Course Schedule
Schedule for June 22 to June 24, 2016
Workshop Q/A Forum
Post your workshop questions here!
Workshop Survey
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Class Picture
Laptop Setup Instructions
Instructions to setup your laptop can be found here.
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
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Introduction to Cytoscape3 - User Interface
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Introduction to Cytoscape3 - Welcome Screen
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Filtering and Editing in Cytoscape 3
Pre-workshop Readings
Before coming to the workshop, read these.
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Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen
Logging into the Amazon Cloud
Instructions can be found here.
- We have set up 31 instances on the Amazon cloud - one for each student. In order to log in to your instance, you will need a security certificate. If you plan on using Linux or Mac OS X, please download this certificate. Otherwise if you plan on using Windows (with Putty and Winscp), please download this certificate.
YouTube Playlist for Recorded Lectures
Day 1
Welcome
Ann Meyer
Module 1: Introduction to Metagenomics and Computing in the Cloud
William Hsiao
Introduction to Cloud Computing
Introduction to Data Resources Self-Guided Tour
Module 2: Marker Gene-based Analysis of Taxonomic Composition
William Hsiao
Module 3: Introduction to PICRUSt
Morgan Langille
Integrated Assignment Part 1
Thea Van Rossum and Mike Peabody
Day 2
Module 4: Metagenomic Taxonomic Composition
Morgan Langille
Module 5: Metagenomic Functional Composition
Morgan Langille
Integrated Assignment Part 2
Thea Van Rossum and Mike Peabody
Day 3
Module 6: Metatranscriptomics
John Parkinson
Module 7: Biomarker Selection
Fiona Brinkman
Data for the Workshop
Tool Installation
Instructions for installing the tools used in the workshops can be found here.
Data Sets
- hmp_metagenomics
- integrated_assignment_day1
- integrated_assignment_day2
- markergenes
- metatranscriptomics