Selected Topics in Zoology (Section 28325):
Cyberinfrastructure-enabled Computational Genome Science - A Laboratory

BIOL Z620 Spring 2013

Time & Location:    Mon, Wed 9:30a - 10:45a (Start date: March 4, 2013); Credits: 1.5); Swain East (SE) 045
Instructors:    Volker Brendel (205C Simon Hall; Tel.: 855-7074); TA Daniel Standage
Email:     VB, vbrendel@indiana.edu;     DS, dstandag@indiana.edu
WWW:     https://brendelgroup.org/
Office Hours:     Mon, Wed after class and by appointment.
Grades:    will be determined as described below.
Schedule:     https://brendelgroup.org/teaching/2013/CGSL13Sschedule.php
Computing Resources:     You will have access to networked computer terminals in class and will need such basic access outside of the classroom for assignments.

HTML version of this syllabus

Synopsis

The course will be a hands-on, working-group style course covering data processing and analysis of "Next Generation Sequence" data. Students will require access to high-performance computing resources at IU (Mason, Big Red) as well as virtual machine instances tailored to the course provided by the iPlant Collaborative research environment (Atmosphere). Students will then install software on their machines and initially analyze sample data. The course will cover the entire range of genomic analysis, from genome assembly, transcript assembly, transcript mapping, and genome annotation to annotation visualization and evaluation. At each step, participants will work together to generate installation and How-to documentation. There will be opportunity to analyze original data as well as the provided sample data. Participants will be introduced to electronic lab notebook keeping and will be expected to keep records of their work in that way. The course recommended programs and generated documentation will form the basis for a new virtual machine image for wider distribution through iPlant, including use at a tentatively scheduled public workshop conducted in collaboration with iPlant colleagues at the end of the class.

Prerequisites

This interdisciplinary course is primarily directed at graduate students in bioinformatics and biology. Students must have a working knowledge of basic Linux systems administration (installation of software requiring root access, updating of system components, editing of configuration files) and are expected to be familiar with the data types and formats as well as biological motivation of genomic research. Students lacking aforementioned knowledge are encouraged to consult with the instructors and should be able to learn the basic skills quickly from any of a wide range of appropriate tutorials available on the Web.

Assignments

Students will need to update their virtual machines and analyze data outside of the class room. Students will provide documentation for programs and reports on analysis results via course associated Wiki pages.

Grading

Grades will be based on class participation. Students are expected to give a short final presentation on one part of their class work at the end of the course.

Selected journals

Students are encouraged to review current research literature that provides many examples of application of the class topics. The following list provides a selection of relevant journals that are electronically accessible.