This is an old revision of the document!
Linux/Unix is the primary platform for computational science. The goal of this course is to train scientists in its use, with particular emphasis on the needs of bioinformatics users. The course covers basic Linux commands and utilities, running and managing computational jobs, and handling and manipulating large biological datasets.
By the end of the course students will
Lectures: Tuesdays and Thursdays, 10:00 - 11:50am in Computer Science 425.
Graduate standing and interest in using Linux/UNIX in your research work. We will focus on using Linux/UNIX in supporting the needs of running computational work in the life sciences.
The Linux Command Line by William Shotts. The books is freely available from the book website.
This semester we will be using Piazza for class discussions. The system is highly catered to getting you help fast and efficiently from classmates and your instructor. Rather than emailing questions to the teaching staff, you are encouraged to post your questions on Piazza. Find our class page at: https://piazza.com/colostate/fall2016/nsci580a4/home
Please direct content-related questions to the Piazza discussion board where the whole class can assist you in finding a solution. Be aware that content-related questions that are e-mailed privately to instructors may be posted anonymously to Piazza for faster response. Please use instructor e-mails for individual-specific questions that do not relate to course content.
Asa Ben-Hur taught previous iterations of this class and has been instrumental in its development.
Your grade for this course will be based on assignments, weekly quizzes, and a final exam. The percentages are as follows:
The calculation of the final letter grade will be made as follows:
These ranges for a letter grade might be shifted a little lower, but will not be raised.
Late assignments will not be accepted, unless you make arrangements with the instructor at least two days before the due date.