Libre Software in Science 1400-236WO

Subject matter of the classes

tl;dr
LaTeX: source code, types of documents, extensions, images, tables, bibliography, multilingual documents, presentations. Command line: database modifications, working with files and directories, speeding up daily activities, information management.

LaTeX

1. Document as source code – better than *.docx
Using LaTeX online, installation on Linux and Windows. Source code – structure and compilation to PDF. LaTeX extensions. Document classes. The first document.

2. Modify images directly in the document.
Inserting graphic files. Automatic positioning. Pictures surrounded by text. Image references.

3. A document for every occasion.
Standard paper sizes. Book, article, CV... Document layout, margins, spacing, single- and double-sided documents. Mathematical formulas.

4. Table from excel in a LaTeX document
Creating tables: simple, multi-page, vertical. Logical layout of the table. Automatic positioning.

5. Beyond English – LaTeX localization
Autocorrect. Document in Polish, typographic rules. Text encoding and diacritics. Multilingual document. Cyrillic.

6. Bibliography is simple in LaTeX
Embedded system vs packages. Bibliography database. Export of citations from online databases. Language localization of the literature list. Citation styles from scientific journals.

7. Drawing in LaTeX
Color schemes. PGF/TikZ graphic package – drawings and charts. Generating chart code in geogebra.

8. Multimedia presentations – quickly and elegantly
beamer package, styles. Good practices. Notes and handouts. Drawing chemical molecules.

Linux

9. Free Software, history and philosophy.
Free Software Foundation (FSF). Free Software vs Open-source software, types of licenses.
Linux command line – for what? File system navigation. Improved work in text mode.

10. Using Linux without installation.
Linux, introduction, diversity, running from a flash drive, installation options. Program management. Linux as a system for professional use.
Command line – file management, data backups. Combining commands into sequences - pipes.

11. Database in a text file.
Sorting and combining files. Creating subsets, including random ones. Selecting columns.

12. Searching for text in a file and recursive search in files – grep. Regular expressions (regex).

13. Replacing text in files – sed. Searching for files and directories according to complex conditions. Files: comparison, downloading from the Internet, archiving and compression, verification of correctness (checksums).

14. Database operations
awk as a spreadsheet. Mathematical operations, selection of lines according to logical conditions. Field value comparisons. bc calculator.

15. Command line – beyond the basics
Combining commands into shell scripts. Project management - git file version control system and GitHub service.

Prerequisites (description)

The aim of the course is to familiarize students with the following in an accessible way: – professional preparation of text documents (LaTeX). – Linux command line (bash), especially how it speeds up and improves everyday work with files and directories. The skills acquired during the course are valuable regardless of the later career path of students. Classes in the classroom are supported by the course space on the kampus2 website. Before the class, I provide a recording of the theoretical part and introductory materials for students' own work. Therefore, classes in the classroom end 60 minutes earlier than scheduled. If necessary, online consultations will be provided. We use web applications during classes – this provides students with constant access to the material discussed.

Course coordinators

Maciej Jończyk

Type of course

elective courses

Mode

Classroom

Learning outcomes

Knowledge

After mastering the material covered by the course, student:

Has in-depth knowledge of copyright.

Knows the advantages of using Linux and Free Software.
Knows Free Software tools used in science.

Skills

After mastering the material covered by the exercises, student:

Creates, under the supervision of a tutor and independently, properly documented studies.
Demonstrates the ability to critically analyze and select information, especially from electronic sources.
Demonstrates the ability to draw conclusions and formulate judgments based on data from various sources.

Social competence

After mastering the material covered by the exercises, student:

Understands the need to constantly improve her/his professional and social competences.
Understands the need for lifelong learning, inspiring the development of this need in others.
Shows initiative and independence in actions, can think and act in an entrepreneurial way.

Understands the importance of Free Software in the modern world

Assessment criteria

Lab grade, based on the sum of points from:
– document created in LaTeX (progress will be assessed on an ongoing basis);
– assignments concerning command-line;
– activity during classes.

Practical placement

Bibliography

1. Barnett B., The Grymoire – home for UNIX wizards, www.grymoire.com/Unix/

2. Goyvaerts J., Regular expressions, www.regular-expressions.info/

3. Kopka H., Daly P.W., 2003. Guide to LaTeX, 4th edition, Addison-Wesley Longman Publishing Co., Inc., USA

4. Shotts W.E., Jr, The Linux Command Line, linuxcommand.org/tlcl.php/tlcl.php

5. Tobias Oetiker and Contributors, lshort – A short introduction to LaTeX2e, ctan.org/tex-archive/info/lshort

6. Wikibooks contributors, LaTeX, Wikibooks, https://en.wikibooks.org/wiki/LaTeX

Additional information

Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system:

Description of 1400-236WO in USOSweb