LaTeX II: Thesis Workflows, Bibliography, and Advanced Tools
Overview
This follow-up session looks at how LaTeX scales to longer academic documents and collaborative writing. The focus is on practical workflows for theses, bibliographies, and modular document organization, as well as tools that integrate LaTeX with the broader research workflow.
Learning Objectives
- Organize larger LaTeX projects for theses and dissertations using multi-file structure
- Manage bibliographies with Zotero, BetterBibTeX, and
biblatex/biber - Use Quarto for literate programming with PDF output via LaTeX
- Create programmatic figures with TikZ
- Start from journal and thesis templates
- Read LaTeX error messages and debug common problems
Topics Covered
Document Structure for Longer Works
reportandbookdocument classes- Multi-file projects:
\inputand\include - Recommended folder structure for theses
Bibliography Management
- How the LaTeX bibliography pipeline works: multiple compilation passes explained
bibervsBibTeX: differences, when to use each, how to configure TeXstudio.bibfile structure and entry types- Citation commands:
\parencite,\textcite,\autocite
Zotero and BetterBibTeX
- Building and organising a Zotero library
- BetterBibTeX: cite key patterns and continuous auto-export
- Keeping references in sync between Zotero and your LaTeX project
Quarto
- Literate programming: combining R/Python code with prose in a single
.qmdfile - Quarto YAML options for PDF output via LaTeX
- Using
keep-tex: truefor journal submission
TikZ
- Programmatic figures: shapes, paths, and annotations
- Flowcharts and process diagrams
- Plots with PGFPlots
- Syntax trees with
tikz-qtree
Templates and Debugging
- Journal templates from Overleaf, publisher websites, and CTAN
- University thesis templates
- Reading LaTeX error messages; common errors and fixes
Materials
- Presentation Slides — Main workshop presentation
- Presentation Source — Quarto source file for the presentation