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: 2016-2017 (for current schools)

Below is a timeline of important dates for the 2016-2017 academic year, with appropriate supporting links and documents.

Cohort 9 members: please click here to show dates specific to you.

Cohort 10 members should click here to view important training and preparation dates for the 2017-2018 academic year.

Date	Event/Item	Add
Nov 18, 2015	Cohort 9 Application Deadline *	11/18/2015 11/18/2015 America/New_York Cohort 9 Application Deadline SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_5
Dec 15 - Dec 31, 2015	Details Decision Letters for New Applicants Sent *	12/15/2015 12/31/2015 America/New_York Decision Letters for New Applicants Sent Schools who have applied to join the SEA-PHAGES program for the 2016-17 academic year will be sent letters informing them of their status. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_32
Jan 28, 2016	Details Orientation Webinar Option A **	01/28/2016 01/28/2016 America/New_York Orientation Webinar Option A The webinar covers the plans and expectations for your first year of implementing the SEA-PHAGES course, as well as offers some time for you to ask questions. Instructions to connect to the webinar will become available here closer to the date. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_14
Feb 2, 2016	Details Orientation Webinar Option B **	02/02/2016 02/02/2016 America/New_York Orientation Webinar Option B The webinar covers the plans and expectations for your first year of implementing the SEA-PHAGES course, as well as offers some time for you to ask questions. Instructions to connect to the webinar will become available here closer to the date. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_15
Mar 16, 2016	Details Identify 2016 Symposium, Faculty Retreat, and Phage Discovery Workshop attendees **	03/16/2016 03/16/2016 America/New_York Identify 2016 Symposium, Faculty Retreat, and Phage Discovery Workshop attendees Use the link to register for the 2016 Symposium, Faculty Retreat, and Phage Discovery Workshop. HHMI Travel Services will use this information to contact the participants and begin arranging travel. Details of events: Symposium: (June 10 - 12, 2016) Attendee: One faculty member from your institution is invited to attend the 2016 Symposium Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the symposium. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Symposium). Faculty Retreat (June 12 - 14, 2016) Attendee: One faculty member from your institution is invited to attend the 2016 Faculty Retreat. This person will preferably be the same person who attends the 2016 Symposium. Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the Faculty Meeting, held at HHMI Headquarters at Chevy Chase, MD. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Faculty Retreat). 2016 Phage Discovery Workshop (June 26 - July 1, or July 10 - July 15) 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 2016. 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 true MM/DD/YYYY seaphages_event_37
Mar 31, 2016	Details Deadline to Submit Completed MTAs **	03/31/2016 03/31/2016 America/New_York Deadline to Submit Completed MTAs As a new member of the SEA-PHAGES program, you will need to put two Material Transfer Agreements in place by this deadline. These agreements allow: • the University of Pittsburgh to share Mycobacterium smegmatis mc2155 and Mycobacteriophage D29 with you at your institution. •your institution to house and share your novel phages with the University of Pittsburgh, SEA-PHAGES community, and other researchers. Click on the link to review instructions for completing the MTA. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_16
Apr 1 - May 31, 2016	Details Order Phage Discovery Lab Supplies **	04/01/2016 05/31/2016 America/New_York Order Phage Discovery Lab Supplies The SEA Team has generated guidelines to assist you in planning and ordering supplies for the Phage Discovery component of the course. Please review the attached documents, which include the full supplies list, ordering guidelines, and HHMI-negotiated Fisher Scientific pricing that is extended to you. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_35
Jun 10 - Jun 14, 2016	Details Attend 2016 Symposium & Faculty Retreat **	06/10/2016 06/14/2016 America/New_York Attend 2016 Symposium & Faculty Retreat Details of events: Symposium: (June 10 - 12, 2016) Attendee: One faculty member from your institution is invited to attend the 2016 Symposium Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the symposium. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Symposium). Faculty Retreat (June 12 - 14, 2016) Attendee: One faculty member from your institution is invited to attend the 2016 Faculty Retreat. This person will preferably be the same person who attends the 2016 Symposium. Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the Faculty Meeting, held at HHMI Headquarters at Chevy Chase, MD. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Faculty Retreat). SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_38
Jun 26 - Jul 1, 2016	Details Phage Discovery Workshop 9A **	06/26/2016 03:00 PM 07/01/2016 01:00 PM America/New_York Phage Discovery Workshop 9A The goal of the workshop is to familiarize the schools new to the program with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_18
Jul 10 - Jul 15, 2016	Details Phage Discovery Workshop 9B **	07/10/2016 03:00 PM 07/15/2016 01:00 PM America/New_York Phage Discovery Workshop 9B The goal of the workshop is to familiarize the schools new to the program with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_19
Jul 16 - Aug 31, 2016	Details Prepare and Test Reagents for Phage Discovery **	07/16/2016 08/31/2016 America/New_York Prepare and Test Reagents for Phage Discovery The SEA Team has provided you with a Reagent Prep Guide, which includes guidelines to prepare and test your reagents and biological for the Phage Discovery component of the course. Use the link provided to review these recommendations, which include when to begin and what to test. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_20
Sep 1 - Oct 31, 2016	Details Virtual Site Visit with SEA-PHAGES Team **	09/01/2016 10/31/2016 America/New_York Virtual Site Visit with SEA-PHAGES 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. To connect, click on this event on the timeline. The link will become active closer to the date. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_2
Sep 30, 2016	Deadline to Add Fall Section Information to seaphages.org	09/30/2016 09/30/2016 America/New_York Deadline to Add Fall Section Information to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_21
Oct 1, 2016	Details Identify Trainees and Register for Bioinformatics Workshop **	10/01/2016 10/01/2016 America/New_York Identify Trainees and Register for Bioinformatics Workshop Use the link to register for the 2016 Bioinformatics Workshop. HHMI Travel Services will use this information to contact the participants and begin arranging travel. Details of events: Date: Dec 5 - 9, 2016 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 2016. 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_24
Nov 18, 2016	Details Deadline to Submit DNA Samples for Sequencing	11/18/2016 11/18/2016 America/New_York Deadline to Submit DNA Samples for Sequencing 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_1
Nov 28 - Dec 16, 2016	Details Students Complete PITS Survey for Fall 2016	11/28/2016 12/16/2016 America/New_York Students Complete PITS Survey for Fall 2016 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 false MM/DD/YYYY seaphages_event_26
Dec 5 - Dec 9, 2016	Details 2016 SEA-PHAGES Bioinformatics Workshop **	12/05/2016 03:00 PM 12/09/2016 01:00 PM America/New_York 2016 SEA-PHAGES 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_25
Dec 15, 2016	Details Archiving Samples Due to the University of Pittsburgh	12/15/2016 12/15/2016 America/New_York Archiving Samples Due to the University of Pittsburgh The University of Pittsburgh has agreed to 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 true MM/DD/YYYY seaphages_event_34
Jan 31, 2017	Deadline to Add Spring Section Information on seaphages.org	01/31/2017 01/31/2017 America/New_York Deadline to Add Spring Section Information on seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_27
Mar 16, 2017	Details Identify Participants and Register for the 2017 Symposium	03/16/2017 03/16/2017 America/New_York Identify Participants and Register for the 2017 Symposium This is the deadline to register for the 2017 SEA-PHAGES Symposium. All faculty, with the exception of Cohort 10, should use this link to identify symposium attendees. Cohort 10 faculty should use the Timeline link provided specifically for Cohort 10. This year, each institution that delivered at least one in silico/bioinformatics section of the SEA-PHAGES course is invited to bring one faculty member and two students to the Symposium. The exception is Cohort 10, who are invited to bring one faculty member to the Symposium. You can use the link within the timeline to register attendees for the symposium. HHMI Travel Services will use this information to contact the participants and begin arranging travel. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_28
Apr 17 - May 5, 2017	Details Students Complete PITS Survey for Spring 2017	04/17/2017 05/05/2017 America/New_York Students Complete PITS Survey for Spring 2017 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 false MM/DD/YYYY seaphages_event_31
May 5, 2017	Details 2017 Symposium Abstracts Due	05/05/2017 05/05/2017 America/New_York 2017 Symposium Abstracts Due This is the deadline for submitting abstracts for the 9th Annual SEA-PHAGES Symposium. WHO SHOULD SUBMIT AN ABSTRACT: Each school participating in the 2017 Symposium is expected to submit one scientific abstract about bacteriophage work accomplished by students this year. This abstract should be presented during the poster session by the students attending the symposium. One poster space will be set aside for each participating school. Each school may also submit a second abstract, to be presented by the attending faculty. Due to space restriction, a limited number of these posters will be selected for presentation at the poster session. As you submit each abstract, please indicate if you would like your abstract to be considered for a talk. Each of these abstracts will be reviewed and considered for a 12-minute talk. Note that abstracts selected to for a talk will also be expected to be presented at the poster session. ABSTRACT GUIDELINES: Abstract titles can be up to 200 characters long. Abstract body text can be up to 3,000 characters long. POSTER GUIDELINES: Note that even if your abstract is selected for a talk, you will also present a poster. The final poster dimensions must fit into an area no larger than 4’ x 4’. The poster heading should include a title, names of authors, and the name of your institution. HOW TO SUBMIT AN ABSTRACT: To submit an abstract for the meeting, you must be a verified SEA-PHAGES faculty member, and you must log in to seaphages.org. After doing so, you can use the link in this timeline to submit an abstract. Alternatively, go to your institution's page and follow the link found there: http://seaphages.org/abstracts/submit/22/ WHEN TO SUBMIT AN ABSTRACT: The abstract is due on Monday, May 5, 2017. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_33
May 15, 2017	Details Annotations for 2016-17 Due for QC	05/15/2017 05/15/2017 America/New_York Annotations for 2016-17 Due for QC Please submit your final DNA Master files, Author List, and Cover Sheet for phages sequenced and annotated during the 2016-17 school year by this date. More information on submitting annotations can be found in Chapter 12 of the Annotation Guide. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_30
Jun 9 - Jun 11, 2017	Details 9th Annual SEA-PHAGES Symposium	06/09/2017 03:00 PM 06/11/2017 01:00 PM America/New_York 9th Annual SEA-PHAGES Symposium The main end-of-year SEA-PHAGES meeting, held at Janelia Research Campus in Virginia and featuring SEA-PHAGES student talks and posters. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_36
Jun 11 - Jun 13, 2017	2017 Genome Announcement Workshop	06/11/2017 05:00 PM 06/13/2017 01:30 PM America/New_York 2017 Genome Announcement Workshop SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_67

