• About
    • Learning Goals
  • Instructor Guide
    • Content overview
    • Sample Schedules
    • What to know
    • Where to get help
    • Grades
  • 1 Introduction
    • 1.1 Welcome to Your Genomics Adventure
    • 1.2 Activity - Create Accounts
      • 1.2.1 Purpose
      • 1.2.2 Activity
    • 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
  • 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
    • 2.4 Lecture - Scientific Literature
    • 2.5 Project - Scientific Literature
      • 2.5.1 Purpose
      • 2.5.2 Learning Objectives
      • 2.5.3 Introduction
      • 2.5.4 Activity 1 - with group in class
      • 2.5.5 Activity 2 - with group homework
      • 2.5.6 Grading Criteria
      • 2.5.7 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 – QC Reads
      • 4.3.5 Activity 2 – Taxonomy Profiling in Galaxy
      • 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 – 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 Instructions
      • 4.6.3 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
    • 5.4 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 GTDBtk 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 an 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
  • 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 QC 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 data collections
      • 13.3.1 Introduction
      • 13.3.2 Activity
      • 13.3.3 Grading Criteria
      • 13.3.4 Footnotes
  • 14 SciServer Tutorials
    • 14.1 Meet R
      • 14.1.1 Introduction
      • 14.1.2 Activity
      • 14.1.3 Grading Criteria
      • 14.1.4 Footnotes
    • 14.2 R for Data Science 1
      • 14.2.1 Introduction
      • 14.2.2 Activity
      • 14.2.3 Grading Criteria
      • 14.2.4 Footnotes
    • 14.3 test-driveR
      • 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
  • About the Authors
  • APPENDIX
  • 15 Example CURE Projects
  • 16 Troubleshooting
    • Share Galaxy History
    • Galaxy Fundamentals
  • 17 Core Competencies
  • References
  • This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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