Update logbook.md

journal/logbook.md

+# 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.
+
+---
+
+## 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.
+
+---
+
+### 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.
+
+---
+
+### 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”).
+
+---
+
+### 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.
+
+---
+
+### 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).
+
+---
+
+## 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).
+
+---
+
+### 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.
+
+---
+
+## 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.
+
+---
+
+## 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.
+
+---
+
+## 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.
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