UTbiocomputing2015
Peer-led working group in Biological Computing at UT Austin, Spring 2015
Rebecca Tarvin (PAT 123) rdtarvin@utexas.edu
Stephanie Spielman (MBB 3.232) stephanie.spielman@gmail.com
Open Coding Hour: Tuesdays 5-6pm in CCBB conference room (GDC 7.514)
Class: 4-5pm on Wednesdays in FNT 1.104
New class website: http://sjspielman.org/UTbiocomputing2015/
Class website: https://github.com/sjspielman/UTbiocomputing2015
Resources: https://github.com/sjspielman/UTbiocomputing2015/blob/master/resources.md
The goal of this class is to take away any fear of programming that you may have so that computing can become an advantage rather than a barrier to your research. On Wednesdays, we will provide lessons suitable for beginners in programming. Each week you should post at least one question and answer on the google group (UTbiocomputing, http://goo.gl/PLnSpP) and complete the homework. On Tuesdays we will help you with homework or if you had no problems, come anyways to meet other people that are computing at UT, and get some handy tips from GSAF's Scott Hunicke-Smith.
Please install the required software no later than the second day of class. Here are some recommended resources for all your computing needs. The resources are not required reading, but they are tremendously useful!
A new and awesome resource: Rosetta Code !!!!!
Another new and awesome resource, sponsored by UT! http://www.lynda.com/ .
To download files (pdf, csv, or text), try viewing in Raw format.
Course Schedule
| Week | Calendar Date | Topic | Description | Teacher |
|---|---|---|---|---|
| WEEK 00 | Jan 21 | Introduction | Welcome! | Becca |
| WEEK 01 | Jan 28 | Unix/Bash | Basic commands | Becca |
| WEEK 02 | Feb 04 | Python 1 | When to use & basic structure | Stephanie |
| WEEK 03 | Feb 11 | Python 2 | Control flow and loops (if, for, while) | Becca |
| WEEK 04 | Feb 18 | Python 3 | Functions | Stephanie |
| WEEK 05 | Feb 25 | Python 4 | File Input & Output | Stephanie |
| WEEK 06 | Mar 04 | Python 5 | Testing | Becca |
| WEEK 07 | Mar 11 | Python 6 | Numpy & Biopython | Stephanie |
| SPRING BREAK | Mar 18 | Spring break | WOOO! | Everybody! |
| WEEK 08 | Mar 25 | PyBash | Merging Python and Unix/Bash | Stephanie and Becca |
| WEEK 09 | Apr 01 | git | Collaboration and version control slides | Cheng Lee |
| WEEK 10 | Apr 08 | R | Statistical analyses | Nathan Pope |
| WEEK 11 | Apr 15 | pandas | data analysis in python | Ben Liebeskind |
| WEEK 12 | Apr 22 | TACC | Using high-performance computing systems | Benni Goetz |
| WEEK 13 | Apr 29 | RNAseq | Computational platforms and pipeline slides | Dariya Sydykova |
| WEEK 14 | May 06 | pyRAD | pipeline for analyzing NextGen SNP data | April Wright |