Table of Contents

Course Description

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

Time and Place

Lectures: Tuesdays and Thursdays, 10:00 - 11:50 am in Biology 134.

Prerequisites

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.

Textbook

The Linux Command Line by William Shotts. The books is freely available from the book website.

Communications

We will be using Canvas Discussions for class-wide communications.

Instructors

Office Office Hours
Erin Nishimura MRB 239 by appointment
Tai Montgomery Biology 240 Wednesday, 3-4 pm

Please direct content-related questions to the whole class using Canvas Discussions. This way, the class can assist you in finding a solution quickly. Content-related questions that are e-mailed to instructors may be posted (anonymously) on Canvas Discussions for a faster response. Please use instructor e-mails for individual-specific questions.

Grading

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.

Expectations

You are expected to be familiar with the CSU Student code of conduct. This course will adhere to the CSU Academic Integrity Policy. At a minimum, violations will result in a grading penalty in this course and a report to the Office of Conflict Resolution and Student Conduct Services.