PRACTICAL COMPUTING FOR BIOLOGISTS

 

Practical Computing for Biologists:

Biology is becoming far more computationally intensive, yet the undergraduate and graduate biology curricula have not kept pace with this new reality.  Practical Computing for Biologists, based on Haddock’s and Dunn’s book of the same name, is a problem-centric course that provides resources for biologists to analyze the increasingly complex data sets generated by new technologies.  We will cover flexible, scalable tools to accomplish a diversity of tasks using open source software.   Topics will include: regular expressions, command line operations, Python programming, and bioinformatics pipelines.  Exercises relevant to the students’ needs will be used to illustrate and develop new skills.  After doing several assigned homework problems, students will have an opportunity to develop a bioinformatic analysis on their own data set.

 

Overall Course Design: 

The primary focus of the course is to provide hands on training to use computational tools to analyze large biological data sets.  

 

Prerequisites:

 Biology major, your own computer

 

Textbook:

Haddock, Steven H. and Dunn, Casey W., Practical computing for biologists.  Sinauer Associates, Inc.  2011.  

 

Software List  - *(Some softwares are exlcusive for Mac):

  • TextWrangler *[App store]

  • X-code *[App store]

  • Java 7.x

  • JEdit