Introduction to Biocomputing 2019 (BIOS/BIOI/HG 606)
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), R (for data analysis), 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 installed.
When: August 19-23 (2019), 9:00 AM - 4:00 PM
Where: 3755 SPH1 (School of Public Health building 1) Map
N.B. Please help us improve this course by completing this pre-course questionnaire. Upon completion please complete our post-course evaluation.
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 with Python
| Session | Time | Topics |
|---|---|---|
| I | 9:00-10:15 AM | Intro to Python and Programming Concepts |
| ☕ | 10:15-10:30AM | Coffee Break |
| II | 10:30-12:00 AM | Variables, Data Structures, and I/O |
| 🍽 | 12:00-1:00PM | Lunch |
| III | 1:00-2:15 PM | Numpy, Control Structures and Functions |
| ☕ | 2:15-2:30 PM | Coffee Break |
| IV | 2:30-4:00 PM | Pandas, System Calls and Plotting |
Day 3. Data Analysis and Graphics with R
| Session | Time | Topics |
|---|---|---|
| I | 9:00-10:15 AM | Introduction to R |
| 10:15-10:30AM | Coffee Break | |
| II | 10:30-12:00 AM | R Control Structures and Functions |
| 12:00-1:00PM | Lunch | |
| III | 1:00-2:15 PM | Data Exploration and Visualization in R |
| 2:15-2:30 PM | Coffee Break | |
| IV | 2:30-4:00 PM | Working with R Packages |
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 |
| 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 scRNA-seq and Overview of Project |
| 10:15-10:30 AM | Coffee Break | |
| II | 10:30-12:00 AM | Analysis of scRNA-seq dataset with python |
| 12:00-1:00 PM | Lunch | |
| III | 1:00-2:15 PM | Analysis of scRNA-seq dataset with R |
| 2:15-2:30 PM | Coffee Break | |
| IV | 2:30-4:00 PM | Group Presentations and Discussion |
Other courses
BIOINF-575: Programing Lab in Bioinformatics
(Winter term)
https://medicine.umich.edu/dept/dcmb/education/course-descriptions#bioinf-575-programming-laboratory-in-bioinformatics-
BIOINF-525: Foundations of Bioinformatics & Systems Biology
(Winter term)
https://medicine.umich.edu/dept/dcmb/education/course-descriptions#bioinf-525-foundations-in-bioinformatics-and-systems-biology-
HG-551: Computational Genomics
(Winter term)
https://medicine.umich.edu/sites/default/files/content/downloads/HG551%20Syllabus%202018.pdf
ARC: Computing Workshops
(Throughout the year)
http://cscar.research.umich.edu/events/category/workshops/
Software Carpentry: Occasional Workshops
(None planned for this year at UM unfortunately)
http://software-carpentry.org