# Genomics ## Built MicroSim Articles — live (three.js) **60 GENOMICS microsims are built and live** on wikitube-3d-microsims.netlify.app, each paired with a microsim-first article at this hub root. Full index: GENOMICS MicroSim Articles. (Batches 3-4 pending.) ## Links (Wikipedia order) <!-- injected from _registry/childlinks/Genomics.json (2026-07-30T02:09:12Z) --> `1000_Genomes_Project` · `16S_ribosomal_RNA` · `23andMe` · `Abiogenesis` · `Aerobiology` · `Agronomy` · `Agrostology` · `Alanine` · `Allan_Maxam` · `Allele` · `Amazon_Standard_Identification_Number` · `Amino_acid` · `Analog-to-digital_converter` · `Anatomy` · `Anne_Wojcicki` · `Anthropology` · `Arabidopsis_thaliana` · `Archaea` · `Archaeogenetics` · `Astrobiology` · `BLAST_(biotechnology)` · `Bacteria` · `Bacteriology` · `Bacteriophage` · `Bacteriophage_MS2` · `Bar_Harbor,_Maine` · `Base_pair` · `Behavioural_genetics` · `Belgium` · `Bennett_Greenspan` · `Biochemistry` · `Biochip` · `Biodiversity` · `Biogeography` · `Biogeology` · [[Bioinformatics]] · [[Biological_engineering]] · `Biomechanics` · `Biophysics` · `Biosemiotics` · `Biostatistics` · `Biotechnology` · `Botany` · `Brigham_and_Women's_Hospital` · `Broad_Institute` · `Caenorhabditis_elegans` · `Caister_Academic_Press` · `Cell_biology` · `Cellular_microbiology` · `Centromere` · `Chemical_biology` · `Cheminformatics` · `Chemogenomics` · `Chloroplast` · `Chromosome` · `Chromosome_conformation_capture` · `Chronobiology` · `Classical_genetics` · `Cognitive_biology` · `Cognitive_genomics` · `Comparative_biology` · `Comparative_genomics` · `Computational_biology` · `Computational_genomics` · [[Connectomics]] · `Conservation_biology` · `Conservation_genetics` · `Crocosphaera_watsonii` · `Cryobiology` · `Cyanobacteria` · `Cytogenetics` · `DNA` · `DNA_Data_Bank_of_Japan` · `DNA_methylation` · `DNA_polymerase` · `DNA_replication` · `DNA_sequencer` · `DNA_sequencing` · `Demography` · `Dendrology` · `Developmental_biology` · `Dichotomyctere_nigroviridis` · `Dideoxynucleotide` · `Drosophila_melanogaster` · `Ecological_genetics` · [[Ecology]] · `Electrophoresis` · `Electrospray_ionization` · `Embryology` · `English_language` · `Epidemiology` · `Epigenetics` · `Epigenome` · `Epigenomics` · `Epistasis` · `Epitranscriptome` · `Euan_Ashley` · `Eukaryote` · `Europe` · `European_Molecular_Biology_Laboratory` · [[Evolution]] · `Evolutionary_biology` · `Expressed_sequence_tag` · `FamilyTreeDNA` · `Fisheries_management` · `Fluorescence` · `Francis_Crick` · `Frederick_Sanger` · `Freshwater_biology` · `Functional_genomics` · `G_banding` · `Gene` · `GeneCalling` · `Gene_expression` · `Gene_prediction` · `Genealogical_DNA_test` · `Genetic_code` · `Genetic_diversity` · [[Genetic_engineering]] · `Genetic_genealogy` · `Genetic_history_of_Africa` · `Genetic_history_of_Europe` · `Genetic_history_of_Italy` · `Genetic_history_of_the_British_Isles` · `Genetic_history_of_the_Middle_East` · `Genetic_monitoring` · `Genetic_variation` · `Geneticist` · `Genetics` · `Genetics_and_archaeogenetics_of_South_Asia` · `Genetics_in_fiction` · `Genographic_Project` · `Genome` · `Genome_Biology` · `Genome_editing` · `Genome_project` · `Genomics_(journal)` · `Geobiology` · [[German_language]] · `Gerontology` · `Ghent` · `Glycomics` · `Haemophilus_influenzae` · `Hans_Winkler` · `Haplogroup` · `Haplotype` · `Harvard_University` · `Heredity` · `Herpetology` · `Heterosis` · `Hi-C_(genomic_analysis_technique)` · `Histology` · `History_of_biology` · `History_of_genetics` · `Homologous_chromosome` · `Homology_modeling` · `Horizontal_gene_transfer` · `Human_Connectome_Project` · `Human_Epigenome_Project` · `Human_Genome_Project