Welcome to Foundations in Computational Skills’s documentation!¶
Schedule¶
The workshops for summer 2018 meet on the following dates:
- Friday, August 10 9-11AM (CILSE 106B): Intro to linux and command line
- Monday, August 13 9-11AM (CILSE 106B): Intro to python
- Wednesday, August 15 9-11AM (CILSE 106B): Real world application workshop 1
- Friday, August 17 9-11AM (LSEB 904): Intro to R <– Note different location!
- Monday, August 20 9-11AM (CILSE 106B): Advanced linux command line tools
- Wednesday, August 22 9-11AM (CILSE 106B): Real world application workshop 2
- Wednesday, October 24th 12-2PM (LSE 904): Shell scripting and cluster computing
- Wednesday, November 7th 12-2PM (LSE 904): Version control with git
Contents¶
- Workshop 0 - CLI Basics
- Workshop 1 - python
- Workshop 2 - High throughput sequencing application
- Workshop 3 - Advanced CLI
- Workshop 4 - Introduction to R
- Workshop 5 - High throughput sequencing application part 2
- Workshop 6 - Shell scripting and cluster computing
- Workshop 7 - Version Control with git
List of topics¶
Note
These workshops are still under construction Please be kind.
Workshop 0 - CLI Basics¶
Workshop 0. Basic Linux and Command Line Usage: Online Materials
Workshop 0. Basic Linux and Command Line Usage: Workshop
| Topic | Length |
|---|---|
| CLI Introduction | 3 min |
| Navigating directories, listing files | 16 min |
| Basic file operations | 9 min |
| Working with files 1 | 10 min |
| Working with files 2 | 10 min |
| I/O redirection and related commands | 20 min |
| Globbing | 6 min |
Workshop 1 - python¶
Workshop 1. Introduction to Python
Workshop 1: Protein Translation using Python
| Topic | Length |
|---|---|
| Introduction | 3 min |
| Builtin Types | 2 min |
| A Simple Program | 6 min |
| if Statements | 3 min |
| Simplifying Solution | 4 min |
| Defining Functions | 4 min |
| More On Types and Iteration | 4 min |
| More Data Structures | |
| File I/O | 22 min |
| Modules | 3 min |
| Executing Scripts with Arguments from the Command Line | 3 min |
| Other File objects |
Workshop 2 - High throughput sequencing application¶
Workshop 2. High Throughput Sequencing Application Session Online Materials
Workshop 2. High Throughput Sequencing Application Session
| Topic | Length |
|---|---|
| App Session Introduction | 2 min |
| Illumina Sequencing Technology | 5 min |
| High Throughput Sequencing Data Primer | 9 min |
| Sequencing Data QC and Analysis Primer | 9 min |
Workshop 3 - Advanced CLI¶
Workshop 3. Advanced CLI and Tools
Workshop 3. Advanced CLI Techniques Workshop Session
| Topic | Length |
|---|---|
| nano | ~7 min |
| vim (part one, two, three) | ~9, ~6, ~6 min |
| emacs | ~24 min |
| piping, silencing stdout/stderr | ~10 min |
| shell tricks | ~10 min |
| bash history | ~4 min |
| pushd/popd, find, xargs/fim | ~10 min |
Workshop 4 - Introduction to R¶
| Topic | Length |
|---|---|
| Reasons why you should learn R | ~7 min |
| RStudio interface | ~10 min |
| Installing packages | ~7 min |
| Console and working environment basics | ~8 min |
| Very quick data types | ~7 min |
| NAs, NaNs, Infs | ~3 min |
| Intro to vectors | ~7 min |
| Data types and structures, Part 2 | 9:30 min |
| If statements and logical operators | 5:30 min |
| Apply function | ~7 min |
| Reshape package | ~6 min |
| Split, Apply and Combine with plyr | 8:30 min |
| Intro to ggplot | 9 min |
Workshop 5 - High throughput sequencing application part 2¶
Workshop 5. NGS Application Session 2
Workshop 5. NGS Application Session 2 Workshop
There are no video online materials for this workshop.
Workshop 6 - Shell scripting and cluster computing¶
Workshop 6. Shell Scripts and Cluster Computing
There is no in-class workshop material for this workshop.
Workshop 7 - Version control with git¶
Contributors¶
The primary contributors to the BU Bioinformatics Programming Workshop Taskforce:
- Gracia Bonilla
- Rachael Ivison
- Vinay Kartha
- Josh Klein
- Adam Labadorf
- Katharine Norwood
We would also like to thank Gary Benson for his mentorship and support.