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Instituto de Ciências Biomédicas
Disciplina: BMP0260 - Introduction to scientific computing for biological data analysis
Carga Horária Total:
This course´s goal is to provide and advanced training in computer usage (mainly 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.
763756 - João Marcelo Pereira Alves
- The importance of the command-line interface (cli) in large-scale research. - Introduction to unix-like systems, basic architecture, directory structure, shell. - Remote system access and usage (graphical and command line interfaces). - User/group and permission model - who can access what and where? - File types and manipulation 9copy, move, rename, append, data streams, directories, etc.) - Main cli bioinformatics tools and bioinformatic file formats - Basic programming (bash, r) for automation of cli tasks, file manipulation and analyses.
1. Introduction to computing, computers and the Unix family of operating systems. The graphical (gui) and command-line (cli) user interfaces. Why use the cli? Accessing the shell (bash), locally or remotely (ssh) and bash basics. 2. Finding and executing programs, moving around the directory tree (CD). Navigating/understanding the system (memory, disk space, etc.). Getting help with man, info, apropos, and internet search engines. 3. System structure. File Types, directories. User and group permission model. 4. Standard streams and redirection. Piping. 5. Finding and manipulating files and directories (create, delete, move, copy, rename, append, concatenate, etc.).Compressing and decompressing data (tar, gz, zip, etc). Basic regular expressions. 6. Describing and summarizing file content (wc, file). Changing file acess (owner, group, permissions). Getting data into the system (wget, scp, ftp). 7. Exploring (head, tail, more, less, cat, zcat, uniq,etc), sub setting (grep, cut), editing (nano, sed, paste), comparing (diff, comm), and sorting (sort) file content. 8. Compiling third-party programs. 9. Automating the cli with basic bash scripting. 10. Exploring data using basic r.
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. Short pre-class readings will be designated as necessary. The whole course, including exams, takes place in a computer lab. There will be one midterm and one final exam, with cumulative content, as well as in-class quizzes and practical exercises (in-class and homework) distributed along the course. Grades range from 0 to 10 points. There will be no make-up exams.
Final grade will be calculated as the weigthed average of midterm exam ( me:weight 2). Final exam (Fe:weight 2), in-class quizzes ( Q:weight1), and practicalexercises (P?weight3), i.e.:fg= [(ME x 2) + (FE x 2) + (q x 1) + (P x 3)]/8. A passing grade consist of 5,0 or higher final average and at least 70% attendance. students with regular semester final grades between 3,0 and 4,9 and attendance above 70% can take a supplementary exam, in which case the second final grade will be the weighted average of the final grade above (FG:weight 1) and supplementary exam (SE:weight 2), I.E.: F=[FG +(SE x 2)]/3.
Norma de Recuperação
According to resolution COG3583/89, a supplementary exam ("recuperação") will be offered to those students who did not get a passing grade ( 5,0 or higher) in the regular semester exams. Only students with a final grade of at least 3.0 and minimum attendance of 70% during the regular semester qualify for taking the supplementary exam. Like the final, this exam will also be comprehensive ( i.e. anything taught during the regular semester) and contain both theorical and practical components. The suplementary exam will take place either in february ( second semester course) or july ( first semester course.
- "The Linux Command Line, a Complete Introduction" by William E. Shotts jr. (2013) - Freely available at http://linuxcommand.org) - "Ubuntu Pocket Guide and Reference" , by Keir Thomas (2009), chapter 5 ( freely available at http://ubuntupocketguide.com) - "Introduction to the Command Line", by the Free Software Foundation (2013) (freely available at http://en.flossmanuals.net/command-line/) - "Bash Guide for Beginners", by Machtelt Garrels (2008)(Freely available at http://ww.tldp.org/ldf/bash-beginners-guide/bash-begginers-guide.pdf)
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