{"id":39348207,"url":"https://github.com/kimtth/science-companion-mindmap","last_synced_at":"2026-01-18T02:25:23.765Z","repository":{"id":322387873,"uuid":"1087821881","full_name":"kimtth/science-companion-mindmap","owner":"kimtth","description":"🧪References and notes for science mindmap — College-level science overview","archived":false,"fork":false,"pushed_at":"2025-11-21T11:16:27.000Z","size":736,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-11-21T11:24:09.026Z","etag":null,"topics":["biology","chemistry","college","mermaid-diagrams","physics","science"],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kimtth.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-11-01T18:01:36.000Z","updated_at":"2025-11-21T11:16:24.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/kimtth/science-companion-mindmap","commit_stats":null,"previous_names":["kimtth/science-companion-mindmap"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/kimtth/science-companion-mindmap","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kimtth%2Fscience-companion-mindmap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kimtth%2Fscience-companion-mindmap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kimtth%2Fscience-companion-mindmap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kimtth%2Fscience-companion-mindmap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kimtth","download_url":"https://codeload.github.com/kimtth/science-companion-mindmap/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kimtth%2Fscience-companion-mindmap/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28526569,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T00:39:45.795Z","status":"online","status_checked_at":"2026-01-18T02:00:07.578Z","response_time":98,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biology","chemistry","college","mermaid-diagrams","physics","science"],"created_at":"2026-01-18T02:25:22.978Z","updated_at":"2026-01-18T02:25:23.745Z","avatar_url":"https://github.com/kimtth.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# 🧪🔬🧬 Science Companion Mindmaps\n\n\u003e **Comprehensive visual learning guides for college-level science courses**\n\n[![Mermaid](https://img.shields.io/badge/Made%20with-Mermaid-ff69b4)](https://mermaid.js.org/)\n[![College Level](https://img.shields.io/badge/Level-College-blue)](https://github.com)\n\nThis repository is inspired by [Grokipedia](https://grokipedia.com/), which demonstrates how LLMs can understand world knowledge.\n\n## 📖 Overview\n\nThis repository contains **interactive flowchart mindmaps** for four core science and mathematics disciplines, designed to help students visualize and understand the hierarchical relationships between concepts in:\n\n- ⚛️ **General Physics** - From mechanics to quantum physics\n- 🧬 **General Biology** - From cells to ecosystems  \n- 🧪 **General Chemistry** - From atoms to organic molecules\n- 🔢 **College Mathematics** - From calculus to mathematical foundations\n\nEach mindmap is created using **Mermaid diagrams** with color-coded categories, concise descriptions, and practical context for every concept.\n\n**✅ Comprehensive Coverage:** All diagrams provide complete coverage of standard college-level introductory courses, aligned with leading textbooks (Campbell Biology, Zumdahl Chemistry, Halliday/Resnick Physics).