Bioinformatics Tools at SHARCNET

Description: Bioinformatics is a multidisciplinary field that develops methods for turning the so-called ‘biological big data’ into knowledge. Although most problems in biology are not as embarrassingly parallelizable as the physics codes that HPC systems are usually designed for, this has been starting to change in recent years. The number of bioinformatics tools that can fully exploit HPC systems is increasing slowly but steadily because of emerging technologies like heterogeneous computing (e.g. GPUs, integrated CPUs, DSPs, FPGAs and etc.) and PGAS.

In this half-a-day session, we will talk about a few commonly used bioinformatics software packages with a focus on those that can take advantage of HPC facilities available on SHARCNET clusters. The packages are presented in two main categories: 1. genomics and 2. structural bioinformatics. Some of the topics that will be covered are efficient compression of genomic data, de novo genome/transcriptome assembly, comparative/evolutionary genomics, phylogenomics, docking and homology modeling.

Instructor: Armin Sobhani, SHARCNET, University of Ontario Institute of Technology.

Prerequisites: Basic Unix competence and basic knowledge of bioinformatics applications are required.

Course materials: