Details Students Complete Fall Semester PITS Survey [Semester Schools]	12/10/2019 12/10/2019 America/New_York Students Complete Fall Semester PITS Survey [Semester Schools] The Persistence in the Sciences (PITS) Survey is one of the major assessment tools used SEA-PHAGES-wide. As with any survey, having more respondents is incredibly valuable, as is the institution-specific output data when making the case to administrators or colleagues that this class is worthwhile. Please have as many of your students as possible complete the survey! SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_107
Jan 8, 2020	Details Submit DNA Samples [Quarter Schools]	01/08/2020 01/08/2020 America/New_York Submit DNA Samples [Quarter Schools] Schools should make an effort to send DNA samples to the University of Pittsburgh for sequencing by this date. This is a generalized date, and we understand that different circumstances exist (flipped semesters, quarter-system schools, contamination issues, etc.). If you cannot make this deadline, please email info@seaphages.org so that we know when to expect your DNA. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_108
Jan 31, 2020	Deadline to Add Spring Section Data to seaphages.org	01/31/2020 01/31/2020 America/New_York Deadline to Add Spring Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_124
Mar 13, 2020	Identify 2020 Symposium attendees	03/13/2020 03/13/2020 America/New_York Identify 2020 Symposium attendees SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_109
Apr 24, 2020	Submit Student Abstract for 2020 Symposium	04/24/2020 04/24/2020 America/New_York Submit Student Abstract for 2020 Symposium SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_110
May 8, 2020	Details Students Complete Spring Semester PITS Survey [Semester Schools]	05/08/2020 05/08/2020 America/New_York Students Complete Spring Semester PITS Survey [Semester Schools] "The survey takes 15 minutes to do and allows us to assess the outcomes of the SEA-PHAGES course as a research experience. The survey should be done during the last two weeks of class. Please contact David Hanauer at hanauer@pitt.edu." SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_111
May 15, 2020	Details Submit Genome Annotations for Quality Control	05/15/2020 05/15/2020 America/New_York Submit Genome Annotations for Quality Control Please submit your final DNA Master files, Author List, and Cover Sheet for phages sequenced and annotated during the 2019-20 school year by this date. More information on submitting annotations can be found in Bioinformatics Guide. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_112
Jun 5 - Jun 7, 2020	12th SEA Symposium	06/05/2020 06/07/2020 America/New_York 12th SEA Symposium SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_122

* This item/event is for new applicants.

** This item/event is for newly accepted schools in their first year. Namely, Cohort 12 schools.

Phage Discovery Component

Supplies, Quotes, & Ordering Information

Reagent Prep Guidelines

Course Guides

Other Course-related Materials

MTA Instructions

Archiving Instructions

Sequencing Instructions

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 three options:
- Option 1: Obtain a Windows Virtual Machine (and license) from your home institution. Install the Windows Virtual Machine into Virtual Box, and then install the free program DNA Master.
  Download Virtual Box (you may also use other emulation software)
- Option 2: 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 3 (beta): You can add DNA Master into the SEA-PHAGES Virtual Machine.
  Instructions to Install DNA Master on the SEA-PHAGES VM

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 (https://seaphagesbioinformatics.helpdocsonline.com)
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

Once activated, use this link to register for the 2018 Bioinformatics Workshop.
HHMI Travel Services will use this information to contact the participants and begin arranging travel.

Details of events:

Date: Dec 10 - 14, 2018

Venue: HHMI HQ in Chevy Chase, MD

Atendees: Two faculty members from your institution, who will teach the Bioinformatics component of the SEA PHAGES course, are invited to attend the Bioinformatics workshops in 2018. You may nominate and justify the attendance for a third person, typically a faculty member or support staff that will directly contribute towards the Bioinformatics component. If spaces are available, an invitation will be sent to the third person.

Costs: HHMI will cover the cost of travel to and from the workshop, and provide lodging and meals throughout the workshop. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Bioinformatics Workshop).

Once you have entered information on phagesDB for all phage lysates to be archived, you should submit a request for archiving materials to the University of Pittsburgh. Instructions for doing so are provided in the link within the Timeline. You will then be sent the appropriate number of cryo-tubes for archiving.

The University of Pittsburgh will house the archive of lysates for phages found through the SEA-PHAGES program, and to distribute samples when necessary. Please review the guidelines provided in Archiving Instructions before you begin the process to archive your institution’s phages.

Schools should make an effort to send DNA samples to the University of Pittsburgh for sequencing by this date. This is a generalized date, and we understand that different circumstances exist (flipped semesters, quarter-system schools, contamination issues, etc.). If you cannot make this deadline, please email info@seaphages.org so that we know when to expect your DNA.

An intensive week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics.

The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop.

The Persistence in the Sciences (PITS) Survey is one of the major assessment tools used SEA-PHAGES-wide. As with any survey, having more respondents is incredibly valuable, as is the institution-specific output data when making the case to administrators or colleagues that this class is worthwhile. Please have as many of your students as possible complete the survey!

Symposium (June 7 - 9, 2019)
Attendee: One faculty member and one student from your institution is invited to attend the 2019 Symposium. The symposium is scheduled for June 7 - 9 at HHMI’s Janelia Research Campus in Ashburn, VA.

Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the meeting. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the meetings). International members will be expected to contribute towards the costs of travel, as described in the Acceptance Letter.

On the 16th of April you will receive a link to the PITS survey that needs to be distributed to your students. The survey takes 15 minutes to do and allows us to assess the outcomes of the SEA-PHAGES course as a research experience. The survey should be done during the last two weeks of class.

If you do not find the link in your inbox on the 16th of April please check your spam or junk mail folder. If you still cannot find it please contact David Hanauer at hanauer@pitt.edu and he will work with you to find a solution.

Please submit your final DNA Master files, Author List, and Cover Sheet for phages sequenced and annotated during the 2018-19 school year by this date. More information on submitting annotations can be found in Bioinformatics Guide

We are welcoming applications for Cohort 12 to join the SEA-PHAGES program during the 2019-20 academic year.

A live webinar will be led by program leadership, and will cover the goals and expectations for the upcoming year, as well as offer some time for you to ask questions. The webinars are scheduled for:
January 29, 2019 at 4 pm US Eastern Standard Time
February 1, 2019 at 11 am US Eastern Standard Time

You may attend either session.

You may access the live webinars by using the following links:

Join Zoom Meeting
https://zoom.us/j/400423828

Dial by your location
+1 646 558 8656 US (New York)
+1 669 900 6833 US (San Jose)
+1 647 558 0588 Canada
+55 11 4680 6788 Brazil
+55 21 3958 7888 Brazil
Meeting ID: 400 423 828
Find your local number: https://zoom.us/u/acShQS1cuV

To ensure that you are able to obtain all the supplies you need for the course, we encourage you to begin the ordering process as early as possible. While you will not need many of these supplies until after you have attended the summer workshops, a limited quantity for a subset of supplies (as indicated in the Supplies List; see Order by April 2019) will be needed prior to you receiving the biologicals for the program, which will be sent to you between April and May, 2019. As such, you should plan to begin purchasing supplies as soon as possible. Please carefully review the Ordering Guide before purchasing supplies, and contact info@seaphages.org if you have any questions.

Implementing the SEA-PHAGES program assessment survey (PITS Survey) at your university requires appropriate IRB approval. We currently have in place an IRB approval from the Indiana University of Pennsylvania Institutional Review Board stating that compliance by your institution can be satisfied by a simple letter from you and co-signed by your Department Head (or Dean, Vice Dean or Provost) stating that you are aware of this data collection process in the SEA-PHAGES course.
To download this IRB Approval Letter, go to the Program Assessment section of the Faculty Info Page, below.
You will need to print the attached letter with your institution’s letterhead, have it signed by yourself and your Department Head, then scanned and emailed back to us at info@seaphages.org, by March 15, 2019.

Below is information for upcoming meetings, and we encourage you to begin identifying attendees for all 3 meetings.

Symposium (June 7 - 9, 2019)
Attendee: One faculty member from your institution is invited to attend the 2019 Symposium. The symposium is scheduled for June 7 - 9 at HHMI’s Janelia Research Campus in Ashburn, VA.

Phage Discovery Workshop (June 22 - June 28, or July 7 - July 13, 2019)
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 2019. 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.

Costs: HHMI will cover the cost of travel to and from the meetings, and provide lodging and meals throughout the workshop. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Phage Discovery Workshop). International members will be expected to contribute towards the costs of travel, as described in the Acceptance Letter.

Instructions for receiving and reviving biologicals from the program will be sent to Cohort 12 primary faculty by email.
You will be informed of a short window of time when you can expect to receive your biologicals from the program. Upon receiving these biologicals (bacteria and phage), you will propagate, test, and store them. Instructions on how to handle these biologicals are included in "Reagent Prep Guide".

2019 Phage Discovery Workshop (June 22 - 28, or July 7 - 13)
Attendee: 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 workshops in 2019. 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.
Costs: HHMI will cover the cost of travel to and from the workshop, and provide lodging and meals throughout the workshop. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Phage Discovery Workshop).

"The SEA Team will arrange for a time early in your first implementation of the Phage Discovery component of the course to check-in with you, via video-conferencing. This meeting is intended to provided you with an opportunity to share your successes and challenges, and for us to learn how to best assist you.

Instructions to connect will be provided by email"

"Once activated, use this link to register for the 2019 Bioinformatics Workshop.
HHMI Travel Services will use this information to contact the participants and begin arranging travel.
Details of events:
Date: Dec 9 - 13, 2019
Venue: HHMI HQ in Chevy Chase, MD
Atendees: Two faculty members from your institution, who will teach the Bioinformatics component of the SEA PHAGES course, are invited to attend the Bioinformatics workshops 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 Bioinformatics component. If spaces are available, an invitation will be sent to the third person.
Costs: HHMI will cover the cost of travel to and from the workshop, and provide lodging and meals throughout the workshop. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Bioinformatics Workshop)."

"An intensive week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics.
The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop."

"The survey takes 15 minutes to do and allows us to assess the outcomes of the SEA-PHAGES course as a research experience. The survey should be done during the last two weeks of class.
Please contact David Hanauer at hanauer@pitt.edu."

Please submit your final DNA Master files, Author List, and Cover Sheet for phages sequenced and annotated during the 2019-20 school year by this date. More information on submitting annotations can be found in Bioinformatics Guide.