• sequencing technologies

• read quality assessment & improvement

• genome assembly

• variant discovery

• RNA-Seq analysis

• experiment design

• data visualization

• bioinformatics IT issues

• cloud computing mini-bootcamp

The course includes a rich collection of lectures and hands-on sessions, including guest speakers from industry and academia. All hands-on exercises will use the Galaxy platform (http://usegalaxy.org), and we will focus on Illumina and PacBio read data. Exercises will offer the chance to explore software and protocols for handling next-generation data analysis. There are no prerequisites other than familiarity with (and excitement for) general biological concepts. We will not spend time on programming concepts or command line training, but can provide pointers to those who desire experience in those fields. Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

Course seating is limited to 35 students in order to foster an effective learning environment and ensure sufficient one-on-one attention. Course tuition is $1,500 for academic or non-profit participants / $1,800 for other participants.

Register

Also, in an attempt to serve the Sacramento based UC Davis community, we are going to hold additional bootcamps on the UC Davis Medical Center campus in Sacramento during 3 Fridays in May (10th,24th, and 31st).  Enrollment for the May bootcamps will be capped at 35 participants.  Enrollment for June (Davis) bootcamps will be limited to 18 participants, and only 10 for Cloud Computing.

Participants can choose to mix and match dates and locations if they like. The following courses will be offered:

• Next Generation Sequencing Technology Fundamentals & Applications (May 10 or June 18, 2013)
• Introduction to Galaxy (May 24 or June 19, 2013)
• Introduction to RNAseq (May 31 or June 20, 2013)
• Cloud Computing for Bioinformatics (June 21, 2013)

Pricing

The cost for each Boot Camp is $200 (academic) or $250 (non-academic). There is an additional discount of $25 per day if registering for more than one day (e.g. Academic for: 1 day=$200, 2 days=$350, 3 days=$525, 4 days=$700. Non-academic for: 1 day=$250, 2 days=$450, 3 days=$675, 4 days=$900).

Questions

If you have any questions, please don’t hesitate to contact us:
Core email: ucdbio@gmail.com
Core main telephone line: 530-752-2698

***Registration is full***

Bootcamp Description

Next generation sequencing (NGS) technologies allow laboratories to do genome-wide research that was previously only possible at large genome centers. This bootcamp teaches key concepts and applications of major sequencing technologies (Illumina, 454, SOLiD, Ion Torrent & PacBio) including technology basics, technology-specific error modes, experiment design considerations, common data analysis workflows (like RNA-Seq, genome assembly, ChIP-Seq, SNP- and other variant discovery, etc.) and associated IT concerns. Completion of this bootcamp will prepare you for application-specific bootcamps like RNA-Seq Data Analysis.

Who Should Attend

• Principal investigators
• Lab managers and technicians
• Biology oriented project scientists and postdocs
• Students

Dates/Locations

NGS Fundamentals will be offered on 2 separate dates at 2 separate locations:

• May 10 - 2921 Stockton Blvd, Sacramento, CA
• June 18 – UC Davis campus

Bootcamp Description

Galaxy is a web-based front-end to a suite of bioinformatics software and tools that is completely open and free.  It gives you the ability to do accessible, reproducible, and transparent computational biology research.  In this bootcamp we will teach you the fundamentals of navigating the Galaxy interface as well as applications to bioinformatics problems.  We will give you the tools and experience necessary to start using Galaxy for your own research and projects.  If you would like to be able to use the wealth of free bioinformatics tools available, but do not have the time to learn the Unix command line, then this is the bootcamp for you!

Who Should Attend

• Graduate students
• Biology oriented project scientists and postdocs
• Undergrads

How You’ll Benefit From This Bootcamp

• Get a basic understanding of how to use Galaxy
• Learn how to analyze data from NGS technology experiments using Galaxy
• Learn how to leverage free software to do RNA-Seq Data Analysis, Genome Assembly, etc.
• Learn how to create workflows, enabling reproducible science

Bootcamp Topics

• Galaxy Fundamentals
• Importing and grooming your data
• Quality Assurance and Improvement
• NGS Data Analysis
• Workflows

Dates/Locations

Introduction to Galaxy will be offered on 2 separate dates at 2 separate locations:

• May 24 - 2921 Stockton Blvd, Sacramento, CA
• June 19 – UC Davis campus

Bootcamp Description

RNA-seq has emerged as a standard tool to study transcriptomes through massively parallel sequencing. The ability to generate millions of cDNA sequences makes it possible to study novel organisms as well as model organisms with unprecedented sensitivity and reproducibility. In this bootcamp, we will introduce the basic concepts of RNA-Seq and illustrate data analysis workflows through lectures and hands-on activities, including best practices for quality control, read alignment, and expression analysis. Other topics will include experimental design and basic statistical analysis of unreplicated and replicated biological sample data, alignment browsers and high performance computing techniques for dealing with transcriptomic data. Participants will spend most of their time using the Galaxy platform to work through the most common RNA-Seq data analysis workflows.

Prerequisites

Prior experience with next generation sequences, or our Next Generation Sequencing Technology Fundamentals & Applications bootcamp, is highly recommended. It is also recommended that students have some prior experience with Galaxy, or have taken our Introduction to Galaxy bootcamp.

Dates/Locations

Introduction to Galaxy will be offered on 2 separate dates at 2 separate locations:

• May 31 - 2921 Stockton Blvd, Sacramento, CA
• June 20 – UC Davis campus

Bootcamp Description

The Cloud Computing for Bioinformatics Bootcamp will be held June 21, 2013. The course will cover the basics of cloud computing with a focus on Amazon Web Services (AWS) including account signup, overview of services offered focusing on those key to bioinformatics, identity and security, creation and customization of machine images, data movement and processing, monitoring, and more. The cloud computing bootcamp is specifically designed for researchers in small and medium-sized labs who need to leverage IT resources for data analysis as well as bioinformaticians looking to leverage the quick turnaround time cloud services offer.

This bootcamp is ideal for both novices to cloud computing as well as experienced bioinformaticians. Class size will be limited to ensure a fully immersive hands-on experience as well as access to instructors.

Who Should Attend

• Undergrads, Grad students, Post-docs, and PIs that want to use powerful computing resources but don’t have access locally
• Bioinformaticians that don’t want to deal with the overhead of having local computing infrastructure
• Researchers that have some local access, but need more computing power

Dates/Locations

• June 21 – UC Davis campus

Introduction to Services.pdf

Launching Into the Cloud.pdf

Anatomy of a Cloud Computer.pdf

Saving, Sharing, & Public Data Sets.pdf

Mounting Drives.pdf