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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

  • 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

Time and Place

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:

Course Staff

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.

Contact Info
Instructor: Erin Osborne Nishimura email
Instructor: Tai Montgomery email

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:

  • Assignments: 60%
  • Quizzes: 10%
  • 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%

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.


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.

linux_syllabus.1530648097.txt.gz · Last modified: 2018/07/03 14:01 by dokuroot