` · `Human_Metabolome_Database` · `Human_Microbiome_Project` · `Human_biology` · `Human_evolution` · `Human_genome` · `Human_mitochondrial_genetics` · `ISFET` · `Ichthyology` · `Illumina_dye_sequencing` · `Immunogenetics` · `Immunology` · `Immunomics` · `In_silico` · `In_vitro` · `Index_of_genetics_articles` · `International_Society_of_Genetic_Genealogy` · `Introduction_to_genetics` · `Ion_semiconductor_sequencing` · `J._Craig_Venter_Institute` · `Jackson_Laboratory` · `James_E._Womack` · `Japan` · `Joint_Genome_Institute` · `Jonathan_Eisen` · `Karyotype` · `Landscape_genetics` · `Landscape_genomics` · `Lipidology` · `Lipidome` · `Lipidomics` · `List_of_genetic_codes` · `List_of_genetics_research_organizations` · `List_of_omics_topics_in_biology` · `Living_DNA` · `Locus_(genetics)` · `Lyngbya_majuscula` · `Mammalogy` · `Marine_biology` · `Maryland` · `Massachusetts_General_Hospital` · `Mathematical_and_theoretical_biology` · `Medical_genetics` · [[Medicine]] · `Mendelian_inheritance` · `Metabolome` · `Metabolomics` · `Metagenomics` · `Microarray` · `Microbial_ecology` · `Microbial_genetics` · `Microbiological_culture` · `Microbiology` · `Microbiome` · `Microevolution` · `Missing_heritability_problem` · `Model_organism` · `Molecular_biology` · `Molecular_evolution` · `Molecular_genetics` · `Multicellular_organism` · `Multiomics` · `Multiplex_(assay)` · `Mutation` · `MyHeritage` · `Mycology` · `Mycoplasma_genitalium` · `Mycoplasma_laboratorium` · `National_Human_Genome_Research_Institute` · `National_Institutes_of_Health` · `Natural_environment` · `Nature_(journal)` · `Nebula_Genomics` · `Neologism` · `Neontology` · [[Neuroscience]] · `Nobel_Prize` · `Nobel_Prize_in_Physiology_or_Medicine` · `Nodularia` · `North_America` · `Nucleotide` · `Nutritional_science` · `Omics` · `Oncogenomics` · `Open_reading_frame` · `Ornithology` · `Osteology` · `Outline_of_biology` · `Outline_of_genetics` · `Paleontology` · `Paleopolyploidy` · `Parasitology` · `Pascal_Mayer` · `Pathogen` · `Pathogenomics` · `Pathology` · `Paul_Berg` · `Personal_genomics` · `Personalized_medicine` · `Pharmacogenomics` · `Pharmacology` · `Phi_X_174` · `Philip_Leder` · `Phosphodiester_bond` · `Photobiology` · `Photosynthesis` · `Phycology` · `Phylogenetics` · `Physiology` · `Pipeline_(computing)` · `Pipeline_(software)` · `Plant_genetics` · `Pleiotropy` · `Polyacrylamide` · `Polymerase` · `Polymerase_chain_reaction` · `Pomology` · `Population_genetics` · `Population_genomics` · `Primatology` · `Primer_(molecular_biology)` · `Prochlorococcus` · `Prochloron` · `Prophage` · `Protein` · `Protein_structure` · `Protein_structure_prediction` · `Protein–protein_interaction` · `Proteome` · `Proteomics` · `Protistology` · `Pyrosequencing` · `Quantitative_genetics` · `Quantum_biology` · `RNA` · `Recombinant_DNA` · `Replicon_(genetics)` · `Reproductive_biology` · `Reverse_genetics` · `Robert_W._Holley` · `Rosalind_Franklin` · `SV40` · `Saccharomyces_cerevisiae` · `Sanger_sequencing` · `Sequence_alignment` · `Sequence_assembly` · `Sequencing` · `Sex_chromosome` · `Shotgun` · `Shotgun_sequencing` · `Sociobiology` · `Sociogenomics` · `Spatial_biology` · `Spencer_Wells` · `Stephen_J._O'Brien` · `Stephen_Oliver_(scientist)` · `Structural_bioinformatics` · `Structural_biology` · `Structural_genomics` · `Subclade` · `Surname_DNA_project` · `Symbiosis` · `Synechococcus` · `Synthetic_biology` · `Systematics` · [[Systems_biology]] · `Taxonomy_(biology)` · `Teratology` · `Three-dimensional_space` · `Timeline_of_biology_and_organic_chemistry` · `Timeline_of_the_history_of_genetics` · `Toxicogenomics` · `Toxicology` · `Transcriptome` · `Transcriptomics_technologies` · `Translation_(biology)` · `Virology` · `Virophysics` · `Virus` · `Walter_Gilbert` · [[Wayback_Machine]] · `Welfare_biology` · `Wellcome_Sanger_Institute` · `Whole_genome_sequencing` · `Xenobiology` · `Zoology` The **GENOMICS** acronym spells eight branches of the life sciences, in order: **G**enetics · **E**cology · **N**euroscience · **O**ncology · **M**icrobiology · **I**mmunology · **C**ytology · **S**ystematics. This article is the **worklist**. It was seeded from the link-graph crawl in `G.E.N.O.M.I.C.S..csv` — **2,816 validated Wikipedia links** across the parent pages. Each branch below carries a short summary plus the most microsimmable child articles, grouped by p5.js MicroSim pattern and led by a build-first **top-10**. ← Related: [[Physics|PHYSICS]] · REACTION · COSMOS · POETICS · GENERATIVE · standards in P5 JS EDITOR · best practices in MicroSim Best Practices · collision control in MicroSim-Registry *Slug note:* worklist links use the **human-readable** form of each Wikipedia slug. *Sheet note:* this CSV's columns are flipped from the others — **column A is the parent, column B is the validated link**. **Status legend:** `- [ ]` unclaimed · `- [x] … *✅ <editor URL>*` shipped. --- > ## ⚠️ Two notes on this hub > > **1. The 8th section is Systematics.** The parent column spells GENOMIC**S**; the missing eighth branch is **Systematics** (classification & phylogeny), now populated below via a live Chrome crawl of the `Systematics` page. > > **2. Biology is *partly* microsimmable.** The life sciences sit between the hard sciences (PHYSICS/REACTION/COSMOS — densely microsimmable) and the humanities (POETICS — barely). The genuinely microsimmable seams are the **dynamic, quantitative processes**: population dynamics (predator–prey, logistic growth), the action potential, DNA replication/transcription/translation, Punnett squares and Hardy–Weinberg, [[Diffusion|diffusion]] and membrane transport, tumour-growth and epidemic (SIR) models, mitosis/meiosis. The large catalog of **named genes, proteins, species, diseases, and anatomy** is *different-visualization* material (cards, trees, annotated diagrams), dropped from these worklists. --- ## Overview The **life sciences** study [[Living_systems|living systems]] — from molecules and cells to organisms, populations, and ecosystems. The eight GENOMICS branches: Genetics (genes, inheritance, and variation), [[Ecology|Ecology]] (organisms and their environment), [[Neuroscience|Neuroscience]] (the [[Nervous_system|nervous system]]), Oncology (cancer biology), Microbiology (microorganisms), Immunology (the immune [[System|system]]), Cytology (cell biology), and Systematics (classification & phylogeny). Each is a "room" with its own worklist below. | Branch | Letter | Candidate links in sheet | Worklist status | |--------|:------:|:-----:|-----------------| | Genetics | G | 605 | ✅ 112 selected | | Ecology | E | 722 | ✅ 133 selected | | Neuroscience | N | 462 + re-crawl | ✅ 73 selected | | Oncology | O | 272 + re-crawl | ✅ 52 selected | | Microbiology | M | re-crawled | ✅ 57 selected | | Immunology | I | 276 | ✅ 55 selected | | Cytology | C | re-crawled | ✅ 55 selected | | Systematics | S | crawled | ✅ 50 selected | --- ## G — Genetics Genetics is the study of genes, heredity, and variation — how the [[Information|information]] encoded in DNA is copied, read out, recombined, mutated, and shifted in frequency across generations. It is among the most microsimmable corners of the life sciences because almost every core idea is a **process** or a **quantitative model** rather than a static object: replication unzips and copies