# MODULE 1 : Note-Taking for Reproducible Research and Beyond

## 0. Introduction
- Note-taking extends beyond reproducible research; it's essential for everyone dealing with information overload.
- **Historical context**: Predecessors faced similar challenges; learn from their techniques.
- **Modern tools to implement**:
  - Text files with lightweight markup languages for efficient, structured notes.
  - Version control (e.g., GitLab) for persistent, evolving notes without loss.
  - Labels/tags and indexing software to navigate notes and avoid rediscovering lost information.
- **Goal**: Enhance note-taking on paper and digital media for better organization and retrieval.

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## 1. Note-Taking Concerns Everyone

### 1.1. Note-Taking Concerns Everyone
- Reproducible research requires meticulous notes, but note-taking is universal.
- **Examples**:
  - Scholars annotating books/manuscripts (e.g., 14th-century Aristotle manuscripts).
  - Galileo's 1610 observations of Jupiter's moons → rejection of geocentrism, support for heliocentrism; Inquisition trial (1633).
  - Shift from codices to paper/index cards post-printing press → affordability; rotating cabinets (Placcius & Leibniz, 17th century).
  - **Warning**: Over-accumulation risks chaos (e.g., Anatole France’s *Penguin Island* parody).
  - Practical cases: Éric Tabarly’s 1969 logbook; historical logbooks for climate reconstruction or slave trade quantification.
- **Key questions for note-taking**:
  - Tools: Annotated books, notebooks, loose sheets/binders, computer files, drawings/photos/films.
  - Organization: Handle heterogeneity; structure/index notes for persistence and updatability.
  - Risk: Unorganized notes rely solely on memory; modern tools can help.

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### 1.2. Interview with Anne Estrade (Math Professor, Université Paris-Descartes)
- **Work style**: Primarily on paper (loose sheets, dated/numbered); board for group work (preserves errors via cross-outs).
- **Process**:
  - Exploration → theorem proof → generates sheets.
  - Tidying at end of day: trash/renumber/copy; store until publication.
  - Keeps unproductive tracks but often forgotten.
- **Retrieval**: No systematic indexing; relies on memory.
- **Bibliography**: Skims digitally, prints for annotation, organizes in thematic folders.
- **Collaboration**: Starts on paper; types when clear; shares via Dropbox, no version control.
- **Impact of computers**: Minimal; still prefers paper first.
- **Training**: Students imitate method naturally.

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### 1.3. Interview with Marie-Noëlle Bourguet (Historian on Alexander von Humboldt)
- **Humboldt (1769–1859)**: German scientist/traveler; expedition 1799–1804.
- **Notebook analysis**:
  - Meteorological measures (dated/placed, e.g., Bologna/Rome).
  - Numbered paragraphs → bibliographical notes, Vatican Library work.
- **Process**:
  - Pencil notes on-site → later copied to ink notebook (selection/correction).
  - Delegated notes (e.g., Buch’s Vesuvius eruption).
- **Roman notes**: Larger folio notebook; continuous numbering; cross-references (“See page 35”).

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### 1.4. Interview with Annie Lacroix-Riz (Emerita History Professor, Paris-Diderot)
- **Data sources**: Archival files → summaries/quotes of all potentially useful info.
- **Method**: Exhaustive, chronological, handwritten → later typed.
- **Tech evolution**:
  - Switched to computer ~1987 (auto footnotes).
  - Laptop use from 1991; typing faster but core unchanged.
- **Synthesis/retrieval**:
  - Before: Paper files → retrieval very time-consuming.
  - Now: Computer search by keywords across hundreds of files.
- **Philosophy**: Deep archival research essential for valid historical interpretation.

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### 1.5. Interview with Isabel Llano (CNRS Neurophysiologist)
- **Work**: Records cerebellar cortex activity (electrophysiology + imaging).
- **Lab notebook**:
  - Fluorescence excitation, temperature, coordinates, stimulation parameters.
  - Sequence of events (e.g., reposition if response low).
- **Digital integration**: Some auto-recorded, but manual redundancy maintained.
- **Experiment**: Stimulate cell → observe fluorescence change (Ca²⁺ increase).

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## 2. Note-Taking: A Quick History

### 2.1. First Part
- **Focus**: Materiality, organization, book-note links.
- **Materials evolution**:
  - Clay tablets (3000 BC).
  - Wax tablets/styli (Antiquity–19th century).
  - Scrolls (3000 BC–4th century).
  - Codices (2nd century).
  - Paper notebooks (*commonplaces*).
  - Index cards (19th century boom).
  - Post-its, digital devices.
- **Innovations**:
  - Eusebian Canons (cross-references for Gospels).
- **China**: 9th century *leishu* (printed anthologies for exams).

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### 2.2. Second Part
- **Cards**: Useful but chaotic if unorganized.
- **Locke’s indexing**:
  - Numbered pages + keywords in red.
  - Alphabet-vowel grid for references.
- **Conclusion**: Paper remains indispensable; digital adds flexibility and indexing.

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## 3. From Text Files to Lightweight Markup Languages
- **Text files**: Readable in editors, UTF-8 encoded.
- **Word processors**: Not plain text; less durable.
- **Limitations**: Lack structure, hyperlinks, collaboration tools.
- **Markup languages**:
  - HTML (structured, not human-friendly raw).
  - Lightweight markup → simple syntax, raw readability.
  - Examples: Markdown, Wikitext, AsciiDoc, ReStructuredText.
- **Benefits**: Portable, convertible, quick note-taking with structure.

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## 4. Notes (and Codes) with Version Control (GitLab)
- **Persistence**: Digital copies ensure durability.
- **Upgradability**: Track changes, cross-outs, revisions.
- **Tools**:
  - Word processors → limited versioning.
  - Wikis → history view but per-page.
  - Version control (Git/GitHub/GitLab) → robust file tracking, collaboration, backups.
- **Pros**: Sophisticated, persistent, collaborative.
- **Cons**: Learning curve.
- **Practice**: Use GitLab interface.

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## 5. Finding One’s Way with Tags and Desktop Search
- **Issue**: Navigating large collections of notes.
- **Methods**:
  - Single file → search menu.
  - Cards → index system.
- **Heterogeneous files**: Use labels/tags + search apps.
  - Example: DocFetcher (cross-platform, relevance ranking).
- **Enhancing**:
  - Labels as anchors in Markdown (`:tag-1:`).
  - Add tags to image metadata (ExifTool) or PDF metadata.
- **Conclusion**: Tags + search tame note profusion, prevent rediscovery of lost data.