* This item/event is for new applicants.

** This item/event is for newly accepted schools in their first year. Namely, Cohort 9 schools.

Timeline: 2017-2018 (for current and incoming schools)

Below is a timeline of important dates for the upcoming 2017-2018 academic year, with appropriate supporting links and documents.

Members of Cohort 10 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
Nov 18, 2016	Cohort 10 Application Deadline *	11/18/2016 11/18/2016 America/New_York Cohort 10 Application Deadline SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_6
Jan 26, 2017	Details Orientation Webinar Option A **	01/26/2017 01/26/2017 America/New_York Orientation Webinar Option A The webinar covers the plans and expectations for your first year of implementing the SEA-PHAGES course, as well as offers some time for you to ask questions. Instructions to connect to the webinar have been provided by email. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_39
Jan 30, 2017	Details Orientation Webinar Option B **	01/30/2017 01/30/2017 America/New_York Orientation Webinar Option B The webinar covers the plans and expectations for your first year of implementing the SEA-PHAGES course, as well as offers some time for you to ask questions. Instructions to connect to the webinar have been provided by email. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_40
Mar 16, 2017	Details Submit Completed PITS Assessment IRB Approval Letter **	03/16/2017 03/16/2017 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 16, 2017. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_41
Mar 16, 2017	Details Identify 2017 Symposium Participant & Phage Discovery Workshop Trainees: for Cohort 10 only **	03/16/2017 03/16/2017 America/New_York Identify 2017 Symposium Participant & Phage Discovery Workshop Trainees: for Cohort 10 only For Cohort 10: Use this link to register for the 2017 Symposium and Phage Discovery Workshop. HHMI Travel Services will use this information to contact the participants and begin arranging travel. Link: You may copy and paste this link into a web browser: https://www.surveymonkey.com/r/seacohort10 or you may click the active link within the timeline. Details of events: Symposium: (June 9 - 11, 2017) Attendee: One faculty member from your institution is invited to attend the 2017 Symposium Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the symposium. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Symposium). 2017 Phage Discovery Workshop (June 24 - 30, or July 8 - July 14) 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 2017. 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 true MM/DD/YYYY seaphages_event_43
Apr 1 - Jun 1, 2017	Details Order Phage Discovery Lab Supplies **	04/01/2017 06/01/2017 America/New_York Order Phage Discovery Lab Supplies The SEA Team has generated guidelines to assist you in planning and ordering supplies for the Phage Discovery component of the course. Please review the attached documents, which include the full supplies list, ordering guidelines, and HHMI-negotiated Fisher Scientific pricing that is extended to you. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_44
Jun 9 - Jun 11, 2017	Details Attend 9th SEA-PHAGES Symposium **	06/09/2017 06/11/2017 America/New_York Attend 9th SEA-PHAGES Symposium Details of events: Symposium: (June 9 - 11, 2017) Attendee: One faculty member from your institution is invited to attend the 2017 Symposium Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the symposium. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Symposium). SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_46
Jun 24 - Jun 30, 2017	Details Phage Discovery Workshop Option A **	06/24/2017 06/30/2017 America/New_York Phage Discovery Workshop Option A Details of events: 2017 Phage Discovery Workshop (June 24 - 30, or July 8 - July 14) 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 2017. 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_47
Jul 8 - Jul 14, 2017	Details Phage Discovery Workshop Option B **	07/08/2017 07/14/2017 America/New_York Phage Discovery Workshop Option B Details of events: 2017 Phage Discovery Workshop (June 24 - 30, or July 8 - July 14) 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 2017. 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_48
