Introduction to Biocomputing 2015 (BIOS/BIOI/HG 606)
For details of the 2016 version of this class please see our new web site.
Overview: This hands-on boot camp introduces new graduate students to computational tools, techniques and best practices that foster reproducible research in bioinformatics, genome informatics and biostatistics.
Description: Concepts and tools covered include the Unix system, version control, data management, software compilation, task automation and cluster computing. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. Our tools of choice will be Python (for programming), Git (for version control) and PBS (for cluster resource management). However, lessons learned should be widely applicable for those looking to incorporate more productive computational approaches into their daily research work.
Audience: Students with little to no UNIX experience and no formal programming training.
Requirements: Participants must bring a laptop with specific software packages installed.
When: August 24-28, 9:00 AM - 4:00 PM
Where: 3755 SPH1 (School of Public Health building 1) Map
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Day 1. Introduction to UNIX
| Session | Time | Topics |
|---|---|---|
| I | 9:00-10:15 AM | Setup and Motivation |
| 10:15-10:30 AM | Coffee Break | |
| II | 10:30-12:00 AM | Beginning Unix |
| 12:00-1:00 PM | Lunch | |
| III | 1:00-2:15 PM | Working with Unix |
| 2:15-2:30 PM | Coffee Break | |
| IV | 2:30-4:00 PM | How to Get Working |
Day 2. Introduction to Programming
| Session | Time | Topics |
|---|---|---|
| I | 9:00-10:15 AM | Intro to Python and Programming Concepts |
| 10:15-10:30 AM | Coffee Break | |
| II | 10:30-12:00 AM | Variables, and Data Structures |
| 12:00-1:00 PM | Lunch | |
| III | 1:00-2:15 PM | Control Structures and Functions |
| 2:15-2:30 PM | Coffee Break | |
| IV | 2:30-4:00 PM | System Calls, Plotting, and iPython Notebooks |
Day 3. Data Formats and Visualization
| Session | Time | Topics |
|---|---|---|
| I | 9:00-10:15 AM | Mini-Practice : FASTQ File Manipulation |
| 10:15-10:30AM | Coffee Break | |
| II | 10:30-11:15 AM | Lecture : Data Formats and Conversions |
| III | 11:15-12:00 AM | Mini-Practice: Select a subset of variant/genotype calls |
| 12:00-1:00PM | Lunch | |
| IV | 1:00-2:15 PM | Practice : Analysis with Genomic Data Formats |
| 2:15-2:30 PM | Coffee Break | |
| V | 2:30-4:00 PM | Visualization: Overview and Practice |
Day 4. Version Control and Cluster Computing
| Session | Time | Topics |
|---|---|---|
| I | 9:00-10:15 AM | Version Control with Git |
| 10:15-10:30 AM | Coffee Break | |
| II | 10:30-12:00 AM | Collaborating with GitHub & BitBucket |
| 12:00-1:00 PM | Lunch | |
| III | 1:00-2:15 PM | Concepts in Cluster Computing |
| 2:15-2:30 PM | Coffee Break | |
| IV | 2:30-4:00 PM | Parallelization Strategies and Workflow Management |
Day 5. Unified Analytical Group Projects
| Session | Time | Topics |
|---|---|---|
| I | 9:00-10:15 AM | Introduction to eQTLs and Overview of Project |
| 10:15-10:30 AM | Coffee Break | |
| II | 10:30-12:00 AM | Obtaining, Parsing and Formatting Data |
| 12:00-1:00 PM | Lunch | |
| III | 1:00-2:15 PM | Parallel Association Testing and Visualization |
| 2:15-2:30 PM | Coffee Break | |
| IV | 2:30-4:00 PM | Group Presentations and Discussion |
Other courses
Mini course: Introduction to Python
(Sept. 14 – 21, 8:30-10 AM)
http://tinyurl.com/bioboot-1
Workshops: ARC On-campus HPC training
(Sept. 14 – Oct. 8, 1-5 PM)
http://tinyurl.com/bioboot-3
Full course: BIOINF-575 Programing Lab in Bioinformatics
(Winter term)
http://tinyurl.com/bioboot-4
Symposium: Computational Discovery in Complex System Biology
(Sept. 22, 9-5 PM)
http://tinyurl.com/bioboot-2