• About
    • Learning Goals
  • Instructor Guide
    • Content overview
    • Sample schedule
    • What to know
    • Where to get help
    • Grades
  • 1 Introduction
    • C-MOOR Overview
    • CURE Microbial Mysteries Overview
    • 1.1 Welcome to Your Genomics Adventure
    • 1.2 Activity: Create Accounts
      • 1.2.1 Purpose
      • 1.2.2 Activity
      • 1.2.3 Grading Criteria
      • 1.2.4 Footnotes
    • 1.3 The Scientic Process
    • 1.4 Homework: Post Introductions
      • 1.4.1 Purpose
      • 1.4.2 Learning Objectives
      • 1.4.3 Introduction
      • 1.4.4 Activity 1 - Create a Topic in a Private Category
      • 1.4.5 Activity 2 - Reply to a Topic in a Public Category
      • 1.4.6 Grading Criteria
      • 1.4.7 Footnotes
  • Exploration and Discovery
  • 2 Scientific Literature
    • 2.1 Lecture: What’s in Your XYZ
    • 2.2 Prelab: Scientific Literature
      • 2.2.1 Purpose
      • 2.2.2 Learning Objectives
      • 2.2.3 Introduction
      • 2.2.4 Activity
      • 2.2.5 Grading Criteria
      • 2.2.6 Footnotes
    • 2.3 Discussion: Scientific Literature
      • 2.3.1 Activity
      • 2.3.2 Footnotes
    • 2.4 Lecture: Scientific Literature
    • 2.5 Activity: Scientific Literature
      • 2.5.1 Purpose
      • 2.5.2 Learning Objectives
      • 2.5.3 Introduction
      • 2.5.4 Part 1 - Paper Overview
      • 2.5.5 Part 2 - Methods and Figure Analysis
      • 2.5.6 Part 3 - Conclusions
      • 2.5.7 Grading Criteria
      • 2.5.8 Footnotes
    • 2.6 Presentation: Scientific Literature
      • 2.6.1 Activity
      • 2.6.2 Footnotes
  • 3 Microbial Genomes
    • 3.1 Lecture: Microbial Genome
    • 3.2 Prelab: Microbial Genomes
      • 3.2.1 Purpose
      • 3.2.2 Learning Objectives
      • 3.2.3 Activity 1 – GenBank
      • 3.2.4 Activity 2 – Genomes, Genes, and Other Databases
      • 3.2.5 Activity 3 - Taxonomy and Tree of Life
      • 3.2.6 Grading Criteria
      • 3.2.7 Footnotes
    • 3.3 Discussion: Microbial Genomes
      • 3.3.1 Activity
      • 3.3.2 Footnotes
    • 3.4 Project: Microbial Genomes
      • 3.4.1 Purpose
      • 3.4.2 Learning Objectives
      • 3.4.3 Activity 1 – MAGs and Taxonomy
      • 3.4.4 Activity 2 – Genomes, Genes, and Databases
      • 3.4.5 Activity 3 – Go Deeper
      • 3.4.6 Grading Criteria
      • 3.4.7 Footnotes
    • 3.5 Presentation: Microbial Genomes
      • 3.5.1 Activity
      • 3.5.2 Footnotes
  • Testing Ideas
  • 4 Taxonomy Profiling
    • 4.1 Activity: Taxonomy Profiling Spreadsheet
      • 4.1.1 Purpose
      • 4.1.2 Learning Objectives
      • 4.1.3 Introduction
      • 4.1.4 Activity 1 – Explore Zymo Gut Standard Metagenomic Diversity
      • 4.1.5 Activity 2 (OPTIONAL) – Compare results with the Zymo Fecal Reference
      • 4.1.6 Grading Criteria
      • 4.1.7 Footnotes
    • 4.2 Lecture: Taxonomy Profiling
    • 4.3 Prelab: Taxonomy Profiling
      • 4.3.1 Purpose
      • 4.3.2 Learning Objectives
      • 4.3.3 Introduction
      • 4.3.4 Activity 1 – Import data and QC Reads
      • 4.3.5 Activity 2 – Taxonomy Profiling
      • 4.3.6 Grading Criteria
      • 4.3.7 Footnotes
    • 4.4 Discussion: Taxonomy Profiling
      • 4.4.1 Activity
      • 4.4.2 Footnotes
    • 4.5 Project: Taxonomy Profiling
      • 4.5.1 Purpose
      • 4.5.2 Learning Objectives
      • 4.5.3 Introduction
      • 4.5.4 Activity 1 – Data import and QC
      • 4.5.5 Activity 2 – Taxonomy Profiling
      • 4.5.6 Grading Criteria
      • 4.5.7 Footnotes
    • 4.6 Presentation: Taxonomy Profiling
      • 4.6.1 Activity
      • 4.6.2 Footnotes
  • 5 Finding AMRs
    • 5.1 Lecture: Finding AMRs
    • 5.2 Prelab: Finding AMRs
      • 5.2.1 Purpose
      • 5.2.2 Learning Objectives
      • 5.2.3 Introduction
      • 5.2.4 Activity 1 – Flye assembly
      • 5.2.5 Activity 2 – Visualizing contigs
      • 5.2.6 Activity 3 – Finding AMRs
      • 5.2.7 Grading Criteria
      • 5.2.8 Footnotes
    • 5.3 Discussion: Finding AMRs
      • 5.3.1 Activity
      • 5.3.2 Footnotes
    • 5.4 Project: Finding AMRs
      • 5.4.1 Purpose
      • 5.4.2 Learning Objectives
      • 5.4.3 Introduction
      • 5.4.4 Activity 1 – Genome assembly with Flye
      • 5.4.5 Activity 2 – Contig visualization with Bandage
      • 5.4.6 Activity 3 – Finding AMRs
      • 5.4.7 Activity 4 – Bin contigs with MetaBAT2
      • 5.4.8 Activity 5 – Read about GTDB-Tk tool in Galaxy
      • 5.4.9 Grading Criteria
      • 5.4.10 Footnotes
    • 5.5 Presentation: Finding AMRs
      • 5.5.1 Activity
  • Project Work
  • 6 Kickstart Project Work
    • 6.1 Lecture: Kickstart Project Work
    • 6.2 Activity: Kickstart Project Work
      • 6.2.1 Learning Objectives
      • 6.2.2 Activity 1 - Import an SRA file into Galaxy
      • 6.2.3 Activity 2 – Taxonomically classify nanopore-soil-subset MAGs with GTDB-Tk in Galaxy
      • 6.2.4 Activity 3 – Import a long-read SRA dataset of interest for your research project
      • 6.2.5 Activity 4 – Use a new Galaxy tool that may be useful for your project
      • 6.2.6 Grading Criteria
      • 6.2.7 Footnotes
  • 7 Identifying Datasets
    • 7.1 Lecture: Possible Datasets
    • 7.2 Activity: Possible Datasets
      • 7.2.1 Activity
      • 7.2.2 Grading Criteria
      • 7.2.3 Footnotes
  • 8 Conducting Your Research
    • 8.1 Project Work Organizer
      • 8.1.1 Round Table Data & Troubleshooting
      • 8.1.2 Written Check-ins
      • 8.1.3 Advisory Meetings
      • 8.1.4 Sample Project Work Document Organizer
      • 8.1.5 Footnotes
    • 8.2 Activity: geNomad
      • 8.2.1 Purpose
      • 8.2.2 Learning Objectives
      • 8.2.3 Activity 1 – Run geNomad
      • 8.2.4 Activity 2 – Explore geNomad output in Galaxy
      • 8.2.5 Activity 3 – Examine geNomad plasmids in RStudio
      • 8.2.6 Grading Criteria
      • 8.2.7 Footnotes
    • 8.3 Activity: RStudio
      • 8.3.1 Purpose
      • 8.3.2 Learning Objectives
      • 8.3.3 Activity 1 – Import files to RStudio on SciServer
      • 8.3.4 Activity 2 – Explore files in RStudio on SciServer
      • 8.3.5 Activity 3 – Plot and modify histogram of contig lengths
      • 8.3.6 Grading Criteria
      • 8.3.7 Footnotes
  • COMMUNITY ANALYSIS AND FEEDBACK
  • 9 Scientific Posters
    • 9.1 Lecture: Scientific Posters
    • 9.2 Activity: Scientific Posters
      • 9.2.1 Activity
      • 9.2.2 Grading Criteria
      • 9.2.3 Footnotes
    • 9.3 Making Group Poster
      • 9.3.1 Preparing to make a poster
      • 9.3.2 Part 1 - Choose a Template
      • 9.3.3 Part 2 - Make an Academic Research Poster
      • 9.3.4 Part 3 - Proofread and Add Final Touches
      • 9.3.5 Part 4 - Canvas Discussion
      • 9.3.6 Grading Criteria
      • 9.3.7 Footnotes
    • 9.4 Activity - Share Your Poster
      • 9.4.1 Introduction
      • 9.4.2 Activity 2 – Present Your Poster
