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

• Be comfortable with the Linux command line and command line programs, including the ability to move/create/edit files/directories
• Know how to connect to a remote server and run/manage jobs on it
• Know how to search, manipulate, and process large datasets
• Write and execute small bash script programs

Lectures: Tuesdays and Thursdays, 10:00 - 11:50 am on ZOOM. The lectures will be very interactive, so attendance is encouraged. However, attendance is not mandatory. A recording of each lecture will be posted later in the day on Canvas, the same day of class.

We will be offering virtual Study Sessions every Friday from 1 pm - 2 pm on ZOOM. Instructors or TA's will be available during those times to offer assistance.

Graduate standing is encouraged but not required. An interest in using Linux/UNIX in your research work is encouraged. We will focus on using Linux/UNIX to support research primarily in the life sciences. However, the content is broadly applicable to many fields.

BEFORE the first day of class, ensure you have purchased, uploaded, or installed all the required hardware and software. See COMPUTER REQUIREMENTS.

The Linux Command Line, 2nd ed by William Shotts. The books is available as a free, downloadable pdf from the book website or as a paperback widely sold by booksellers.

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

Instructor: Erin Nishimura, PhD
TA: David King, PhD
Support: Romario Romain

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.

Your grade for this course will be based on assignments, weekly quizzes, and a final exam. The percentages are as follows:

• Assignments: 70%
• Final exam: 30%

The calculation of the final letter grade will be made as follows:

• A 90 - 100%
• B 80 - 89.9%
• C 70 - 79.9%
• D 60 - 69.9%
• F below 60%

We do give out plusses or minuses depending on performance. These ranges for a letter grade might be shifted a little lower, but will not be raised.

Late assignments will be accepted provided you make arrangements with the instructor at least two days before the due date.

• Assignments make up 70 % of your course grade.
• There will be 6 assignments.
• If you need to turn in an assignment late, you may turn in an assignment up to 48 hours late with PRIOR approval. Approval must be requested at least 24 hr before the due date.

Erin's section will have a 5-minute quiz at the beginning of each class. These are not graded.

You are expected to be familiar with the 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.

Colorado State University has clear Principles of Community. We each have the responsibility to uphold these values as we interact with one another and learn.