Bioinformatic Methods I

University of Toronto

Use of available (mainly web-based) programs for analyzing biological data. This is an introductory course with a strong emphasis on hands-on methods. Some theory is introduced, but the main focus is on using extant bioinformatics tools to analyze data and generate biological hypotheses.

Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful information pertaining to the system being studied. This course focuses on employing existing bioinformatic resources – mainly web-based programs and databases – to access the wealth of data to answer questions relevant to the average biologist, and is highly hands-on.

Topics covered include multiple sequence alignments, phylogenetics, gene expression data analysis, and protein interaction networks, in two separate parts.

The first part, Bioinformatic Methods I, deals with databases, Blast, multiple sequence alignments, phylogenetics, selection analysis, RNA-seq, and metagenomics.

The second part, Bioinformatic Methods II, covers motif searching, protein-protein interactions, structural bioinformatics, gene expression data analysis, and cis-element predictions.

This pair of courses is useful to any student considering graduate school in the biological sciences, as well as students considering molecular medicine.

Syllabus

Bioinformatic Methods I
Week 1: NCBI/Blast I
Week 2: Blast II/Comparative Genomics
Week 3: Multiple Sequence Alignments
Week 4: Phylogenetics  
Week 5: Selection Analysis
Week 6: 'Next Gen' Sequence Analysis (RNA-seq) / Metagenomics

Recommended Background

Some knowledge of molecular biology is recommended, say a second year university introductory course on this subject.

Suggested Readings

Suggested readings are provided at the end of each lab. Additionally, we will provide links to other lectures, e.g. those from the Toronto Bioinformatics Users Group.

Course Format

Each week's material will consist of a 20-30 minute introductory lecture covering a bit of the biological background and a bit of theory behind the tools being explored that week, followed by a lab that you perform on your own computer. Each section has in addition two quizzes, and one assignment. The assignment is not optional.

FAQ

  • Will I get a Statement of Accomplishment after completing this class?

    Yes. Students who successfully complete the class will receive a Statement of Accomplishment signed by the instructor.

  • What resources will I need for this class?

    For this course, all you need is an Internet connection, and the time to perform the labs presented here.

  • What is the coolest thing I'll learn if I take this class?

    You'll be exposed to some interesting data sets and tools for exploring biological data from the kilometer to nanometer scales.


Dates:
  • 6 January 2014, 6 weeks
Course properties:
  • Free:
  • Paid:
  • Certificate:
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  • Language: English Gb

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