BCH2021H
BCH2020L
BCH2022L
BCH2024H
BCH2029H
JBB2025H
JBB2026H
JTB2010H
JTB2020H

BCH 1371H
BCH 1422H
BCH 1426H
BCH 1440H
BCH 1441H
BCH 1471Y

JBB1425H
JBL1507H
JNP1017H
JNR1444Y
JTB2020H
Applied Bioinformatics


Overview
Evaluations
Course Outline

A course for the fulfilment of program requirements of the Collaborative Program in Genome Biology and Bioinformatics.

It can be argued that all of post-genomic life-science requires a bioinformatics component. Most of us use some Web-based resources to that end. But the Web-based paradigm of bioinformatics is not well suited

  • to support multiple queries based on lists of genes,
  • to rerun queries at specific times, as databases grow
  • to integrate information from various sources
  • and to integrate results into the workflow of wet-lab scientific inquiry.
This is increasingly becoming a limiting factor in the lab. Fortunately modern scripting languages such as Perl, on UNIX based computers have matured to a point where it is reasonable for wet-lab scientist to acquire the fundamentals of constructing their own, integrated processes and build on these as their requirements change.

JTB2020 is designed to do just that. It is offered within the academic program of The Collaborative Graduate Program in Genome Biology and Bioinformatics and satisfies a part of the program's requirements. Significant computer and programming skills are not a course requirement, rather the course aims to teach and train the necessary fundamentals. A basic understanding of bioinformatics concepts, databases and procedures is a prerequisite; JTB2020 is not an overview course but intended to help applying bioinformatics concepts to our students' own research. Our students will learn what are appropriate objectives for the bioinformatics components of their projects, what strategies can be applied, what they can realistically achieve by themselves, for what they will need help and how to go about getting it.

In this course, we will analyse the re-implementation of a complex bioinformatics procedure for the functional annotation of genes through data integration. We will define a useful platform though which to implement the procedure or a part thereof. Then we will design an implementation and prototype it.

The detailed topics will depend on the needs and interests of the participants, a rough guide is following list:

  • UNIX commands and shell scripts
  • Perl and CGI
  • Wiki concepts, collaboration, process modeling
  • HTML and PHP
  • MySQL
  • UCSC, GBrowse, DAS, Ensembl, data integration
  • BioPerl, ontologies and synonyms
  • R
  • Classification, dimensionality reduction
  • Clustering
  • [...]

For detailed information, please visit the Course Wiki.

Coordinator
Professor B. Steipe
Informational Protein Folding
Medical Sciences Building, Room 5368
416-946-7741 boris.steipe@utoronto.ca


Prerequisites
An introductory level 4th year undergraduate or graduate course in bioinformatics or computational biology is a course prerequisite. The following courses can be applied towards this requirement:

BCH441H Bioinformatics
BIO472H1 / JBZ 1473H Computational Genomics and Bioinformatics
MBP1011H Foundations of Bioinformatics

Other courses or prior experience can be approved by the course coordinator.

 

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