Keywords: introduction, real-course

Learning objectives:

• Construct absolute and relative paths that identify specific files and directories.
• Construct command pipelines with two or more stages.
• Create a directory hierarchy that matches a given diagram.
• Create files in that hierarchy using an editor or by copying and renaming existing files.
• Delete, copy and move specified files and/or directories.
• Demonstrate how to see what commands have recently been executed.
• Demonstrate the use of tab completion and explain its advantages.
• Explain Unix's 'small pieces, loosely joined' philosophy.
• Explain how the shell relates to the keyboard, the screen, the operating system, and users' programs.
• Explain the difference between a variable's name and its value.
• Explain the similarities and differences between a file and a directory.
• Explain what is meant by 'text' and 'binary' files, and why many common tools don't handle the latter well.
• Explain what usually happens if a program or pipeline isn't given any input to process.
• Explain when and why command-line interfaces should be used instead of graphical interfaces.
• Explain why spaces and some punctuation characters shouldn't be used in file names.
• Have a basic understanding of history of biology from Darwin to today.
• Have a basic understanding of the history of sequencing
• Learn the fundamentals of programming in Python
• Learning about dynamic programming
• Learning about how to translate DNA in Python
• Process a file instead of keyboard input using redirection.
• Re-run recently executed commands without retyping them.
• Redirect a command's output to a file.
• Trace the values taken on by a loop variable during execution of the loop.
• Translate an absolute path into a relative path and vice versa.
• Understand Python basics
• Understand data manipulation in Pandas
• Understand manipulation of FASTQ data in Python
• Understand manipulation of files in Python
• Understand quality metrics
• Understanding of lists and dictionaries
• Use find to find files and directories whose names match simple patterns.
• Use grep to select lines from text files that match simple patterns.
• Use options and arguments to change the behaviour of a shell command.
• Use the output of one command as the command-line argument(s) to another command.
• Write a loop that applies one or more commands separately to each file in a set of files.

Event types:

• Workshops and courses