Jul 17 - Aug 31, 2017	Details Prepare & Test Reagents for Phage Discovery **	07/17/2017 08/31/2017 America/New_York Prepare & Test Reagents for Phage Discovery The SEA Team has provided you with a Reagent Prep Guide, which includes guidelines to prepare and test your reagents and biological for the Phage Discovery component of the course. Use the link provided to review these recommendations, which include when to begin and what to test. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_49
Jul 17 - Aug 31, 2017	Details Receive Shipment of Biologicals from Program **	07/17/2017 08/31/2017 America/New_York Receive Shipment of Biologicals from Program You will be inform of a short window of time when you can expect to receive your biologicals from the program. Instructions on how to handle these biologicals are included in "Prepare & Test Reagents for Phage Discovery" SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_50
Sep 18 - Oct 31, 2017	Details Virtual Site Visit with SEA Team **	09/18/2017 10/31/2017 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. To connect, click on this event on the timeline. The link will become active closer to the date. SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_52
Sep 29, 2017	Deadline to Add Fall Section Data to seaphages.org	09/29/2017 09/29/2017 America/New_York Deadline to Add Fall Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_51
Oct 3, 2017	Details Identify Bioinformatics Workshop Trainees **	10/03/2017 10/03/2017 America/New_York Identify Bioinformatics Workshop Trainees Once activated, use this link to register for the 2017 Bioinformatics Workshop. HHMI Travel Services will use this information to contact the participants and begin arranging travel. Details of events: Date: Dec 8 - 12, 2017 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 2017. 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_53
Nov 1, 2017	Details Receive Archival Materials from Program	11/01/2017 11/01/2017 America/New_York Receive Archival Materials from Program You will receive a request to provide the number of lysates you have prepared and will archive at the University of Pittsburgh. 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_54
Nov 1 - Dec 1, 2017	Install software for Bioinformatics Workshop and Semester **	11/01/2017 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_57
Nov 21, 2017	Details Submit DNA Samples [Semester Schools]	11/21/2017 11/21/2017 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_55
Nov 21 - Dec 15, 2017	Details Submit Lysates for Archiving	11/21/2017 12/15/2017 America/New_York Submit Lysates for Archiving The University of Pittsburgh has agreed to 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_56
Dec 8 - Dec 12, 2017	Details Bionformatics Workshop **	12/08/2017 12/12/2017 America/New_York Bionformatics 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_59
Dec 11, 2017	Details Students Complete Fall Semester PITS Survey [Semester Schools]	12/11/2017 12/11/2017 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_58
Jan 9, 2018	Details Submit DNA Samples [Quarter Schools]	01/09/2018 01/09/2018 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_60
Jan 30, 2018	Deadline to Add Spring Section Data to seaphages.org	01/30/2018 01/30/2018 America/New_York Deadline to Add Spring Section Data to seaphages.org SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_61
Mar 15, 2018	Identify 2018 Symposium attendees	03/15/2018 03/15/2018 America/New_York Identify 2018 Symposium attendees SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_62
Apr 25, 2018	Submit Student Abstract for 2017 Symposium	04/25/2018 04/25/2018 America/New_York Submit Student Abstract for 2017 Symposium SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_63
May 11, 2018	Details Students Complete Spring Semester PITS Survey [Semester Schools]	05/11/2018 05/11/2018 America/New_York Students Complete Spring 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_64
May 15, 2018	Details Submit Genome Annotations for Quality Control	05/15/2018 05/15/2018 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 2016-17 school year by this date. More information on submitting annotations can be found in Chapter 12 of the Annotation Guide. SEA-PHAGES Program info@seaphages.org true MM/DD/YYYY seaphages_event_65
Jun 8 - Jun 10, 2018	10th SEA Symposium	06/08/2018 06/10/2018 America/New_York 10th SEA Symposium SEA-PHAGES Program info@seaphages.org false MM/DD/YYYY seaphages_event_66