\n\n## 🎯 Features\n\n✨ **Comprehensive Coverage** - 2,600+ concepts across 27 detailed diagrams covering all major topics in introductory college-level science and mathematics courses  \n🎨 **Color-Coded** - Physics (blue), Biology (green), Chemistry (orange), Mathematics (purple) with 3-4 tier visual hierarchy  \n📊 **Hierarchical Structure** - 3-4 levels of depth showing concept relationships from foundational principles to specific applications  \n💡 **Contextual Learning** - Each node includes 2-3 line descriptions: concept name, definition, and practical significance  \n📱 **Interactive** - Renders in any Mermaid-compatible viewer and natively on GitHub  \n📚 **Textbook-Aligned** - Based on standard college textbooks with equations, formulas, and key principles included  \n🎓 **Exam-Ready** - Perfect for MCAT, DAT, AP courses, and undergraduate science requirements  \n✅ **Verified Structure** - All diagrams verified with proper node connections and consistent color coding\n\n## 📂 Repository Structure\n\n```\nscience-companion-mindmap/\n│\n├── 📘 **Navigation Hub Files** (Root Level)\n│   ├── biology.md          # 🧭 Biology navigation hub → biology/*.md\n│   ├── chemistry.md        # 🧭 Chemistry navigation hub → chemistry/*.md\n│   ├── math.md             # 🧭 Mathematics navigation hub → math/*.md\n│   └── physhics.md         # 🧭 Physics navigation hub → physics/*.md (note: filename typo preserved for compatibility)\n│\n├── 📗 **biology/** - Biology Topic Diagrams (Green Theme)\n│   ├── biology-cell.md                 # Cell structure, metabolism, division\n│   ├── biology-genetics.md             # DNA, inheritance, gene expression\n│   ├── biology-evolution.md            # Natural selection, speciation\n│   ├── biology-ecology.md              # Populations, ecosystems, conservation\n│   ├── biology-organisms.md            # Plant \u0026 animal systems\n│   └── biology-diversity.md            # Taxonomy, phylogeny, biodiversity\n│\n├── 📙 **chemistry/** - Chemistry Topic Diagrams (Orange Theme)\n│   ├── chemistry-atomic.md             # Atomic structure, periodic table\n│   ├── chemistry-bonding.md            # Ionic, covalent, molecular geometry\n│   ├── chemistry-stoichiometry.md      # Moles, reactions, states of matter\n│   ├── chemistry-thermochem-kinetics.md # Energy, reaction rates\n│   ├── chemistry-equilibrium.md        # Equilibrium, Le Châtelier\n│   ├── chemistry-acids-bases.md        # pH, buffers, titration\n│   ├── chemistry-redox.md              # Oxidation-reduction, electrochemistry\n│   ├── chemistry-organic.md            # Hydrocarbons, functional groups\n│   └── chemistry-transition-nuclear.md # Transition metals, radioactivity\n│\n├── 🟣 **math/** - Mathematics Topic Diagrams (Purple Theme)\n│   ├── math-calculus.md                # Limits, derivatives, integrals, series, multivariable\n│   ├── math-linear-algebra.md          # Vectors, matrices, eigenvalues, vector spaces\n│   ├── math-differential-equations.md  # ODEs, PDEs, Laplace transforms, applications\n│   ├── math-probability-statistics.md  # Probability, distributions, inference, regression\n│   ├── math-discrete.md                # Logic, set theory, combinatorics, graph theory\n│   └── math-logic-foundations.md       # Set theory, number theory, formal systems\n│\n├── 📗 **physics/** - Physics Topic Diagrams (Blue Theme)\n│   ├── physics-mechanics.md            # Mechanics, kinematics, dynamics\n│   ├── physics-waves.md                # Waves, SHM, sound\n│   ├── physics-thermodynamics.md       # Heat, entropy, engines\n│   ├── physics-electromagnetism.md     # Fields, circuits, EM waves\n│   ├── physics-optics.md               # Geometric \u0026 wave optics\n│   └── physics-modern.md               # Relativity, quantum, nuclear\n│\n├── 📘 **note/** - Study Guides \u0026 Formulas\n│   ├── physhics-note.md                # Physics formulas \u0026 concepts\n│   ├── biology-note.md                 # Biology formulas \u0026 concepts\n│   ├── chemistry-note.md               # Chemistry formulas \u0026 concepts\n│   └── math-note.md                    # Mathematics formulas \u0026 concepts\n│\n└── 📋 README.md                        \n```\n\n**📌 Navigation:** Start with root-level hub files (`biology.md`, `chemistry.md`, `math.md`, `physhics.md`) which link to detailed topic diagrams in their respective folders.