Infectious Diseases

Padovaid Project — Memory File

Last updated: 2026-04-05

Project Overview

Quarto-based medical education website for infectious diseases teaching at the University of Padua (Prof. Russell E. Lewis). Deployed to docs/ directory. Live site: www.padovaid.com

Technology Stack

  • Source format: Quarto Markdown (.qmd)
  • Build system: Quarto with R/RStudio (padovaid.Rproj)
  • Output formats: HTML website, RevealJS slides, PDF handouts, speaker notes
  • Styling: custom.scss, custom2.scss, styles.css
  • Citations: BibTeX + diagnostic-microbiology-and-infectious-disease.csl
  • Deployment: Output to docs/, published via _publish.yml

File Naming Conventions (standardized April 2026)

All files follow lowercase kebab-case:

Category Pattern Example
QMD landing pages topic.qmd diarrhea.qmd
QMD full webpages topic-webpage.qmd fuo-webpage.qmd
QMD slide decks topic-slides.qmd malaria-slides.qmd
Image folders images-topic/ images-fuo/
Bibliography files refs-topic.bib refs-fuo.bib
Included modules _topic-content.qmd _diarrhea-content.qmd

Active Website Structure (_quarto.yml sidebar)

File Topic
index.qmd Home / site index
antibiotic-principles.qmd Antibiotic principles landing page
allergies.qmd Drug allergies landing page
intraabdominal.qmd Intra-abdominal infections landing page
immunosuppression.qmd Immunosuppression landing page
febrile-neutropenia.qmd Febrile neutropenia landing page
diarrhea.qmd Infectious diarrhea landing page
malaria.qmd Malaria & Leishmaniasis landing page

Global bibliography in _quarto.yml: refs-diarrhea.bib, refs-intraabdominal-2.bib

QMD Source Files by Topic

Fever of Unknown Origin (FUO)

  • fuo.qmd — landing page
  • fuo-slides.qmd — RevealJS slides
  • fuo-webpage.qmd — full content webpage

Malaria & Leishmaniasis

  • malaria.qmd — landing page
  • malaria-slides.qmd — RevealJS slides
  • malaria-webpage.qmd — full content webpage
  • malaria-webpage-v2.qmd — alternate version (uses different image paths; consider merging)

Infectious Diarrhea

  • diarrhea.qmd — landing page
  • diarrhea-slides.qmd — RevealJS slides
  • diarrhea-webpage.qmd — full content webpage
  • _diarrhea-content.qmd — included content module (used by other files)

Intra-abdominal Infections

  • intraabdominal.qmd — landing page
  • intraabdominal-1-webpage.qmd — Part 1: Peritonitis
  • intraabdominal-2-webpage.qmd — Part 2: Appendicitis & Liver/Biliary
  • intraabdominal-1-slides.qmd — Part 1 slides (polished, 1920×1080)
  • intraabdominal-1-slides-v2.qmd — Part 1 slides (older scrollable version)
  • intraabdominal-2-slides.qmd — Part 2 slides

Febrile Neutropenia

  • febrile-neutropenia.qmd — landing page
  • febrile-neutropenia-webpage.qmd — full content webpage

Immunocompromised Host

  • immunosuppression.qmd — landing page
  • immunocompromise-webpage.qmd — full content webpage

Stubs / Other

  • antibiotic-principles.qmd — landing page stub
  • allergies.qmd — landing page stub
  • resistance.qmd — stub (Antimicrobial Resistance in ESCAPE Pathogens)
  • ifi.qmd — stub (Invasive Fungal Infections)
  • treviso.qmd — Zoom lecture links for Treviso group

Image Folders

Folder Used By
images-fuo/ fuo-slides.qmd (and some figures in malaria-webpage.qmd)
images-fuo-webpage/ fuo-webpage.qmd
images-malaria/ malaria-slides.qmd, malaria-webpage-v2.qmd
images-diarrhea-slides/ diarrhea-slides.qmd
images-diarrhea-webpage/ diarrhea-webpage.qmd, _diarrhea-content.qmd
images-febrile-neutropenia/ febrile-neutropenia-webpage.qmd
images-immunocompromise-slides/ Immunocompromise slide decks
images-immunocompromise-webpage/ immunocompromise-webpage.qmd
images-immunocompromise-extra/ Not referenced in any QMD; has 6 extra files — archive/review
images-intraabdominal-1/ Intra-abdominal Part 1 files
images-intraabdominal-2/ Intra-abdominal Part 2 files

Bibliography Files

File Used By
refs-fuo.bib fuo-webpage.qmd, fuo.qmd
refs-diarrhea.bib diarrhea-webpage.qmd; global in _quarto.yml
refs-diarrhea-slides.bib Older diarrhea bib — check if still needed
refs-malaria.bib malaria-webpage.qmd
refs-malaria-slides.bib Older malaria bib — check if still needed
refs-febrile-neutropenia.bib febrile-neutropenia-webpage.qmd
refs-immunocompromise.bib immunosuppression.qmd, immunocompromise-webpage.qmd
refs-intraabdominal-1.bib intraabdominal-1-webpage.qmd
refs-intraabdominal-2.bib intraabdominal-2-webpage.qmd, intraabdominal-2-slides.qmd; global in _quarto.yml
refs-general.bib intraabdominal-2-slides.qmd, intraabdominal-1-slides.qmd

Supporting Assets (root level)

  • translate.html — Google Translate widget; included in every page via _quarto.yml
  • custom.scss, custom2.scss, styles.css — site styling
  • diagnostic-microbiology-and-infectious-disease.csl — citation style
  • 800-unipd.png/svg, University_of_Padua_seal.svg — institutional branding
  • _extensions/fontawesome/ — FontAwesome icon support for slides

Items Needing Future Attention

  • malaria-webpage.qmd vs malaria-webpage-v2.qmd: Two versions of the malaria webpage differing in image paths; consider merging into one
  • images-immunocompromise-extra/: Not referenced by any QMD; 6 unique images — review and either incorporate or delete
  • refs-diarrhea-slides.bib and refs-malaria-slides.bib: Older bibs; verify whether any QMD still needs them

Build Command

quarto render

Output goes to docs/.