* This item/event is for new applicants.

** This item/event is for newly accepted schools in their first year. Namely, Cohort 10 schools.

Phage Discovery Component

Supplies, Quotes, & Ordering Information

Reagent Prep Guidelines

Course Materials

MTA Instructions

Archiving Instructions

Sequencing Instructions

Bioinformatics Component

Software Overview (Required and Add-ons)

Required Software to Install:

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
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

Course Material

Annotation Guide (updated November, 2015)
- Click Here for What's New to the Annotation Guide and Annotation Procedures for 2016-17
- Click Here for Last year's Updates to the Annotation Guide
- Click here for Revised tRNA evaluation protocol (Section 9.5). Mobyl Pasteur site is no longer available.
DNA Master
Starterator
- Click Here for UPDATED Starterator Guide
- Create a link to Starterator reports on your desktop
Phamerator
- Server Address
Video Tutorials
Submit Annotated Genomes
- Annotation Cover Sheet

* 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*

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 October 31 for the following academic year, but check the timeline above for precise dates.

Apply for 2017-18 Now

Below are links to important application materials.

Call for Applications

Application Instructions

Application Form

You can also collect application material from 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

Schools who have applied to join the SEA-PHAGES program for the 2016-17 academic year will be sent letters informing them of their status.

The webinar covers the plans and expectations for your first year of implementing the SEA-PHAGES course, as well as offers some time for you to ask questions. Instructions to connect to the webinar will become available here closer to the date.

Use the link to register for the 2016 Symposium, Faculty Retreat, and Phage Discovery Workshop.
HHMI Travel Services will use this information to contact the participants and begin arranging travel.

Details of events:

Symposium: (June 10 - 12, 2016)
Attendee: One faculty member from your institution is invited to attend the 2016 Symposium
Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the symposium. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Symposium).

Faculty Retreat (June 12 - 14, 2016)
Attendee: One faculty member from your institution is invited to attend the 2016 Faculty Retreat. This person will preferably be the same person who attends the 2016 Symposium.
Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the Faculty Meeting, held at HHMI Headquarters at Chevy Chase, MD. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Faculty Retreat).

2016 Phage Discovery Workshop (June 26 - July 1, or July 10 - July 15)
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 2016. 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).

As a new member of the SEA-PHAGES program, you will need to put two Material Transfer Agreements in place by this deadline. These agreements allow:

• the University of Pittsburgh to share Mycobacterium smegmatis mc2155 and Mycobacteriophage D29 with you at your institution.

•your institution to house and share your novel phages with the University of Pittsburgh, SEA-PHAGES community, and other researchers.

Click on the link to review instructions for completing the MTA.

The SEA Team has generated guidelines to assist you in planning and ordering supplies for the Phage Discovery component of the course. Please review the attached documents, which include the full supplies list, ordering guidelines, and HHMI-negotiated Fisher Scientific pricing that is extended to you.

Details of events:

Symposium: (June 10 - 12, 2016)
Attendee: One faculty member from your institution is invited to attend the 2016 Symposium
Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the symposium. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Symposium).

Faculty Retreat (June 12 - 14, 2016)
Attendee: One faculty member from your institution is invited to attend the 2016 Faculty Retreat. This person will preferably be the same person who attends the 2016 Symposium.
Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the Faculty Meeting, held at HHMI Headquarters at Chevy Chase, MD. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Faculty Retreat).

The goal of the workshop is to familiarize the schools new to the program with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution.

One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

The SEA Team has provided you with a Reagent Prep Guide, which includes guidelines to prepare and test your reagents and biological for the Phage Discovery component of the course. Use the link provided to review these recommendations, which include when to begin and what to test.

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.

To connect, click on this event on the timeline. The link will become active closer to the date.

