Selected Topics in Bioinformatics and Computational Biology:
Applications of NGS data processing software in genomics.
Applications of NGS data processing software in genomics.
BCB/GDCB F 660 Fall 2011
Time & Location: Tu, Th 11:00a - 12:20p (Units: 2); 1340 MBB
Instructors: Volker Brendel (2112 MBB; Tel.: 294-9884) Amy Toth (309 Bessy Hall; Tel.: 294-3121)
Email:
VB, vbrendel@iastate.edu;
AT, amytoth@iastate.edu
WWW:
http://brendelgroup.org/
Wiki
http://brendelgroup.org//WikiVB/doku.php?id=home:bcb660wiki:start
Office Hours:
Tu, Th after class and by appointment.
Grades: will be determined as described below.
Schedule:
http://brendelgroup.org/teaching/bcb660F11schedule.php
Computing Resources:
You will have access to Linux-based virtual machines adequate for class projects.
A working knowledge of basic Linux system administration is prerequisite for the class.
Synopsis
The course will be a hands-on, working group style course covering data processing and analysis of "Next Generation Sequence" data. Students will be given access to virtual machine instances tailored to course from the iPlant Collaborative research environment. 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, participant 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. 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 public workshop conducted in collaboration with iPlant colleagues at the end of the class.
Prerequisites
This interdisciplinary course is primarily directed at advanced graduate students in bioinformatics and computational 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 will need to bring laptops to class.
Please address any special needs or special accommodations with the instructor at the beginning of the semester or as soon as you become aware of your needs. Those seeking accommodations based on disabilities should obtain a Student Academic Accommodation Request (SAAR) from the Disability Resources (DR) office (515-294-6624). DR is located in Room 1076 of the Student Services Building.
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 will be expected to read current research literature in the field. The following list provides a selected relevant journals that are electronically accessible from ISU accounts. For more choices, see e-Journals @ ISU.