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Events/SaoPaulo2014

Universidade de São Paulo

DNA Sequence Bioinformatics Analysis with the Galaxy Platform

Instructors: Dave Clements, Robson Francisco de Souza, José Belizario

28th July - 1st August 2014
9:00-17:00

The course is hosted by the Institute of Biomedical Science at University of São Paulo (USP) and will take place at the CEFAP main auditorium.

The CEFAP in collaboration with the Brazilian Society of Immunology will host this workshop at no cost to researchers who require training in NGS data analysis. Note, catering will not be provided for the course, but the institute has one cafeteria where participants can purchase refreshments. The workshop is open to all researchers and graduate students. Admission is competitive and will be based on the strength of your application.

Each applicant is required to submit a detailed motivation outlining how the course will contribute to their current research. Preference will be given to those who have already generated data which requires further analysis.

Audience

Are you a life scientist who needs to do complex analysis on large datasets?

Galaxy is an open, web-based platform for data intensive life science research that enables non-bioinformaticians to create, run, tune, and share their own bioinformatic analyses.

This hands-on workshop will teach participants how to integrate data, and perform simple and complex analysis within Galaxy. It will also cover data visualization and visual analytics, and how to share and reuse your bioinformatic analyses, all from within Galaxy.

No programming or Linux command line experience is required.


Nuvem

Platform

Hands-on exercises will be run on the University of São Paulo's compute cloud Nuvem. The USP cloud is based on a Citrix cloud architecture.

Content

Time & Topics

Monday

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

Morning Slides, Afternoon Slides

Tuesday

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

Slides

Wednesday

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

Slides, Community Slides

Thursday

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

Slides, mt.fasta

Friday

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

Slides

Support

Institute of Biomedical Science
Universidade de São Paulo    CEFAP    Brazilian Society of Immunology    Amazon Web Services

This workshop is generously supported by Institute of Biomedical Science at University of São Paulo (USP), CEFAP, the Brazilian Society of Immunology, and an AWS in Education grant award.

Questions?

Contact Robson Francisco de Souza or Dave Clements.