About this site

Personal medical-microbiology encyclopedia by Vahhab Piranfar.
Use search or the graph to explore; every note links to its neighbours.

Microbiology Encyclopedia

Personal knowledge base for medical microbiology — concepts, organisms, lab methods, history, and research notes linked into one graph.

Start Here

Path	Note
Microbiology Map (canvas)	Visual index of the whole vault
Encyclopedia Map	Full structure + remaining backlog
Dashboard - Vault Health	Auto-generated quality report
MOC - Fundamentals of Microbiology	Cell structure, genetics, history
Medical Microbiology History	Timeline of pioneers
MOC - Diagnostic & Lab Methods	Microscopy → culture → molecular
MOC - Bacteriology	Classification + starter pathogens
MOC - Diseases by System	Infections by organ system
MOC - Bioinformatics in Microbiology	WGS pipelines & databases
MOC - AI in Microbiology	ML, AlphaFold, diagnostic AI
Jawetz, Melnick & Adelberg’s Medical Microbiology - Chapter 1	Active book chapter

Knowledge Domains

Core Science

• MOC - Fundamentals of Microbiology
• MOC - Bacteriology
• MOC - Virology
• MOC - Mycology
• MOC - Parasitology
• MOC - Immunology

Clinical & Applied

• MOC - Diseases by System — anatomy-first disease map
• MOC - Clinical Microbiology — specimen/workflow-first
• MOC - Diagnostic & Lab Methods
• MOC - Antimicrobials
• MOC - Antimicrobial Resistance (AMR)
• MOC - Public Health & Epidemiology — surveillance, outbreaks, prevention

Computational

• MOC - Bioinformatics in Microbiology — sequencing → assembly → typing → metagenomics
• MOC - AI in Microbiology — ML foundations, AlphaFold, diagnostics, discovery
• Computational Microbiology Study Path — ordered reading route through both
• Bioinformatics and AI Glossary · Genomics Command-Line Cheatsheet

Support Layers

• Glossary Index — all definition layers in one place
• Learning Media Hub — diagrams, clinical examples, videos
• Image Sources and Attribution — where real images come from, and the AI-image rule
• Books · Papers
• Figures & Timeline
• Dashboard - Vault Health — auto-generated status of every note

Vault Structure

Home
├── 01_References          → books, papers, source notes
├── 02_Core_Concepts       → MOCs (hubs)
├── 03-Glossary            → short definitions
├── 04_Figures_and_Media   → diagrams, timelines, Excalidraw
├── 05_Templates           → note templates
└── 09-Microbiology
    ├── Fundamentals/          → concept notes
    ├── Microbiology History/
    ├── Lab/                   → method notes
    ├── Organisms/             → pathogen pages
    ├── Diseases by System/    → CNS, lung, UTI, SSTI…
    ├── Antimicrobials and AMR/ → drugs, mechanisms, stewardship
    ├── Public Health/         → epidemiology, IPC, vaccines, One Health
    └── AI and Bioinformatics/ → computational notes

Plus, at the root: Microbiology Map.canvas (visual index) and Encyclopedia.base (database views).

Note Types

Type	Template	Purpose
MOC	Template - MOC	Hub / map of a domain
Concept note	Template - Note	One idea, deep
Glossary	Template - Glossary	Short definition
Lab method	Template - Lab Tools & Methods	Procedure + clinical use
Book chapter	Template - Book Chapter	Source → atomic notes
History / organism	(see existing notes)	Figure or pathogen pages
Learning aids	Template - Learning Aids	Diagram + example + video block
Disease	Template - Disease	Single infectious disease note

Build Status (high level)

Phase	Status
0 Navigation	✅
1 Foundations	✅ core done
2 Diagnostics	✅ molecular spine expanded (extraction → PCR family → NGS wet lab)
3 Bacteriology	✅ 25 bacterial pathogens + advanced genetics + AMR deep-dives
4 Clinical / Abx / AMR hubs	✅ scaffolds + AMR deep-dives
5 Virus / fungi / parasite / immuno	✅ 4 priority viruses; fungi/parasite/immuno still scaffolds
6 Bioinformatics + AI	✅ BI/AI + algorithm atlas (supervised→GNN/generative, how-to playbooks)
7 Source pipeline	🔄 ongoing
8 Infrastructure (dashboards, base, canvas, CSS, glossary)	✅ Vault Audit 2026-08-01

See Encyclopedia Map for the detailed backlog.