High-Throughput Biology: From Sequence to Networks

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Course Objectives

With the introduction of next generation sequencing platforms, it is becoming feasible to consider sequencing approaches to address many research projects. Now more than ever, having knowledge of the available bioinformatic resources and the informatic skills to analyze such data is critical.

The Canadian Bioinformatics Workshops, in collaboration with Cold Spring Harbor Laboratory, has developed a comprehensive 7-day course covering the key bioinformatics concepts and tools required to analyze DNA- and RNA-sequence reads using a reference genome. Participants will gain experience in cloud computing and data visualization tools, which will be applied throughout the course. Beginning with an understanding of the workflow involved to move from platform images to sequence generation, participants will gain practical experience and skills to be able to evaluate sequence read quality, map reads to a reference and analyze sequence reads for variation and expression level. The workshop will conclude with analyzing and conducting pathway and network analysis on the resultant ‘gene’ list. The tutorials are designed as self-contained units that include example data (e.g. Illumina paired-end data) and detailed instructions for installation of all required bioinformatics tools.

Prerequisites for attendance:

Basic familiarity with Linux environment and S, R, or Matlab. Must be able to complete and understand the following simple Linux and R tutorials before attending:

You will also require your own laptop computer with wireless internet capability Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements). If you do not have access to your own computer, you may loan one from the CSHL. Please contact CSHL in advance to request a laptop.”

Course Material