\n\n## 🔬 Subject Guides\n\n### ⚛️ Physics (Blue Theme) - 6 Detailed Diagrams\n\n1. **physics-mechanics.md** (~220 nodes)  \n   Kinematics • Dynamics (Newton's laws) • Energy \u0026 Work • Momentum • Rotation • Fluids\n\n2. **physics-waves.md** (~180 nodes)  \n   Simple Harmonic Motion • Wave Properties • Sound (Doppler, intensity)\n\n3. **physics-thermodynamics.md** (~190 nodes)  \n   Temperature \u0026 Heat • Gas Laws • First Law (ΔU = Q - W) • Second Law (entropy, Carnot)\n\n4. **physics-electromagnetism.md** (~210 nodes)  \n   Electric Fields (Coulomb, Gauss) • Electric Potential • Circuits (Ohm, Kirchhoff) • Magnetism • EM Induction (Faraday, Lenz)\n\n5. **physics-optics.md** (~185 nodes)  \n   Geometric Optics (mirrors, lenses, Snell's law) • Wave Optics (interference, diffraction, polarization)\n\n6. **physics-modern.md** (~200 nodes)  \n   Special Relativity (E=mc²) • Quantum Mechanics (uncertainty, Schrödinger) • Atomic Physics (Bohr model) • Nuclear Physics (fission/fusion)\n\n### 🧬 Biology (Green Theme) - 6 Detailed Diagrams\n\n1. **biology-cell.md** (~180 nodes)  \n   Cell Theory • Prokaryotes vs Eukaryotes • Organelles • Membrane Transport • Cell Signaling • Cell Cycle (mitosis/meiosis)\n\n2. **biology-genetics.md** (~175 nodes)  \n   DNA Structure \u0026 Replication • Gene Expression (transcription/translation) • Gene Regulation • Inheritance (Mendel's laws) • CRISPR\n\n3. **biology-evolution.md** (~165 nodes)  \n   Natural Selection • Evidence (fossils, comparative anatomy) • Speciation • Population Genetics (Hardy-Weinberg) • Phylogeny\n\n4. **biology-ecology.md** (~155 nodes)  \n   Population Ecology (growth models) • Community Ecology (competition, succession) • Ecosystem Ecology (energy flow, nutrient cycles) • Conservation\n\n5. **biology-organisms.md** (~170 nodes)  \n   Plant Structure \u0026 Reproduction • Animal Organ Systems (circulatory, respiratory, digestive, nervous, endocrine, immune) • Homeostasis\n\n6. **biology-diversity.md** (~165 nodes)  \n   Viruses • Prokaryotes (bacteria, archaea) • Protists • Fungi • Plant Diversity • Animal Diversity (invertebrates/vertebrates) • Phylogeny\n\n### 🧪 Chemistry (Orange Theme) - 9 Detailed Diagrams\n\n1. **chemistry-atomic.md** (~155 nodes)  \n   Subatomic Particles • Isotopes • Electron Configuration (quantum numbers, Aufbau, Pauli, Hund) • Periodic Table • Periodic Trends\n\n2. **chemistry-bonding.md** (~180 nodes)  \n   Ionic/Covalent/Metallic Bonding • Lewis Structures • VSEPR Theory (5 geometries) • Polarity • Intermolecular Forces • Hybridization\n\n3. **chemistry-stoichiometry.md** (~220 nodes)  \n   Mole Concept (Avogadro 6.022×10²³) • Balancing Equations • Limiting Reactant • Gas Laws (PV=nRT) • Phase Changes • Solutions • Colligative Properties\n\n4. **chemistry-thermochem-kinetics.md** (~190 nodes)  \n   Thermochemistry (enthalpy, ΔG=ΔH-TΔS, Hess's law) • Kinetics (rate laws, Arrhenius equation, activation energy, catalysis)\n\n5. **chemistry-equilibrium.md** (~160 nodes)  \n   Equilibrium Constant (K, Kp) • Reaction Quotient Q • Le Châtelier's Principle • ICE Tables • Solubility (Ksp)\n\n6. **chemistry-acids-bases.md** (~175 nodes)  \n   Acid-Base Theories (Arrhenius, Brønsted-Lowry, Lewis) • pH Scale • Henderson-Hasselbalch • Buffers • Titrations\n\n7. **chemistry-redox.md** (~150 nodes)  \n   Oxidation States • Balancing Redox • Electrochemistry (galvanic/electrolytic cells, Nernst equation) • Batteries\n\n8. **chemistry-organic.md** (~185 nodes)  \n   Hydrocarbons (alkanes/alkenes/alkynes/aromatic) • Functional Groups (7 major) • Isomers (structural/geometric/optical) • Polymers • Biological Molecules\n\n9. **chemistry-transition-nuclear.md** (~170 nodes)  \n   Transition Metals (coordination compounds, crystal field theory) • Nuclear Chemistry (radioactive decay, fission/fusion, half-life)\n\n### 🔢 Mathematics (Purple Theme) - 6 Detailed Diagrams\n\n1. **math-calculus.md** (~150 nodes)  \n   Limits \u0026 Continuity • Derivatives (4 rules, optimization) • Integration (5 techniques, FTC) • Sequences \u0026 Series (convergence tests, Taylor series) • Multivariable (partial derivatives, Lagrange multipliers) • Vector Calculus (Green's, Stokes', Divergence theorems)\n\n2. **math-linear-algebra.md** (~120 nodes)  \n   Vectors (dot/cross products) • Matrices (operations, RREF, inverses) • Systems of Equations • Determinants • Eigenvalues/Eigenvectors • Vector Spaces • Linear Transformations • Inner Product Spaces (Gram-Schmidt)\n\n3. **math-differential-equations.md** (~180 nodes)  \n   First Order ODEs (separable, linear, exact) • Second Order ODEs (characteristic equation) • Systems • Laplace Transform • Series Solutions • PDEs (heat/wave/Laplace) • Numerical Methods (Euler, RK4)\n\n4. **math-probability-statistics.md** (~200 nodes)  \n   Probability Theory (Bayes' theorem, counting) • Random Variables (PMF, PDF, CDF) • Distributions (binomial, normal, CLT, chi-square, t) • Descriptive Statistics • Point/Interval Estimation (MLE, CI) • Hypothesis Testing (p-value, Type I/II errors) • Regression • ANOVA\n\n5. **math-discrete.md** (~190 nodes)  \n   Logic \u0026 Proofs (induction, contradiction) • Set Theory (relations, functions) • Combinatorics (P(n,r), C(n,r), binomial theorem) • Graph Theory (Euler/Hamiltonian, trees, MST, BFS/DFS/Dijkstra) • Algorithms (Big O, sorting, dynamic programming)\n\n6. **math-logic-foundations.md** (~140 nodes)  \n   Set Theory (ZFC axioms, cardinals ℵ₀, Cantor's theorem) • Number Theory (GCD, primes, modular arithmetic, RSA) • Mathematical Induction • Formal Systems (Gödel's incompleteness, computability, Turing machines)\n\n## 🚀 How to Use\n\n**View on GitHub** - All diagrams render natively in `.md` files  \n**Mermaid Live Editor** - Copy/paste diagrams to [mermaid.live](https://mermaid.live/)  \n**VS Code** - Install [Markdown Preview Mermaid Support](https://marketplace.visualstudio.com/items?itemName=bierner.markdown-mermaid), press Ctrl+Shift+V  \n**Navigation** - Start with hub files (`biology.md`, `chemistry.md`, `math.md`, `physics.md`) → Navigate to topic diagrams in folders  \n**Study Notes** - Formulas and equations in `note/` folder\n\n## 📚 Based on Standard Textbooks\n\n**Physics** - Halliday/Resnick *University Physics*  \n**Chemistry** - Zumdahl *Chemistry*  \n**Biology** - Campbell *Biology* 12th ed  \n**Mathematics** - Stewart *Calculus*, Strang *Linear Algebra*, Boyce \u0026 DiPrima *Differential Equations*, Ross *Probability*, Rosen *Discrete Mathematics*\n\n## 📊 Coverage\n\n**Total:** ~2,600+ nodes across 27 diagrams\n\n- **Biology** (~1,010 nodes): Cell Biology • Genetics • Evolution • Ecology • Organisms • Diversity\n- **Chemistry** (~1,385 nodes): Atomic Structure • Bonding • Stoichiometry • Thermochem/Kinetics • Equilibrium • Acids/Bases • Redox • Organic • Transition/Nuclear\n- **Physics** (~1,185 nodes): Mechanics • Waves • Thermodynamics • Electromagnetism • Optics • Modern Physics\n- **Mathematics** (~1,020 