a double helix, transcription and translation run a tape through a machine, a Punnett square is a combinatorial grid, meiosis lines up homologues and crosses them over, a mutation flips one base in a running [[Sequence|sequence]], and selection, drift, and gene flow push allele frequencies like sliders on a population. A learner can drive every one of these from a p5.js canvas. **112 articles** selected from the 605 validated candidates — the second-largest pool in the sheet — by the quality bar *"can this be shown as an effective interactive MicroSim?"*, grouped by p5.js pattern and led by a build-first top-10. The pool was heavily diluted and most of it dropped. The single largest block was the **Branches of biology** navbox that every biology page carries (Anatomy, Botany, Ecology, Immunology, Microbiology, Neuroscience, Zoology … — each a different room or off-theme entirely), followed by the long roster of **geneticists** (Mendel, Darwin, Galton, Morgan, Sturtevant, Watson, Crick, Franklin, McClintock, Sanger, Mullis …) and their **places, books, journals, and projects** (Brno, Trinity College, *On the Origin of Species*, the *Genetics* journal, the Human Genome Project, Celera). Per the life-[[Science|science]] rule, the large catalog of **named genes and proteins** (the histone family H1–H4, the CENP centromere proteins, p53, Ras, the Trp repressor), **species and model organisms** (*Drosophila*, *E. coli*, *Arabidopsis*, yeast, *C. elegans*, zebrafish, mouse), **diseases** (sickle-cell anaemia, phenylketonuria, schizophrenia), and **anatomical / structural catalog** (karyotype, centromere, telomere, chromatid, the chromosome-type and -arm taxonomy, organs, tissues, plant and body systems) was also dropped as different-visualization material, along with the `*_(identifier)`, `Category:*`, `Template_talk:*`, `List_/Index_/Outline_/Glossary_/Timeline_of_*` cruft and the `-genetics` / `-genomics` **sub-discipline** names (medical, molecular, classical, behavioural, conservation, ecological, pharmaco-, population-*genomics* …). Cancer-genetics items (oncogene, tumour suppressor, metastasis) were left to the **O — Oncology** room and the cell-cycle / organelle items to **C — Cytology** — cross-page sharing is allowed and the registry routes each to its single canonical article. Synonym twins were collapsed to one slug each (Deoxyribonucleic_acid → `DNA`; Dominant_/Recessive_allele and Dominance_relationship → `Dominance_(genetics)`; Selective_breeding → `Artificial_selection`; Nature_and_nurture → `Nature_versus_nurture`). ⚠️ **Note on the pool:** the crawl contains **no Hardy–Weinberg article**, so the canonical equilibrium sim isn't listed here — `Population_genetics` and `Allele_frequency` carry the allele-frequency dynamics instead. ### Top 10 — start here (10) · *the most canonical, visually striking genetics sims; build these first* - [ ] DNA replication - [ ] Transcription (genetics) - [ ] Translation (biology) - [ ] Punnett square - [ ] Mendelian inheritance - [ ] Meiosis - [ ] Mitosis - [ ] Genetic code - [ ] Natural selection - [ ] Genetic drift ### DNA, RNA & molecular structure (11) · *structure / spatial builder; assemble the helix, pair the bases, then melt and re-anneal the strands* - [ ] DNA - [ ] RNA - [ ] Double helix - [ ] Base pair - [ ] Nucleotide - [ ] Hydrogen bonding - [ ] Genome - [ ] Gene - [ ] Chromosome - [ ] Genetic variation - [ ] Denaturation (biochemistry) ### Central dogma — expression, regulation & development (11) · *process animation / parameter sim; run transcription → translation and tune the switches that turn genes on and off* - [ ] Gene expression - [ ] Protein biosynthesis - [ ] Central dogma of molecular biology - [ ] Protein folding - [ ] Post-transcriptional modification - [ ] Regulation of gene expression - [ ] Transcription factor - [ ] [[Negative_feedback]] - [ ] Epigenetics - [ ] Paramutation - [ ] Morphogenesis ### Mendelian & classical inheritance (16) · *Punnett-square / cross; parameter explorer over alleles, zygosity, and dominance* - [ ] Dominance (genetics) - [ ] Allele - [ ] Genotype - [ ] Phenotype - [ ] Homozygous - [ ] Heterozygous - [ ] Diploid - [ ] Haploid - [ ] Ploidy - [ ] Locus (genetics) - [ ] Wild type - [ ] Heredity - [ ] Epistasis - [ ] Sex linkage - [ ] Pedigree chart - [ ] Blending inheritance ### Recombination, segregation & cell division (9) · *spatial process; line up the homologues, cross over, and segregate into gametes* - [x] Cell division *✅ https://wikitube-3d-microsims.netlify.app/Cell_division.html* - [ ] Chromosomal crossover - [ ] Genetic linkage - [ ] Independent assortment - [ ] Origin and function of meiosis - [ ] Gamete - [ ] Sexual reproduction - [ ] Asexual reproduction - [ ] Sex-determination system ### Mutation & chromosomal rearrangement (14) · *event / process sim; flip a base, shift the frame, then duplicate, delete, invert, and translocate* - [ ] Mutation - [ ] Single-nucleotide polymorphism - [ ] Frameshift mutation - [ ] Gene duplication - [ ] Gene deletion - [ ] Chromosomal inversion - [ ] Chromosomal translocation - [ ] Chromosome abnormality - [ ] Aneuploidy - [ ] Polyploidy - [ ] Polyploidization - [ ] Somatic mutation - [ ] DNA repair - [ ] Mutagenic ### Population & evolutionary genetics (17) · *dynamical-system / agent sim; push allele frequencies with selection, drift, flow, and time* - [ ] Population genetics - [ ] Allele frequency - [ ] Gene flow - [ ] Genetic hitchhiking - [ ] Artificial selection - [ ] Fitness (biology) - [ ] Speciation - [ ] [[Adaptation]] - [ ] Molecular clock - [ ] Neutral theory of molecular evolution - [ ] Nearly neutral theory of molecular evolution - [ ] Genetic diversity - [ ] Microevolution - [ ] Macroevolution - [ ] Common descent - [ ] Sequence homology - [ ] Evolutionary tree ### Quantitative & complex traits (7) · *statistics / variance sim; partition heritability and stack additive polygenic effects* - [ ] Quantitative genetics - [ ] Quantitative trait locus - [ ] Heritability - [ ] Complex traits - [ ] Human skin color - [ ] Twin study - [ ] Nature versus nurture ### Lab & genomic techniques (17) · *process / algorithm sim; amplify, cut, ligate, run the gel, sequence, and assemble* - [ ] Polymerase chain reaction - [ ] Gel electrophoresis - [x] DNA sequencing *✅ https://wikitube-3d-microsims.netlify.app/DNA_sequencing.html* - [ ] Sanger sequencing - [ ] Next-generation sequencing - [ ] CRISPR - [ ] Genome editing - [ ] [[Genetic_engineering]] - [ ] Restriction enzymes - [ ] Recombinant DNA - [ ] Molecular cloning - [ ] Cloning - [ ] Plasmid - [ ] Genome assembly - [ ] Transformation (genetics) - [x] Bacterial conjugation *✅ https://wikitube-3d-microsims.netlify.app/Bacterial_conjugation.html* - [ ] Horizontal gene transfer ## E — Ecology Ecology is the study of the relationships between organisms and their environment — how populations grow and crash, how species compete, eat, and depend on one another, how [[Energy|energy]] and matter flow through food webs, and how communities assemble, are disturbed, and recover across space and time. It is the canonical home of the agent-based and dynamical-system MicroSim: almost every core idea is a **process** or a **quantitative model** a learner can drive from a canvas. A logistic curve bends toward its carrying capacity, Lotka–Volterra predator and prey chase each other around a phase loop, a trophic cascade ripples down an ecological pyramid, an island fills to its immigration–extinction equilibrium, dispersing agents knit a metapopulation together, and a wildfire or an invasion spreads cell by cell across a grid. **133 articles** selected from the 722 validated candidates — the largest pool in the sheet — by the quality bar *"can this be shown as an effective interactive MicroSim?"