Use the link to register for the 2016 Bioinformatics Workshop.
HHMI Travel Services will use this information to contact the participants and begin arranging travel.

Details of events:

Date: Dec 5 - 9, 2016

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 2016. 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).

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.

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!

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 University of Pittsburgh has agreed to 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.

This is the deadline to register for the 2017 SEA-PHAGES Symposium.
All faculty, with the exception of Cohort 10, should use this link to identify symposium attendees. Cohort 10 faculty should use the Timeline link provided specifically for Cohort 10.

This year, each institution that delivered at least one in silico/bioinformatics section of the SEA-PHAGES course is invited to bring one faculty member and two students to the Symposium. The exception is Cohort 10, who are invited to bring one faculty member to the Symposium.

You can use the link within the timeline to register attendees for the symposium. HHMI Travel Services will use this information to contact the participants and begin arranging travel.

This is the deadline for submitting abstracts for the 9th Annual SEA-PHAGES Symposium.

WHO SHOULD SUBMIT AN ABSTRACT:
Each school participating in the 2017 Symposium is expected to submit one scientific abstract about bacteriophage work accomplished by students this year. This abstract should be presented during the poster session by the students attending the symposium. One poster space will be set aside for each participating school.
Each school may also submit a second abstract, to be presented by the attending faculty. Due to space restriction, a limited number of these posters will be selected for presentation at the poster session.
As you submit each abstract, please indicate if you would like your abstract to be considered for a talk. Each of these abstracts will be reviewed and considered for a 12-minute talk. Note that abstracts selected to for a talk will also be expected to be presented at the poster session.

ABSTRACT GUIDELINES:
Abstract titles can be up to 200 characters long.
Abstract body text can be up to 3,000 characters long.

POSTER GUIDELINES:
Note that even if your abstract is selected for a talk, you will also present a poster.
The final poster dimensions must fit into an area no larger than 4’ x 4’.
The poster heading should include a title, names of authors, and the name of your institution.

HOW TO SUBMIT AN ABSTRACT:
To submit an abstract for the meeting, you must be a verified SEA-PHAGES faculty member, and you must log in to seaphages.org. After doing so, you can use the link in this timeline to submit an abstract. Alternatively, go to your institution's page and follow the link found there: http://seaphages.org/abstracts/submit/22/

WHEN TO SUBMIT AN ABSTRACT:
The abstract is due on Monday, May 5, 2017.

Please submit your final DNA Master files, Author List, and Cover Sheet for phages sequenced and annotated during the 2016-17 school year by this date. More information on submitting annotations can be found in Chapter 12 of the Annotation Guide.

The main end-of-year SEA-PHAGES meeting, held at Janelia Research Campus in Virginia and featuring SEA-PHAGES student talks and posters.

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 16, 2017.

For Cohort 10: Use this link to register for the 2017 Symposium and Phage Discovery Workshop. HHMI Travel Services will use this information to contact the participants and begin arranging travel.

Link:
You may copy and paste this link into a web browser:
https://www.surveymonkey.com/r/seacohort10
or you may click the active link within the timeline.

Details of events:

Symposium: (June 9 - 11, 2017)
Attendee: One faculty member from your institution is invited to attend the 2017 Symposium
Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the symposium. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Symposium).

2017 Phage Discovery Workshop (June 24 - 30, or July 8 - July 14)
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 2017. 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).

Details of events:

Symposium: (June 9 - 11, 2017)
Attendee: One faculty member from your institution is invited to attend the 2017 Symposium
Costs: HHMI will cover the cost of travel to and from the meeting, and provide lodging and meals throughout the symposium. Participants will be expected to cover the cost of incidentals (e.g. meals during travel, baggage fees, or lodging not required for the Symposium).

Details of events:

2017 Phage Discovery Workshop (June 24 - 30, or July 8 - July 14)
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 2017. 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).

You will be inform of a short window of time when you can expect to receive your biologicals from the program. Instructions on how to handle these biologicals are included in "Prepare & Test Reagents for Phage Discovery"

Once activated, use this link to register for the 2017 Bioinformatics Workshop.
HHMI Travel Services will use this information to contact the participants and begin arranging travel.

Details of events:

Date: Dec 8 - 12, 2017

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 2017. 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).

You will receive a request to provide the number of lysates you have prepared and will archive at the University of Pittsburgh. You will then be sent the appropriate number of cryo-tubes for archiving.