nodes): Calculus • Linear Algebra • Differential Equations • Probability/Statistics • Discrete Math • Logic/Foundations\n\n**Ideal For:** Undergraduate STEM courses • AP courses (Biology, Chemistry, Physics, Calculus, Statistics) • Standardized tests (MCAT, DAT, GRE) • Pre-med, engineering, CS prerequisites\n\n## 💡 Study Tips\n\n🎓 Start with topic-specific diagrams matching your coursework  \n🔍 Follow arrows to understand hierarchical relationships  \n📝 Each node = flashcard (name/definition/context)  \n🔄 Review regularly - visual memory aids retention  \n🤝 Notice cross-disciplinary connections (e.g., thermodynamics in physics \u0026 chemistry)\n\n## 🛠️ Technical Details\n\n**Format:** Mermaid v9+ flowcharts in `.md` files  \n**Colors:** 4-tier CSS hierarchy per subject  \n**Math:** Unicode notation (H₂O, v², E=mc², ∆G, ∫, ∂)  \n**Structure:** 4 hub files + 27 topic diagrams (Physics 6, Biology 6, Chemistry 9, Math 6)  \n**Rendering:** GitHub native, Mermaid Live Editor, VS Code, Notion, Obsidian\n\n## 🎨 Color Scheme\n\nAll nodes in the diagrams are consistently styled with a 4-tier color hierarchy:\n\n| Subject | Primary | Secondary | Tertiary | Quaternary |\n|---------|---------|-----------|----------|------------|\n| ⚛️ **Physics** | Dark Blue (#1e40af) | Blue (#3b82f6) | Light Blue (#60a5fa) | Pale Blue (#93c5fd) |\n| 🧬 **Biology** | Dark Green (#15803d) | Green (#22c55e) | Light Green (#4ade80) | Mint Green (#86efac) |\n| 🧪 **Chemistry** | Dark Orange (#c2410c) | Orange (#ea580c) | Light Orange (#fb923c) | Peach (#fdba74) |\n| 🔢 **Mathematics** | Dark Purple (#7c3aed) | Purple (#a78bfa) | Light Purple (#c4b5fd) | Pale Purple (#ddd6fe) |\n\n**Color Application:**\n- **Primary (:::blue/green/orange/purple)** - Root/Start nodes and major section headers\n- **Secondary (:::lightblue/lightgreen/lightorange/lightpurple)** - Main topic categories\n- **Tertiary (:::paleblue/palegreen/paleorange/palepurple)** - Subtopics and concepts\n- **Quaternary (:::skyblue/mintgreen/peach/lavender)** - Detailed nodes and specific examples\n\n## 🔧 Quality Assurance\n\nAll diagrams in this repository have been verified for:\n\n✅ **Structural Integrity** - Every node is properly connected to the diagram tree (no orphaned nodes)  \n✅ **Color Consistency** - All nodes have appropriate color class definitions matching the 4-tier hierarchy  \n✅ **Unicode Math** - Mathematical notation uses Unicode characters (v², H₂O, ∆G, ∫, ∂) for universal compatibility  \n✅ **Mermaid Compatibility** - Tested and validated across GitHub, Mermaid Live Editor, and VS Code  \n✅ **Rendering Verification** - All 30 diagrams render correctly without errors\n\n### Diagram Standards\n\n**Node Connection:** All concept nodes trace back to the root `Start` node through parent-child relationships  \n**Color Coding:** Consistent 4-tier visual hierarchy with proper CSS class definitions (:::blue, :::lightblue, :::paleblue, :::skyblue)  \n**Mathematical Notation:** Unicode superscripts (⁰¹²³⁴⁵⁶⁷⁸⁹) and subscripts (₀₁₂₃₄₅₆₇₈₉) for formulas  \n**Special Characters:** Greek letters (α, β, γ, θ, ω, λ, μ, π, ρ, σ, τ, φ, Ω), operators (±, ≥, ≤, ≠, ≈, ∞), set theory (∈, ∉, ⊂, ⊆, ∪, ∩), calculus (∂, ∫, ∑, ∏, √), arrows (→, ⇌)  \n**Line Breaks:** HTML `\u003cbr/\u003e` tags for multi-line node descriptions\n\n## 📜 License\n\nThis educational resource is provided as-is for learning purposes.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkimtth%2Fscience-companion-mindmap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkimtth%2Fscience-companion-mindmap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkimtth%2Fscience-companion-mindmap/lists"}