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:
BCH2021H
JTB2020H
Overview
Evaluations