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Linux 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 - 11:50 am in Biology 134.


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.

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


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


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


Office Office Hours
Erin Nishimura MRB 239 by appointment
David King MRB 227 by appointment
Tai Montgomery Biology 240

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.


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%

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.


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 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.1536953313.txt.gz · Last modified: 2018/09/14 13:28 by dokuroot