The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Considerations for Implementing SEA-PHAGES in 2020 - 2021

Considerations for Implementing PHAGES in 2020 - 2021

Faculty Discussions Summary:

SEA Faculty met virtually, in groups of 5 – 10, to discuss ideas for implementing SEA-PHAGES this coming academic year, focusing on strategies for maintaining safe distancing, preparing for the possibility of being fully online, and maintaining high student engagement. Below is a summary of suggested considerations, the majority of which are written in the context of Phage Discovery, though many are also applicable for Phage Genomics.

  1. Maintaining Safe Distancing.
  2. Preparing for Reversal to Fully Online Classes.
  3. Developing Students as Scientists


1. To Maintain Safe Distancing:
This will require modifying scheduling, space, and/or enrollment.

  • Request for increased/adequate space to avoid altering scheduling and enrollment.
  • Enroll fewer students to avoid altering scheduling and space.
  • Have students attend in-person labs in shifts, to avoid changes in enrollment or space. For example, with a 2 x 3 hrs weekly setup, students can attend in-person a fraction of the time, either 1 x 3 hrs or 2 x 1.5 hrs per week. This can be facilitated by having students work in teams of 2 or 4, so that the project can progress even if a given student can only be present for half of lab meeting times.
  • All reagents placed on benches to minimize students needing to move around lab.
  • Instructor responsible for moving items to and from incubators and lab.
  • Minimize sharing, by preparing individual aliquots (bacteria, plates, buffer, top agar) and pipettes.
  • Establish decontaminating procedures for student to perform on their bench and pipettes pre and post lab.
  • Consider providing print copies of the PDG that are laminated/covered in plastic sheet at the bench so that they can be disinfected.


2. Preparing for Reversal to Fully Online Classes.

  • Start early. For example: If you have students watch videos and read protocols for sample collection and enrichment, enrichments can begin within first week.
  • Have student watch as many pre-recorded materials before attending in-person, so that time in class can be focused on mentored lab work. Overview and/or demo videos are available for all steps of Phage Discovery, and many instructional videos are also available for Phage Genomics. The videos can be found under the resources tab of this website, and many can be downdloaded for edititng from QUBES.
  • Shorten the amount of time spent on the “isolation” phase:
    • Have students enrich many samples at once,
    • Set the goal for each team to collaboratively find one phage or for the entire class to isolate enough phages for each team (i.e. promote adoption).
    • Use hosts that have higher isolation rates, such as M. smegmatis.
    • May be worthwhile having some back-up phage isolated during the summer, though only to be used if students are unable to isolate ANY phage.
  • Normalize online activities:
    Should classes be forced to return online and instructors/TAs are the only ones allowed in lab, then instructors/TAs could possibly continue Phage Discovery by being the “hands-on” person. It may therefore be worthwhile normalizing they ways in which this will have to be structured, including:
      • Instructors/TAs integrating themselves as collaborators/team members, and occasionally being the hands-on person for a team.
      • Instructors/TAs regularly providing sample data for analyses.
        *this requires a bank of sample data, which all SEA faculty can contribute to.
      • Instructor/TAs joining in on weekly virtual discussions with small groups/teams of students.
  • Run PHAGES with at least 2 instructors or 1 instructors with well-prepared TAs. The goal here is to ensure that if one instructor much self-isolate, the class may continue to meet.
  • Begin introducing students to genome annotation early in the semester, so that they can continue with genome annotation is all access to lab (including for instructors) are restricted. For example, discuss the genomic sequence of SARS-CoV2.
  • Be mindful of barriers that some students may have with regard to technology (hardware and software) and connectivity. If students cannot maintain stable connection to a video-conferencing call/webinar, it may be helpful to ensure that all video calls/webinars are recorded and made available to students. If DNAMaster cannot be reliably run by some students, they may be allowed to use PECAAN while being partnered with a student that runs DNAMaster.


Developing Students as Scientists
Given the necessary modifications to the fall semester, and possible the need to revert to online-only classes, the following strategies may facilitate maintaining high student engagement:

  • Promote Collaborations within members of a team:
    • Use online collaborative tools like Trello for team members to communicate what they’ve completed, what needs to be done, data sharing. This will allow each student to work collaboratively while also maintaining their own e-notebook (or a shared e-notebook).
    • Use online tools like CATME (Comprehensive Assessment of Team Member Effectiveness) to promote smarter teamwork.
    • to promote teamwork
    • If possible, support live-streaming via Facetime, WhatsApp, Google Hangout, etc., during lab sessions.
    • Have students rotate roles, e.g. taking turns to be the note-taker, protocol verifier, hands-on person, data analyzer.
    • Have teams meet virtually once a week to review progress and discuss strategies for the following week.
      *If possible, ask SEA-PHAGES alum to “buddy” with a team and join in their weekly meetings and/or host separate virtual office hours. This may encourage peer discussions about their data and general research expectations).
  • Promote Individual Responsibility/Ownership in a Team:
    • Give students the responsibility to prepare for their teammates by requesting reagents for the next session.
    • While each team member will participate/support all aspects of Phage Discovery, it may be helpful to have each team member serve as the lead person for particular stages of Phage Discovery (e.g. Isolation, or Purification, or DNA Extraction).
    • Each student can take turns reporting out for the team. This can be a summary to the instructor/TA, or the instructor/TA can join their weekly meeting for a short period.
    • Find ways to recognize each student throughout the semester for group progress.
  • Community Building & Maintaining Engagement
    • Entire class meets regularly for
      • Fun (e.g. Trivia, via the Kahoot app or Flipgrid)
      • Report outs by students on team progress
      • Report out by faculty about class progress
    • Connect classmates via social media (Facebook group, Instagram) and provide introductory material (e.g. Perfect Predator video assignments) before the semester starts.
  • Science Identity
    • Connect the skills they are learning to the current pandemic in a way that encourages students to speak knowledgably about with their friends and family. This can include the importance of working aseptically and the utility of wearing a mask, as well as the concept of host range and transmission from wildlife to humans.
    • Have teams of students co-develop an elevator pitch about their work.

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