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BIOL L531 (Z620) Spring 2014

Selected Topics in Zoology (Section 33948):
Cyberinfrastructure-enabled Computational Genome Science Laboratory

BIOL L531 (Z620) Spring 2014


Time & Location:    Mon, Wed 9:30a - 10:45a (Credits: 3.0); Lindley Hall (LH) 030
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/
Wiki     https://brendelgroup.org/WikiBCB/doku.php?id=cgss14:start
Office Hours:     Mon, Wed after class and by appointment.
Grades:    will be determined as described below.
Schedule:     https://brendelgroup.org/teaching/2014/CGSL14Sschedule.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.


btn_printerFriendly.gif version of this syllabus

Synopsis

The course will be a hands-on, working-group style class covering data processing and analysis of "Next Generation Sequence" data. Topics encompass the entire range of genome analysis, from de novo genome assembly, genome re-sequencing, transcript assembly, transcript mapping, and genome annotation to annotation visualization and evaluation and comparative genomics. Students will have access to high-performance computing resources at IU and national cyberinfrastructure portals for biological research. At each step of the learning process, participants will collaborate to produce tutorial/how-to style documentation of their work and will gain practical experience with electronic lab notebook keeping. Sample data will be provided, but students will have abundant opportunity to analyze original data. The course experience will culminate with a term project that encourages participants to explore topics of their particular interest in greater depth or to progress with their own research work.


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

Class assignments will come in two general flavors. First, small simple assignments with detailed step-by-step instructions will be provided as an introduction to each topic. Participants will be expected to reproduce these assignments by following the provided steps and taking notes of the process: what worked, what didn't, what was learned, potential pitfalls, etc. Second, more open-ended assignments will be given with each topic that provide an opportunity for participants to sample the wide variety of publicly available tools and data (or their own lab's data if they would like). In both cases, participants will be expected to utilize remote computing resources both inside and outside the classroom, and to submit their assignments via the course-associated wiki pages.


Grading

Final grades will be based on class participation. There will be a graded reading quiz for each unit, and students will also have frequent opportunities to present their class work to their peers. These presentations will graded both by the instructor and peers. The primary purpose of these assessments is to motivate participants to be prepared for and participate in class, as well as to provide feedback early and often. A short final presentation on a term project at the end of the course will take the place of a final exam


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.