Scientific writing

Part A

This module will cover the principles of scientific writing (structure of a report and a scientific article), the critical approach to scientific information, the principles of searching for scientific information using appropriate tools, the notions of plagiarism and publication ethics, the principles of methodological rigour and the use of data formatting tools.

 

Table of contents of theory courses


Scientific writing (P Cardol/ P. Tocquin)

Principles of writing and structuring a scientific paper

• Preparation for the company placement report and dissertation
• Principles of scientific writing
• Developing an introduction
• Writing a title, abstract and figure legend
• Presentation of methods, principles of reproducibility, accessibility of data (Data management program, etc.)
• Structuring the results section
• Principle and application of results discussion
• Choice of key words, etc.

• Sources of information, information search tools (types of resources and content) and development of a critical approach to scientific information (pyramid of evidence, etc.);
• Introduction to scientific communication and publishing: costs, abuses, open access issues, copyright policies and plagiarism, new vectors for scientific communication;
• General principles of scientific information research: initial question, documentary question, choice of tools, documentary languages, command languages, access to documents via databases;
• Bibliographic methods and use of bibliographic referencing software (Zotero).

• General theory on the presentation of figures and graphs of results  
• R packages applied to graphs
• Legend writing

• Scientific writing (P Cardol/ P. Tocquin): application of writing principles
• Training in the use of documentary resources (M. Bardiau)
• Data formatting and graphing (F. Bouché and P. Tocquin): practical work 

Part B

This course introduces Markdown as a lightweight markup language for writing scientific documents. Students will learn how to structure textual content in a simple and portable way, use Pandoc to convert these documents to various formats (Word, PDF, HTML) while applying custom Word templates. The course also covers the integration of bibliographic references using Zotero and BibTeX, as well as the creation of dynamic reports with R-Markdown, including executable code, automatically generated figures, and tables. The focus is on reproducibility, separation of content and formatting, and automation of writing workflows.

Part A

• Formulate a research hypothesis and put it into context
• Acquire the ability to structure a scientific report
• Develop a critical approach to scientific texts

Part B

At the end of this course, students will be able to:

• Write structured documents using Markdown syntax (headings, paragraphs, lists, links, images, tables, code blocks).
• Convert Markdown documents to Word, PDF, or HTML using Pandoc.
• Apply custom Word templates to ensure consistent formatting that meets the requirements of scientific journals.
• Manage bibliographic references with Zotero, export to BibTeX, and integrate citations into Markdown documents.
• Create dynamic reports with R-Markdown, including execution of R code, display of figures and tables, and automatic generation of bibliographies.
• Adopt best practices for reproducible and collaborative writing of scientific documents.

Part A

Notion of programming in R.

Part B

This course does not assume any prior knowledge of Markdown, Pandoc, or R-Markdown

For the R-Markdown section, elementary knowledge of R (basic syntax, data manipulation) is required.

Part A

Classroom theory

Tutorials (scientific writing)

Part B

Learning activities combine short theoretical lectures, live practical demonstrations, and guided hands-on exercises on the computer. Participants will:

• Observe demonstrations of Markdown syntax and conversion with Pandoc.
• Practice writing in Markdown using various editors (VS Code, Obsidian, RStudio).
• Experiment with document conversion while applying Word templates.
• Integrate bibliographic references using Zotero and BibTeX.
• Create and compile a dynamic report in R-Markdown.

Part A

Face-to-face course


Further information:

Face-to-face course


Further information:

The course will be organized as follows:

Unless otherwise specified, classes will take place in the morning from 09:00 to 12:30 (4 periods of 50 minutes) and in the afternoon from 13h45 to 17h00 (4 periods of 45 minutes).

Practical sessions are mandatory, as they are essential for the preparation of the report on which part of this module will be assessed. In case of absence, even if justified, students are required to catch up on any missed work.

 

Part B

Face-to-face course

Part A

The slideshows will be made available to students on the eCampus platform.

Part B

Platform(s) used for course materials:
- eCampus

Part A

Written work / report


Further information:

Written work / report


Additional information:

Evaluation will be based on the quality and formal structure of a report written by the students on a topic assigned by the teaching staff.

 

 

 

 

 

Part B

Written work / report


Further information:

Assessment focuses on the source files (Markdown, BibTeX, YAML, etc.) used to generate the final report of the practical internship from the parent course BIOL0034-A "Scientific Writing". Assessment criteria include:

• The quality and structure of Markdown documents (clarity, organization, correct syntax).
• The appropriate integration of bibliographic references BibTeX.
• The functionality of R-Markdown documents (executable code, automatic generation of figures/tables).
• The overall reproducibility of the workflow: ability to regenerate the final report from the source files.

Part A

For practical writing assignments, students are required to bring a computer (or tablet).

Part A

Module coordination :  

Frédéric Bouché

Tél : 04/366 22 69 
Email: fbouche@uliege.be


The teachers are available to answer your questions: either during the lessons/practical work sessions given as part of this module, or by e-mail (during office hours). 


List of teachers : 

Frédéric Bouché (fbouche@uliege.be)
Pierre Cardol (pierre.cardol@uliege.be) 
Marjorie Bardiau (mbardiau@uliege.be)
Pierre Tocquin (ptocquin@uliege.be)

Part B

Responsible teacher: Pierre Tocquin
E-mail address: ptocquin@uliege.be