      • 9.4.3 Grading Criteria
      • 9.4.4 Footnotes
  • 10 Professional Development
    • 10.1 Lecture: Next Steps
    • 10.2 Activity: Next Steps
      • 10.2.1 Introduction
      • 10.2.2 Activity 1 – Complete Feedback
      • 10.2.3 Activity 2 – Research Opportunities
      • 10.2.4 Activity 3 – Explore Communities
      • 10.2.5 (Optional) Activity 4 – Share Work
      • 10.2.6 Grading Criteria
      • 10.2.7 Footnotes
    • 10.3 Science Talks
      • 10.3.1 Science Talks - Activity 1
      • 10.3.2 Science Talks - Activity 2
    • 10.4 Create your CV
  • 11 C-MOOR Scholars
    • 11.1 C-MOOR Scholars
      • 11.1.1 C-MOOR Scholars links
    • 11.2 Pursue further research
      • 11.2.1 Research opportunities at your institution
      • 11.2.2 Find a research lab to join
    • 11.3 BioDIGS
  • 12 Online Community
  • TUTORIALS
  • 13 Galaxy Tutorials
    • 13.1 A short introduction to Galaxy
      • 13.1.1 Introduction
      • 13.1.2 Activity
      • 13.1.3 Grading Criteria
      • 13.1.4 Footnotes
    • 13.2 Quality Control and Galaxy Workflows
      • 13.2.1 Introduction
      • 13.2.2 Activity 1 – Quality Control (QC)
      • 13.2.3 Activity 2 – Creating, Editing and Importing Galaxy Workflows
      • 13.2.4 Grading Criteria
      • 13.2.5 Footnotes
    • 13.3 Galaxy dataset collections
      • 13.3.1 Introduction
      • 13.3.2 Activity
      • 13.3.3 Grading Criteria
      • 13.3.4 Footnotes
  • 14 SciServer Tutorials
    • 14.1 test-driveR
      • 14.1.1 Introduction
      • 14.1.2 Activity
      • 14.1.3 Grading Criteria
      • 14.1.4 Footnotes
    • 14.2 Meet R!
      • 14.2.1 Introduction
      • 14.2.2 Activity
      • 14.2.3 Grading Criteria
      • 14.2.4 Footnotes
    • 14.3 R for Data Science 1
      • 14.3.1 Introduction
      • 14.3.2 Activity
      • 14.3.3 Grading Criteria
      • 14.3.4 Footnotes
    • 14.4 R for Data Science 2
      • 14.4.1 Introduction
      • 14.4.2 Activity
      • 14.4.3 Grading Criteria
      • 14.4.4 Footnotes
  • 15 GenAI Tutorials
    • 15.1 Prelab: GenAI for Graphical Abstracts
      • 15.1.1 Activity 1 - Google Gemini
      • 15.1.2 Activity 2 - Your Choice
      • 15.1.3 Grading Criteria
      • 15.1.4 Footnotes
    • 15.2 Project: GenAI for Graphical Abstracts
      • 15.2.1 Purpose
      • 15.2.2 Learning Objectives
      • 15.2.3 Introduction
      • 15.2.4 Activity 1 - Plan your prompt
      • 15.2.5 Activity 2 - Prepare Graphical Abstract
      • 15.2.6 Activity 3 - Reflect on your GenAI experience
      • 15.2.7 Grading Criteria
      • 15.2.8 Footnotes
  • 16 Galaxy Workflows
    • 16.1 Galaxy Workflows: Build a Workflow
      • 16.1.1 Purpose
      • 16.1.2 Learning Objectives
      • 16.1.3 Activity 1 - Create a Galaxy Workflow from scratch
      • 16.1.4 Activity 2 - Run Workflow
      • 16.1.5 Activity 3 - Modify Workflow
      • 16.1.6 Activity 4 - Share Workflow
      • 16.1.7 Grading Criteria
      • 16.1.8 Footnotes
  • About the Authors
  • APPENDIX
  • 17 Example CURE Projects
  • 18 Troubleshooting
    • Share Galaxy History
    • Galaxy Fundamentals
  • 19 Core Competencies
  • References
  • This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

    Style adapted from: rstudio4edu-book (CC-BY 2.0)

CURE: Microbial Mysteries

Chapter 17 Example CURE Projects

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