*, grouped by p5.js pattern and led by a build-first top-10. The pool was heavily diluted and most of it dropped. The single largest block was the **Branches of ecology** navbox that every page carries — the long roster of **sub-disciplines** (applied, behavioural, chemical, community, conservation, disease, evolutionary, fire, forest, functional, human, industrial, landscape, microbial, molecular, paleo-, plant, political, restoration, soil, spatial, systems, theoretical, thermal, tropical, urban *ecology*, plus autecology, synecology, macroecology, and ecophysiology) — each a discipline rather than a sim. Then came the roster of **ecologists** (Haeckel, Humboldt, Warming, Clements, Hutchinson, MacArthur, Lindeman, Carson, E. O. Wilson, Verhulst …) and their **places, books, journals, and organisations** (the oceans and continents, *On the Origin of Species*, *Silent Spring*, the *Journal of Biogeography*, the Stanford Encyclopedia). Per the life-science rule, the large catalog of **named organisms, species, and taxa** (algae, fungi, lichen, plankton, ants, bees, wasps, beavers, sea otters, corals, kelp — and the taxonomy scaffolding of domain, kingdom, taxon, and species) and of **biomes and habitats** (taiga, tundra, desert, rainforest, wetland, estuary, reef, hydrothermal vent) was dropped as different-visualization material, along with the **trophic-mode terminology** (the auto-/hetero-/mixo-/chemo-/photo-/litho-troph "primary nutritional groups" and the herbivore / carnivore / detritivore feeding roles), the **elements and molecules** of the nutrient cycles (carbon, nitrogen, phosphorus, oxygen, methane, ammonia), the off-theme **meteorology / [[Earth]]-science** tail (weather, wind, rain, tides, the atmosphere's layers, plate tectonics, the Earth-symbol and Solar-System pages), the **applied / environmental-[[Engineering|engineering]]** tail (pollution control, sewage treatment, remediation, recycling, sustainability policy), and the usual `Category:*`, `Template_talk:*`, `List_/Glossary_/Outline_/History_of_*`, `*_(identifier)`, and `(disambiguation)` cruft. Synonym and plural twins were collapsed to one slug each (Food-web → `Food_web`; Mutualisms → `Mutualism_(biology)`; Ecotones → `Ecotone`; Insular_biogeography → `Island_biogeography`; Nutrient_cycling → `Nutrient_cycle`; Resilience_(ecology) → `Ecological_resilience`; Consumer-resource_model → `Consumer–resource_interactions`; Relative_abundance_distribution → `Relative_species_abundance`). Population-genetics and speciation items (natural selection, genetic drift, allele frequency, allopatric speciation) were left to the **G — Genetics** room and osmosis / membrane-transport items to **C — Cytology** — cross-page sharing is allowed and the registry routes each to its single canonical article. ### Top 10 — start here (10) · *the most canonical, visually striking ecology sims; build these first* - [ ] Lotka–Volterra equations - [ ] Logistic function - [x] [[Carrying_capacity]] *✅ https://wikitube-3d-microsims.netlify.app/Carrying_capacity.html* - [ ] Food web - [ ] Trophic cascade - [ ] Ecological pyramid - [ ] Ecological