Course Overview

Many fields of biological research have changed markedly over the past few years with the rise of high-throughput laboratory techniques such as microarrays, massive nucleic acid sequencing and proteomic technologies. These technical developments have brought forth not only a significant, and still ongoing, change in philosophical outlook, but have also transformed how work in certain fields is performed in the lab _ more specifically, the computer lab. Generation of huge data files that are only useful after extensive computational processing became a frequent task in many biological research groups. Proper training in basic computational concepts and tools that can greatly aid in such endeavors have thus become essential in order to extract all the information that many modern large-scale techniques of biological research can provide.

Learning Achievement

This course's goal is to provide intensive and advanced training in computer usage on the command-line interface (CLI) for large-scale data analysis. At the end of the course, students from biologically-oriented backgrounds should be able to use the CLI to view, edit, manipulate, and summarize large data files, successfully extracting biological information and insight from the high-throughput analyses that generated those files.

Competence

Course prerequisites

Grading Philosophy

Avaliation Form: Final grade will be calculated as the weighted average of midterm exam (weight 2), final exam (weight 2), in-class quizzes (weight 1), and practical exercises (weight 3). A passing grade consists of 5.0 or higher final average and at least 75% attendance. Students with regular semester final grades between 3.0 and 4.9 and attendance above 75% can take a supplementary exam, in which case the second final grade will be the average of the final grade above and the supplementary exam.

Course schedule

• Introduction to computers and the Unix family of operating systems. • Accessing the shell (Bash), locally or remotely, and Bash basics. • Getting help with man, info, apropos, and Internet search engines. • Moving around the directory tree; finding and executing programs; navigating/understanding the system (memory, disk space etc.). • System structure; file types; user and group permission model; Changing file access (owner, group, permissions). • Standard streams and redirection; piping. • Finding and manipulating files and directories (create, delete, move, copy, rename, append, concatenate etc.). • Describing and summarizing file content (wc, file); getting data into the system (wget, scp, ftp). • Creating, exploring, and sub-setting files. • Comparing, sorting, and editing files. • Compressing and decompressing data (tar, gz, zip etc.). • Basics of regular expressions. • Compiling third-party programs. • Automating the CLI with basic Bash scripting.

Course type

Online Course Requirement

Instructor

Jo_o Marcelo Pereira Alves

Other information

The course is structured in short lectures intermingled with class activity sessions, in order to make the course as practice-oriented as possible. In order to better reflect everyday research practice, the most widespread file formats used in the field will also be introduced and used in as many practical examples as possible. The whole course, including exams, takes place in a computer lab. The use of the command-line environment of Unix-like operating systems (such as Mac OS X and Linux-based systems) will be intensively explored, in order to give students all the working knowledge necessary to run most bioinformatics tools and efficiently analyze their output.

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