Faculty Information
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.
Members of the incoming cohort 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 | Identify 2019 Symposium attendees |
03/15/2019
03/15/2019
America/New_York
Identify 2019 Symposium attendees
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
|
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.
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 | Order Phage Discovery Lab Supplies ** |
03/01/2019
03/31/2019
America/New_York
Order Phage Discovery Lab Supplies
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 & Faculty Meeting (June 9 - 11, 2018)
Attendee: One faculty member from your institution is invited to attend the 2018 Symposium and Faculty Meeting. The symposium is scheduled for June 9 - 11 at HHMI’s Janelia Research Campus in Ashburn, VA, and a Faculty Meeting is scheduled for June 11 - 13 at HHMI’s headquarters in Chevy Chase Maryland for a smaller group of SEA faculty to attend, which will likely not include incoming faculty.
Phage Discovery Workshop (June 23 - June 29, or July 7 - July 13, 2018)
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 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 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 - 27, or July 6 - 12)
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 6 - Jul 12, 2019 |
Details
Phage Discovery Workshop Option B
**
|
07/06/2019
07/12/2019
America/New_York
Phage Discovery Workshop Option B
2019 Phage Discovery Workshop (June 22 - 27, or July 6 - 12)
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
|
Phage Discovery Component
Supplies, Quotes, & Ordering Information
Course Guides
- Phage Discovery Guide
- Phage Discovery Instructor's Guide
- [Phage Discovery & Instructor's Guide - 2017 Edition]
Other Course-related Materials
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
- 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.
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
Old Material (2017 and earlier)
- Annotation Guide (updated November, 2015)
- DNA Master
- Phamerator
- Starterator
* 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
- Suggestions to increase the diversity of the phages you're isolating*
- Restriction digest tips/tricks/modifications*
- Money-saving tips for a SEA-PHAGES course*
Advanced Experiments/Ideas
- Using DOGEMS to sequence all your genomes and find hidden gems*
- Doing RNA-Seq experiments in a SEA-PHAGES context*
- Exploring bacteriophage biology
Community Research Projects
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 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.
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).
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 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.
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.
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
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
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
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.
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 & Faculty Meeting (June 9 - 11, 2018)
Attendee: One faculty member from your institution is invited to attend the 2018 Symposium and Faculty Meeting. The symposium is scheduled for June 9 - 11 at HHMI’s Janelia Research Campus in Ashburn, VA, and a Faculty Meeting is scheduled for June 11 - 13 at HHMI’s headquarters in Chevy Chase Maryland for a smaller group of SEA faculty to attend, which will likely not include incoming faculty.
Phage Discovery Workshop (June 23 - June 29, or July 7 - July 13, 2018)
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 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 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.
Symposium & Faculty Meeting (June 9 - 11, 2018)
Attendee: One faculty member from your institution is invited to attend the 2018 Symposium and Faculty Meeting. The symposium is scheduled for June 9 - 11 at HHMI’s Janelia Research Campus in Ashburn, VA, and a Faculty Meeting is scheduled for June 11 - 13 at HHMI’s headquarters in Chevy Chase Maryland for a smaller group of SEA faculty to attend, which will likely not include incoming faculty.
Phage Discovery Workshop (June 23 - June 29, or July 7 - July 13, 2018)
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 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 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".
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 - 27, or July 6 - 12)
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).
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 - 27, or July 6 - 12)
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).
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"
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)."
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 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 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.
"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 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.