BIOL 6297: Programming for Biologists
This course will introduce students with no prior background to computing. It will enable students to "get their feet wet" with computational analyses. Topics will include: how to use a UNIX machine and work from the command-line, how to submit and monitor jobs using a cluster, how to compile software, and how to organize and manage large projects.
We will learn about diverse tools to accomplish computational tasks, including shell scripts, UNIX one-liners, generic scripting languages (Python), and languages for data visualization and statistical analysis (R). This course is intended to provide students who have no prior programming experience with the basic skill set needed to undertake computational projects as part of their research training.
Articles on Programming:
- A great article that explains the necessity of our course: 'data wrangling' is the main hurdle to getting bioinformatics research done.
"It's time to reboot bioinformatics education" (Toddot Blog)
Practice exercises: Command-Line Exercises LCTHW: Command-line crash course Reference: UNIX reference card
Bash practice exercises
Lecture 9: Python (cont'd): Dictionaries, Lists, Writing Functions
Lecture 15: IPython Notebook