Laptop Setup Instructions
Instructions for setting up your laptop can be found here: Laptop Setup Instructions
Pre-Workshop Tutorials
1) UNIX Preparation tutorials: Please complete tutorials #1-3 on UNIX at http://www.ee.surrey.ac.uk/Teaching/Unix/
2) Cytoscape Preparation tutorials: Complete the introductory tutorial to Cytoscape: http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3
- Introduction to Cytoscape3 - User Interface
- Introduction to Cytoscape3 - Welcome Screen
- Filtering and Editing in Cytoscape 3
Pre-Workshop Readings
-
Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen
Logging into the Amazon cloud
Instructions can be found here.
- These instructions will ONLY be valid in the classroom and not from home. The Cloud will be set up for the class.
Day 1
Module 1: Introduction to Metagenomics and Cloud Computing
*Faculty: Robert Beiko*Lecture:
Metagenomics_2015_Module1_Lecture.pdf
Metagenomics_2015_Module1_Lecture.ppt
Metagenomics_2015_Module1_Lecture.mp4
Lab Practical:
Metagenomics Databases Lab practical
Papers:
Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice
Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics
Metabolic signatures of bacterial vaginosis
Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences
Module 2: Marker Gene-based Analysis
*Faculty: William Hsiao*Lecture:
Metagenomics_2015_Module2_Lecture.pdf
Metagenomics_2015_Module2_Lecture.ppt
Metagenomics_2015_Module2_Lecture.mp4
Lab Practical:
Marker Gene-based Lab practical
Data set:
Programs used:
Integrated Assignment - Day 1
*Faculty: Dhwani Desai and Michael Hall*Lab Practical:
Metagenomics Integrated Assignment Metagenomics IntegratedAssignment AnswerKey
Day 2
Module 3: Metagenomic Taxonomic Composition
*Faculty: Morgan Langille*Lecture:
Metagenomics_2015_Module3_Lecture.pdf
Metagenomics_2015_Module3_Lecture.ppt
Lab Practical:
Metagenomics Taxonomic Composition Lab Practical
Metagenomics Taxonomic Composition Lab Practical Answers
Data set:
- Custom dataset generated from samples from the HMP DACC
Programs used:
Module 4: Metagenomic Functional Composition
*Faculty: Morgan Langille*Lecture:
Metagenomics_2015_Module4_Lecture.pdf
Metagenomics_2015_Module4_Lecture.ppt
Metagenomics_2015_Module4_Lecture.mp4
Lab Practical:
Metagenomics Functional Composition Lab practical
Metagenomics Functional Composition Lab Answers
Data set:
- Custom dataset generated from samples from the HMP DACC
Programs used:
Bonus Module: PICRUSt
*Faculty: Morgan Langille*Lecture:
Metagenomics_2015_Bonus_PICRUSt_Lecture.pdf
Lab Practical:
Integrated Assignment - Day 2
*Faculty: Dhwani Desai and Michael Hall*Lab Practical:
Metagenomics Integrated Assignment Integrated assignment Day 2 Answer Key
Day 3
Module 5: Metatranscriptomics
*Faculty: John Parkinson*Lecture:
Metagenomics_2015_Module5_Lecture.pdf
Metagenomics_2015_Module5_Lecture.ppt
Metagenomics_2015_Module5_Lecture.mp4
Lab Practical:
Metatranscriptomics Lab practical
Module 6: Biomarker Selection
*Faculty: John Parkinson*Lecture:
Metagenomics_2015_Module6_Lecture.pdf
Metagenomics_2015_Module6_Lecture.ppt
Metagenomics_2015_Module6_Lecture.mp4
Tips, tricks, and resources
Data Sets from Entire Workshops
* Module2 Data
* Integrated Assignment - Day 1 Data
* Module3 & Module 4 Data
* Integrated Assignment - Day 2 Data
* Module 5 Data without blast database
Results from Instructor’s Instance on Amazon
* Module2 mothur result
* Module2 qiime result
* Integrated Assignment - Day 1 result
* Module3 result
* Module4 result
* Bonus Module: PICRUSt result
* Integrated Assignment - Day 2 result
* Module5 result
Tools with installation instructions on our Amazon server
Instructions for installing the tools used in the workshops can be found here.
Launching CBW AMI
Steps to launch CBW public AMI
- AMI ID: ami-b7de25dc
- AMI Name: CBW Metagenomics Workshop 2015