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Faculty Information

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

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).

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)."

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 one day annotation Hack-a-Thons are to remind SEA-PHAGES faculty of the basic resources and tasks that are needed to annotate a phage genome so that they can refresh their skills. There will be a series of hack-a-thons during this period, with each hack-a-thon agenda focused on the needs of attending faculty.

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!

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.

We are looking forward to seeing you at the upcoming SEA Symposium and Faculty Meeting, and we are excited to welcome all of the students that will participate this year. Please find additional details about the upcoming meetings in the following message, and keep in mind that the pre-registration deadline is March 16, 2020.


1. Location
Our SEA community has grown so much that the HHMI Conference Center at the Janelia Research Campus is no longer able to accommodate our symposium. We’re excited to announce that we’ve found a new venue, the National Conference Center, which happens to be just a short distance away from Janelia and with a much greater capacity so that we can continue to gather with representatives from each member institution.

2. Duration
The symposium will continue to be held June 5 - 7, 2020. When students leave the symposium in the afternoon of June 7th, we will begin our faculty meeting at the same venue, for 1 day, from June 7th - 8th. Given the duration and timing of these two meetings, we are requesting that the same faculty member(s) represents each institution at both the Symposium and Faculty Meeting.

3. Participants: We will invite one faculty member and one student from each institution that is offering the full PHAGES sequence to attend the symposium. With the GENES project now underway, we will also invite one faculty member and one student participating in the GENES project to share their discoveries at the symposium. There will also be room for a faculty member from each school that may be on a break but who intend to contribute again in the near future. In mid-March, once all schools have registered for the meeting and we have a head-count, we anticipate being able to invite additional students, particularly from schools that are selected to present a talk. HHMI will continue to cover the cost of travel to and from the meetings, and provide lodging and meals throughout the meetings. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the meeting).

Important notes:

i. HHMI is monitoring the SARS-CoV-2 outbreak, and is currently following CDC recommendations about travel. At the moment, we will continue making arrangements for our upcoming meetings as planned, and will notify you should these plans change. 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.

ii. Final details of the agenda are being developed, and we hope to include sessions for many, if not all, of the Faculty Meeting topics you have suggested on the seaphages.org forum. Please keep sharing your ideas and feedback.

iii. Guests should expect to arrive at the Symposium by 3:00 PM EDT on Friday, June 5. The meeting will end for students by 1:00 PM EDT on Sunday, June 7, and for faculty by 3:00 PM on Monday, June 8.

iv. Each school with a student participating in the Symposium will be expected to submit an abstract that represents the work the students have done. Schools offering both the PHAGES and GENES projects can submit one or two poster abstracts. The deadline for abstract submission is April 24, 2020. Information about abstract collection will be provided closer to the time of the submission deadline.

"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.

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

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