Community Phages Get in touch

Lab protocols and resources.

Lab protocols, bioinformatics chapters, notebook guidance, glossary, and instructor materials.

Program schedule Instructor information

Lab protocols.

Bench protocols, bioinformatics chapters, glossary entries, and notebook guidance.

Community Phages banner
Community Phages Program protocols and reference material.

Resource index.

Lab protocols, bioinformatics chapters, student resources, and instructor information.

12 lab protocols 3 bioinformatics chapters 6 student resources 4 program references
01

Lab Protocols

Bench methods for samples, bacterial lawns, plaque work, lysates, DNA, and host range experiments.

  1. 1. Project introduction Program question, host strains, and phage discovery overview.
  2. 2. Pipetting exercises Practice with volumes, technique, and accuracy before plaque and titer experiments begin.
  3. 3. Basic techniques Core microbiology practices for sterile work, bacteria, media, and safe bench habits.
  4. 4. Acquiring and processing environmental samples How samples are collected, labeled, filtered, and prepared for screening.
  5. 5. Direct plating of environmental samples First-pass plaque hunting on host bacterial lawns.
  6. 6. Phage enrichment Increasing the chance of finding phages from environmental samples.
  7. 7. Phage purification Turning a plaque into a clean isolate through repeated purification.
  8. 8. Preparing high titer lysates Building enough phage stock for DNA extraction and characterization.
  9. 9. Extracting phage genomic DNA Preparing DNA from high-titer lysates for digest and sequencing work.
  10. 10. Restriction digest Checking phage DNA and comparing digest patterns.
  11. 11. Phage killing experiment Testing how phages affect bacterial growth across conditions.
  12. 12. Host range experiments Comparing which bacterial strains are sensitive or resistant to each phage.
02

Bioinformatics

Sequence assembly, BLAST, genome annotation, and the computational work behind poster figures.

  1. 1. Introduction Command line basics, sequence context, BLAST, and how phage genomes are read.
  2. 2. Assembling whole phage genomes Using sequencing data to assemble complete or near-complete phage genomes.
  3. 3. Annotating genomes Finding genes, assigning likely functions, and building interpretable genome maps.
03

Student Resources

First-day orientation, lab notebook guidance, glossary, videos, and daily reference material.

  1. Day 1 Where to arrive, what to bring, dress code, and first lab activities.
  2. Useful videos Short background videos and explainers for phage biology and lab techniques.
  3. IT instructions Computer, browser, network, and software setup notes for the program.
  4. Everyday lab checklist A daily reference for lab readiness, notebook habits, and cleanup.
  5. Lab notebook instructions How to record experiments, observations, calculations, and decisions.
  6. Lab glossary A reference for program vocabulary, techniques, and phage biology terms.
04

Instructor Information

Instructor references, schedule context, people, history, and partner material.

  1. Instructor info Instructor reference notes and weekly teaching materials.
  2. Program schedule The 8-week schedule and daily blocks.
  3. People and mentors Current team, faculty sponsors, instructors, and mentors.
  4. Program history Prior years and acknowledgments.

Instructor information.

Schedule, protocol, notebook, glossary, and poster references for instructors.

Schedule

Review the weekly plan

The 8-week outline and daily lab blocks.

During lab

Use the protocols

Use the protocol pages for pipetting, lawns, purification, titers, DNA, and bioinformatics.

Before posters

Prepare figures

Figure-making, PhagesDB context, and final presentation practice.