Learning Media Hub

Central index of diagrams, clinical examples, and videos for this encyclopedia.

Parent: Home · Map: Encyclopedia Map

How media works in this vault

Type	Where it lives	How to use
Mermaid figures	04_Figures_and_Media/Diagrams/	Embed with ![[Figure - Name]] or open the note
Excalidraw	04_Figures_and_Media/Timeline/ etc.	Already used for history timeline
Clinical examples	Callout > [!example] inside topic notes	Short vignette + answer
Videos	YouTube links in topic notes	Prefer ≤15 min teaching clips
Template	Template - Learning Aids	Copy block into new notes

Obsidian tip: install Media Extended (optional) if you want inline YouTube embeds. Links work without any plugin.

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Diagram library

Figure	Teaches	Used in
Figure - Gram Envelope Comparison	Gram+ vs Gram− wall	Gram Stain · Bacterial Cell Wall
Figure - Bacterial Growth Curve	Lag → death phases	Bacterial Growth Curve
Figure - Horizontal Gene Transfer	Transformation / transduction / conjugation	Horizontal Gene Transfer
Figure - Koch Postulates Flow	Causality steps + modern limits	Koch’s Postulates
Figure - Diagnostic Workflow	Specimen → answer	MOC - Diagnostic & Lab Methods
Figure - AI and Bioinformatics in Microbiology	Data → BI → AI → validation	MOC - AI in Microbiology · MOC - Bioinformatics in Microbiology
Figure - WGS Bioinformatics Pipeline	FASTQ → report	WGS Bioinformatics Pipeline
Figure - Machine Learning Workflow in Microbiology	Question → validation → monitoring, with failure points	Machine Learning Basics for Microbiology · Model Evaluation in Clinical Microbiology
Figure - Omics Layers in Microbiology	Genome → transcript → protein → phenotype	Genotype to Phenotype Prediction
Figure - Sequencing Platform Comparison	Choosing a platform by question	Sequencing Technologies
Figure - Timeline of Medical Microbiology	History milestones	Medical Microbiology History
Timeline - History of Medical Microbiology.excalidraw	Visual timeline	History hub

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Image library

Real images and AI-generated images follow different rules — read Image Sources and Attribution before adding any.

Image	Type	Used in
banner-computational-microbiology.png	Decorative banner (AI)	MOC - Bioinformatics in Microbiology
banner-history-microbiology.png	Decorative banner (AI)	Medical Microbiology History
schematic-gram-envelope.png	Conceptual schematic (AI, reviewed)	Figure - Gram Envelope Comparison

Never AI-generate a micrograph, agar plate, or clinical photo

Use CDC PHIL, Wikimedia, or NIAID instead — the wanted list lives in Image Sources and Attribution.

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Curated video playlist (starter)

Topic	Video	Note
Gram stain concept	Khan Academy — Gram staining	Gram Stain
Gram stain lab technique	Hardy Diagnostics — perfect Gram stain	Gram Stain
Gram stain animation	Animated Gram stain (USMLE-style)	Bacterial Cell Wall
PCR principle	DNA Learning Center — PCR	PCR · qPCR
RT-PCR concept	Clevland Clinic — what is RT-PCR (overview)	RT-PCR · RNA Extraction
NGS overview	Illumina — sequencing by synthesis	Whole-Genome Sequencing · NGS Library Preparation
HGT overview	Genetic exchange: conjugation, transduction, transformation	Horizontal Gene Transfer
Conjugation / HGT lecture	Conjugation, transformation, transduction	Conjugation
Bacteria basics (incl. conjugation idea)	Khan Academy — Bacteria	MOC - Fundamentals of Microbiology
How Illumina sequencing works	Illumina SBS animation	Sequencing Technologies
Nanopore sequencing explained	Oxford Nanopore — how it works	Sequencing Technologies
AlphaFold and the protein folding problem	DeepMind — AlphaFold	AlphaFold in Microbiology
BLAST in practice	NCBI — BLAST quick start	Sequence Alignment and BLAST

Search terms that reliably find good material for this layer: “bacterial WGS pipeline tutorial”, “cgMLST outbreak investigation”, “nf-core bactmap walkthrough”, “machine learning antimicrobial resistance prediction lecture”.

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Notes that already have Learning Aids

• Gram Stain
• Bacterial Cell Wall
• Bacterial Growth Curve
• Horizontal Gene Transfer
• Koch’s Postulates
• MOC - Diagnostic & Lab Methods
• Staphylococcus aureus
• Escherichia coli

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Add media to a note (checklist)

1. Add a ## Learning Aids section (see Template - Learning Aids).
2. Link or embed a figure from this hub.
3. Add one > [!example] clinical vignette.
4. Add 1–2 short videos with why watch + approximate length.
5. List the note here under “Notes that already have Learning Aids.”