Supplies, Quotes, & Ordering Information

• Ordering Guide & Supplies List [updated March 2023]
• Fisher Scientific Quote [updated May 2023]

Course Guides

• Phage Discovery Guide
• Phage Discovery Guide -- beta version -- improved for user accessibilily

Other Course-related Materials

• Phage Discovery Flowchart [pdf] [tif]
• Sample 15-week schedule

MTA Instructions

Archiving Instructions

Sequencing Instructions

Software Overview (Required and Add-ons)

Required Software to Install:

• DNA Master
  Download DNA Master
  DNA Master Installation Guide (includes computer requirements)
  This program runs on Windows ONLY. If you have a Mac, you have two options:
  • Option 1 (preferred): Use Virtual Box to install a Windows virtual machine on your Mac, then install DNA Master on that Windows virtual machine.
    Download Virtual Box (you may also use other emulation software)
    Guide to Install Windows on a Mac
  • Option 2 (not recommended): Use WINE to install DNA Master directly on a Mac with no need for a Windows license.  Installing DNA Master on a Mac using WINE*

Optional software:

• The SEA-PHAGES Virtual Machine
  • The SEA VM is an Ubuntu disc image with the programs Phamerator, Starterator, Newbler, AceUtil and Consed and associated databases pre-installed. The SEA-PHAGES Virtual Machine download is a ~4.6 Gb .zip file, so downloading it will take some time. Unpacked, the file is ~12 Gb.

Download SEA-PHAGES Virtual Machine

Setting up shared folders in Virtual Box

Course Material

• SEA-PHAGES Bioinformatics Guide
• • DNA Master Gene Prediction Settings
  • How to Fix a Corrupted DNA Master file
  • How to Rearrange a Genome Annotation in DNA Master
• Video Tutorials
• Submit Annotated Genomes
  • Annotation Cover Sheet and Checklist 
  • Approved List of Phage Gene Functions
• DNA Master
  • DNA Master Info and Installation Guide
• Phamerator
  • Server Address
• Starterator
  • Click Here for UPDATED Starterator Guide
  • Create a link to Starterator reports on your desktop

* These documents were generated wholly or in part through work done at the 2016 SEA-PHAGES Faculty Retreat and Workshop.  Many thanks to the faculty members who helped craft them!

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

• The Host-Range Project | details* | forum
• The Xeno Project | details* | forum

Adding Sections at Your Institution

• What to Expect When You're Expanding: Tips from faculty who have grown their SEA-PHAGES implementations*

Microbial Resource Announcements (used to be Genome Announcements)

• We have created a resource on the SEA QUBES hub describing the process of writing an MRA. Click here to access it.

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!

• Assessment Plan
• PITS (Persistence in the Sciences) Survey Sample
• IRB Approval Letter
• IRB Protocol
• Video of SEA-PHAGES Assesment Strategy
• Assessment Presentation Slides from 2016 SEA Faculty Workshop

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.

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