Bioinformatics for Cancer Genomics

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Course Objectives

Cancer research has rapidly embraced high throughput technologies and Cloud computing into its research. Large amounts of data are being created from various microarray, tissue array, and next generation sequencing platforms. Dedicated compute clouds such as the Cancer Genome Collaboratory [http://cancercollaboratory.org/] facilitate complex analyses on big cancer data sets from projects hosting their data in the Cloud, such as the ICGC and PCAWG. Now more than ever, having the informatic skills and knowledge of available bioinformatic resources specific to cancer and how to access and use available data sets in the Cloud is critical.

This 6-day workshop will cover the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the Cloud.

Participants will gain practical experience and skills to:

  • Visualize genomic data;
  • Analyze cancer -omic data for gene expression, genome rearrangement, somatic mutations, and copy number variation;
  • Analyze and conduct pathway analysis on the resultant cancer gene list;
  • Integrate clinical data;
  • Launch, configure, customize, and scale virtual machines (VM);
  • Navigate and work with data sets from Cloud repositories; and
  • Follow best practices in data and workflow management.

Target Audience

This workshop is intended for clinical researchers, researcher scientists, post-doctoral fellows, and graduate students with cancer genomics research projects.

Prerequisites: UNIX and R familiarity is required. Familiarity can be gained through online activities. You should be familiar with these UNIX concepts (tutorial 1-3) [http://www.ee.surrey.ac.uk/Teaching/Unix/] and these R concepts (chapters 1-5) [http://www.cyclismo.org/tutorial/R/]. A useful hands-on tool for getting started in R is Swirl [http://swirlstats.com/students.html].

You will also require your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 2GB RAM, 10GB free disk space, 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 CBW. Please contact course_info@bioinformatics.ca for more information.

Pre-work and pre-readings can be found at https://bioinformaticsdotca.github.io/bicg_2018.

Course Material