Locked History Actions

Events/GCC2013/TrainingDay/Includes

This page is not meant to be viewed on its own. Rather, it contains sections that are displayed on the GCC2013 Training Day page

SCHEDULE

Time

CAML Rm 3348

C Rm 3347

Logo Rm 2438

Python Rm 2269

Prolog Rm 2465

8:00

Registration Opens and Catered Breakfast

9:00

Galaxy Code and Storage Architecture

 

Statistical Genome Analysis with Galaxy

Installing and Maintaining a Local Galaxy Server

Introduction to Galaxy and the Galaxy Ecosystem

Running Galaxy on the Cloud

11:00

Catered Lunch 

12:30

The Galaxy API

Introduction to Tool and Data Source Configuration

RNA-Seq Analysis with Galaxy

Statistical Genome Analysis with Galaxy

 

Running Galaxy on the Cloud

14:30

Break

15:00

Advanced Tool and Data Source Configuration

Galaxy Tool Shed

 

Variant and SNP Analysis with Galaxy

 

RNA-Seq Analysis with Galaxy

ChIP-Seq Analysis with Galaxy

17:00

Finish

Key:  

General

Biologist centric

Developer & Deployer centric

END_INCLUDE


Prerequisite Includes

LAPTOP

  • A wi-fi enabled laptop. 

END_INCLUDE

WEB BROWSER

  • A modern web browser.  Google Chrome, Firefox and Safari will work best. 

END_INCLUDE

VM_PLAYER

END_INCLUDE

VM

END_INCLUDE

VM_BASIC

END_INCLUDE

VM_ADVANCED

END_INCLUDE

SSH

END_INCLUDE

NOVICE

  • Little or no knowledge of Galaxy. 

END_INCLUDE

UNIX KNOWLEDGE

  • Knowledge and comfort with the Unix/Linux command line interface and a text editor. If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.

END_INCLUDE

INTRO

END_INCLUDE

QC

END_INCLUDE

ROOT ACCESS

  • Root access to a Galaxy server: your own, or a conference provided virtual machine image or cloud image (recommended, details to come).

END_INCLUDE

ADMIN ACCESS

  • Root access to a Galaxy server: your own, or a conference provided virtual machine image or cloud image (recommended, details to come).

END_INCLUDE

TOOL TO WRAP

  • A "simple" executable tool you would like to wrap that takes and/or creates existing Galaxy datatypes like bed/fastq/bam etc such as one of the bedTools executables.

END_INCLUDE

TOOL BASICS

END_INCLUDE

SCRIPTING

  • Knowledge of a programming or scripting language.

END_INCLUDE

PACKAGE MANAGEMENT

  • Basic Linux package management administration (yum / apt-get)

END_INCLUDE

POSTGRES

END_INCLUDE

TEXT EDITOR

  • Knowledge of a simple Text Editor (vi, pico, nano).

END_INCLUDE


Results

TOOL SHED

  1. Starting up your own local tool shed as well as your own local Galaxy instance.  You will be interacting between these 2 applications throughout this workshop.
  2. Creating new repositories in your tool shed, and uploading various Galaxy utilities to them.
  3. Discovering how relationships are built between repositories and repository contents in the tool shed using tool dependency and simple and complex repository dependency definitions. 
  4. Installing repositories that contain each category of Galaxy utilities from the tool shed into your Galaxy instance and understanding the installation behavior of each of the utilities.
  5. Deactivating and reactivating repositories installed into Galaxy and understanding the behavior of the various Galaxy utilities contained in the repositories.
  6. Uninstalling and reinstalling  repositories installed into Galaxy and understanding the behavior of the various Galaxy utilities contained in the repositories.
  7. Building new Galaxy flavors using the tool shed.

END_INCLUDE

RNA-SEQ

  1. Reads to Results analysis of transcript level differences between two conditions

  2. Visualization of the results in Galaxy’s Trackster

END_INCLUDE

CHIP-SEQ OUTCOMES

  1. Quality control of the ChIP experiment
  2. Peak calling and annotation
  3. Identification of transcription factors binding sites
  4. Identification of histone modification

END_INCLUDE


AWS SUPPORT

 Amazon Web Services 
This workshop uses AWS-based compute infrastructure END_INCLUDE

VIRTUAL BOX

Virtual Machine Images
This workshop will require that you have the VirtualBox player (or VMware player) installed on your laptop. END_INCLUDE