From 0ed9b04eaa4109ade861f51fed4d201283d3b802 Mon Sep 17 00:00:00 2001 From: e7422cd3159d46c5212576fce1c4663d Date: Wed, 1 Oct 2025 23:03:54 +0000 Subject: [PATCH] Update logbook.md --- journal/logbook.md | 142 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 142 insertions(+) diff --git a/journal/logbook.md b/journal/logbook.md index e69de29..2567de9 100644 --- a/journal/logbook.md +++ b/journal/logbook.md @@ -0,0 +1,142 @@ +# 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. \ No newline at end of file -- 2.18.1