This page is not intended to be viewed directly. Rather, parts of it are included [here](/events/sao-paulo2014//).

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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