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Events/SaoPaulo2014/Includes

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Day 1

9:00

Intro to Cloud Computing and Using the Nuvem Cloud

10:20

Break

10:40

Intro to Cloud Computing and Using the Nuvem Cloud (cont.)

12:00

Lunch

2:00

Galaxy Project Introduction

2:15

Introduction to Using Galaxy

Basic examples introducing the Galaxy interface and highlighting a wide range of Galaxy's functionality.

3:20

Break

3:40

Introduction to Using Galaxy (cont.)

5:00

Finish

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Day 2

9:00

Intro to Using Galaxy (cont.)

Workflows and Sharing

9:50

Next Generation Sequencing (NGS) Data Quality Control

Options for evaluating quality, trimming data, and tradeoffs involved.

10:20

Break

10:40

Next Generation Sequencing (NGS) Data Quality Control (cont.)

12:00

Lunch

2:00

Open Discussion and Q and A

2:15

ChIP-Seq Analysis

3:20

Break

3:40

ChIP-Seq Analysis (cont.)

4:00

Genome Assembly, Concepts

5:00

Finish

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Day 3

9:00

Genome Assembly, hands on

10:40

Break

10:40

RNA-Seq Analysis Example, Part I

Read Mapping using the Tuxedo Suite of Tools

12:00

Lunch

2:00

Open Discussion and Q and A

2:15

RNA-Seq Analysis Example, Part II

Differential Expression Analysis with the Tuxedo Suite of Tools

3:20

Break

3:40

RNA-Seq Analysis Example, Part III

RNA-Seq Analysis with a different set of tools
Evaluate and discuss alternatives and selecting different approaches for different situations.

5:00

Finish

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Day 4

9:00

SNP and Variant Calling, Part I

10:20

Break

10:40

SNP and Variant Calling, Part II

12:00

Lunch

2:00

Open Discussion and Q and A

2:15

SNP and Variant Calling, Part III

3:20

Break

3:40

SNP and Variant Calling, Part IV

5:00

Finish

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Day 5

9:00

Genome Annotation Concepts

10:20

Break

10:40

Genome Annotation Concepts (cont.)

11:00

Command Line Introduction

12:00

Lunch

2:00

Genome Annotation using MAKER

3:20

Break

3:40

Genome Annotation using MAKER (cont.)

4:00

Galaxy and CloudMan on Amazon Web Services Intro and Demo

4:30

Wrapup

5:00

Finish

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