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
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
This pair of courses is useful to any student
considering graduate school in the biological sciences, as well as
students considering molecular medicine.
Bioinformatic Methods I
Week 1: NCBI/Blast I
Multiple Sequence Alignments
'Next Gen' Sequence Analysis (RNA-seq) /
Some knowledge of molecular biology is recommended, say a second year university introductory course on this subject.
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.
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.
- 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.