Introduction to working with UNIX and bash (IN PERSON)

Beginners

The Unix shell (command line) is a powerful and essential tool for modern researchers, in particular those working in computational disciplines such as bioinformatics and large-scale data analysis. In this course we will explore the basic structure of the Unix operating system and how we can interact with it using a basic set of commands. You will learn how to navigate the filesystem, manipulate text-based data and combine multiple commands to quickly extract information from large data files. You will also learn how to write scripts, use programmatic techniques to automate task repetition, and communicate with remote servers (such as High Performance Computing servers).

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
• After you have booked a place, if you are unable to attend any of the live sessions and would like to work in your own time, please email the Bioinfo Team as Attendance will be taken on all courses. A charge is applied for non-attendance, including for registered university students.
• Further details regarding eligibility criteria are available here

No previous experience required

Number of sessions: 1

UNIX, Linux, Bash, Data handling

During this course you will learn about:

• Navigating the filesystem using a terminal (text-based interface).
• Using bash as a tool for data manipulation and automation.
• Best practices for managing and maintaining scripts written in bash.
• How to work on remote servers.

After this course you should be able to:

• Recognise the uses of the command line for computational work.
• Become comfortable in using the command line, understanding how commands are structured and how to access their documentation.
• Navigate the filesystem from the command line and understand how to specify the location of files and directories.
• Perform basic file manipulations in Bash: combine multiple files together; count number of lines, words and characters in a file; extract text matching a pattern; counting unique values in a file.
• Combine multiple commands to solve more complex tasks.
• Write Bash scripts to record and make your analysis reproducible.
• Understand what a for loop is an how it can be used to automate repetitive tasks.
• Access remote servers and move data to/from them.

• Free for registered University of Cambridge students
• £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
• £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 100/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

1

• Working on HPC clusters (IN-PERSON)