Computational Biology Tools

Lectures

MWF 12:30PM - 1:40PM     Cowell Rm131

Discussion Sections

01A     DIS     20578   W       05:00PM-06:10PM Staff   J Baskin Engr 165
01B     DIS     20579   W       06:30PM-07:40PM Staff   J Baskin Engr 165

 

This course provides an introduction to sequence informatics and workflows relevant to high-throughput computational genomics.  In addition to introducing core topics of sequence alignment and database mining (historically, central to BME110), the curriculum this quarter is designed to give students experience with advanced topics and applications of next-generational sequencing technologies, including: genome-wide alignments of experimental datasets (RNA sequence and chromatin immunoprecipitation sequencing (ChIP-seq)), short-read assembly, and metagenomics.  Biological concepts and online tools presented in this course are expected to be highly valuable to any student interested in developing skills expected of contemporary computational biologists.  

No prior experience with scripting languages or knowledge of unix environment is required.  Class problem sets will utilize the Galaxy web-based platform (http://galaxyproject.org/) -- an online analysis framework common to life science research --  to analyze and integrate publicly available software and genomic datasets.  Additionally, the use of Galaxy is intended to introduce the importance of reproducibility and transparency in data management through the use of published workflows.

The course is open to all science students with basic biochemistry and/or genetics or permission of the instructor as a prerequisite.

You must bring your own laptop to class every day.   If you do not have access to a laptop computer that you can use for this class, please contact the instructors as soon as possible.

You are expected to submit eight problem sets, online quizzes, a midterm, and a final project.


Required Text

The class textbook is currently back ordered through CSHL.  You are advised to place your order in the near future to ensure that it arrives in a timely manner.  Alternatively, you could consider purchasing individual chapters relative to course discussions (available for instant download @ $7/chapter with links provided below):

Next-Generation DNA Sequencing Informatics

Edited by Stuart M. Brown, New York University School of Medicine

http://www.cshlpress.com/default.tpl?action=full&--eqskudatarq=948&typ2=hpl

http://seqinformatics.com/

 

 Please note:  All course information and material will be maintained and updated on the eCommons website.  

 

 

 

Instructors and Assistants