succession - [ ] Island biogeography - [ ] Competitive exclusion principle - [ ] Optimal foraging theory ### Population dynamics & growth models (16) · *dynamical-system / parameter sim; bend an exponential toward its carrying capacity, then add lags, thresholds, and structure* - [ ] [[Population_dynamics]] - [ ] [[Population_growth]] - [ ] Population cycle - [ ] Malthusian growth model - [ ] Random generalized Lotka–Volterra model - [ ] Density dependence - [ ] Allee effect - [ ] Depensation - [ ] R/K selection theory - [ ] Life history theory - [ ] Recruitment (biology) - [ ] Metapopulation - [ ] Source–sink dynamics - [ ] Minimum viable population - [ ] Effective population size - [ ] Population viability analysis ### Competition, niches & coexistence (12) · *parameter / phase-plane sim; overlap two niches and watch who excludes whom, who partitions, and who coexists* - [ ] Competition (biology) - [ ] Interspecific competition - [ ] Intraspecific competition - [ ] Limiting similarity - [ ] Niche differentiation - [ ] Niche construction - [ ] Niche apportionment models - [ ] Ontogenetic niche shift - [ ] Storage effect - [ ] Priority effect - [ ] Consumer–resource interactions - [ ] Paradox of the plankton ### Predation & foraging (8) · *agent / decision sim; tune attack rate and handling time, then let foragers optimise where and what to eat* - [ ] Predation - [ ] Mesopredator release hypothesis - [ ] Intraguild predation - [ ] Prey switching - [ ] Marginal value theorem - [ ] Ideal free distribution - [ ] Resource selection function - [ ] Tritrophic interactions in plant defense ### Food webs, trophic structure & energy flow (15) · *network / flow sim; wire the web, push energy up the levels, and read off the losses* - [ ] Food chain - [ ] Trophic level - [ ] Trophic dynamics - [ ] Trophic state index - [ ] Ecological efficiency - [ ] Energy flow (ecology) - [ ] Primary production - [ ] Productivity (ecology) - [ ] Photosynthetic efficiency - [ ] Ecological stoichiometry - [ ] Biomass (ecology) - [ ] Green world hypothesis - [ ] Microbial loop - [ ] Ecological network - [ ] Non-trophic networks ### Symbiosis & species interactions (8) · *agent / co-dynamics sim; pair two species and slide the interaction from + + to + − to − −* - [ ] Symbiosis - [ ] Mutualism (biology) - [ ] Commensalism - [ ] Parasitism - [ ] Coevolution - [ ] Pollination - [ ] Ecological facilitation - [ ] Mimicry ### Movement, dispersal & collective behavior (6) · *agent-based sim; let individuals walk, flock, and disperse across a landscape* - [ ] Biological dispersal - [ ] Animal migration - [ ] Shoaling and schooling - [ ] [[Self-organization]] - [ ] [[Kin_selection]] - [ ] Group selection ### Spatial, landscape & biogeography (12) · *grid / spatial sim; fragment the habitat, cross the gradient, and fill the islands* - [ ] Species–area relationship - [ ] Habitat fragmentation - [ ] Edge effects - [ ] Patch dynamics - [ ] Ecotone - [ ] Environmental gradient - [ ] Cline (biology) - [ ] Cross-boundary subsidy - [ ] Land change modeling - [ ] Species distribution - [ ] Species distribution modelling - [ ] Latitudinal gradients in species diversity ### Diversity, community structure & keystone roles (9) · *sampling / rank-abundance sim; accumulate species, rank their abundances, and pull a keystone* - [ ] Species richness - [ ] Species diversity - [ ] Relative species abundance - [ ] Unified neutral theory of biodiversity - [ ] Occupancy–abundance relationship - [ ] Keystone species - [ ] Foundation species - [ ] Ecosystem engineer - [ ] Invasive species ### Succession, disturbance, stability & regime shifts (14) · *time-series / tipping-point sim; disturb a community and watch it recover — or flip to an alternative state* - [ ] Seral community - [ ] Climax community - [ ] Disturbance (ecology) - [ ] Intermediate disturbance hypothesis - [ ] Ecological resilience - [ ] Resistance (ecology) - [ ] Ecological stability - [ ] Alternative stable state - [ ] Regime shift - [ ] Ecological threshold - [ ] Panarchy (ecology) - [ ] Ecological collapse - [ ] Extinction debt - [ ] Wildfire ### Biogeochemical cycles & ecosystem processes (10) · *flow / box-model sim; route matter through the pools and watch it accumulate and magnify* - [ ] Biogeochemical cycles - [ ] Nutrient cycle - [ ] Nitrogen fixation - [ ] Decomposition - [ ] Bioturbation - [ ] Bioaccumulation - [ ] Biomagnification - [ ] Evapotranspiration rates - [ ] Soil formation - [ ] Thermally layered zones ### Ecological laws, rules & quantitative theory (8) · *scaling / parameter sim; plot the law and sweep its exponent or limiting factor* - [ ] Liebig's law of the minimum - [ ] Allometry - [ ] Kleiber's law - [ ] Metabolic theory of ecology - [ ] Foster's rule - [ ] Thorson's rule - [ ] Rapoport's rule - [ ] Ascendency ### Ecosystem models & applied dynamics (5) · *model / management sim; forecast a system and harvest it without crashing it* - [ ] [[Ecosystem_model]] - [ ] Ecological forecasting - [ ] Maximum sustainable yield - [ ] Overexploitation - [x] [[Ecological_footprint]] *✅ https://wikitube-3d-microsims.netlify.app/Ecological_footprint.html* ## N — Neuroscience Neuroscience studies the nervous system — how neurons generate and propagate electrical signals, talk to one another across synapses, wire into circuits and large-scale networks, develop, adapt, and give rise to behavior. Its microsimmable seam is narrow but deep: the parts that are genuinely dynamic and quantitative are among the most rewarding sims in the life sciences. A membrane crosses threshold and fires an all-or-nothing spike, the Hodgkin–Huxley gating variables open and close around a phase-plane loop, vesicles release transmitter across a cleft, a recurrent network settles into an [[Attractor|attractor]], grid cells tile an arena with hexagonal firing fields, a circadian oscillator free-runs and re-entrains, and brain-[[Wave|wave]] rhythms rise and fall on an EEG trace — every one of these a learner can drive from a p5.js canvas. **40 articles** selected from the 462 validated candidates, grouped by p5.js pattern and led by a build-first top-10. ⚠️ **Note on the pool:** despite being one of the larger crawls in the sheet, Neuroscience yields fewer sims than Genetics or Ecology — its candidate list is overwhelmingly biographical, disciplinary, and anatomical rather than dynamic. The single largest block is the long roster of **neuroscientists** — nearly the whole Nobel Prize in Physiology or [[Medicine]] lineage (Golgi, Cajal, Sherrington, Adrian, Dale, Loewi, Eccles, Hodgkin, Huxley, Katz, Hubel, Wiesel, Sperry, Kandel, Neher, Sakmann, the Mosers, O'Keefe, Axel, Buck …) plus the historical figures (Galen, Vesalius, Descartes, Willis, Broca, Wernicke, Brodmann, Penfield, Pavlov). Next came roughly seventy **"neuro-X" sub-discipline and applied-field names** (computational, cognitive, molecular, cellular, systems, behavioral, clinical, social, affective, cultural, evolutionary neuroscience; neuroeconomics, neurolaw, neuroethics, neurophilosophy, neuromarketing, neurogastronomy, neuroaesthetics …) — each a discipline rather than a sim, dropped exactly as the "-genetics" subdisciplines were in the **G** room. Per the life-science rule, the large catalog of **named brain anatomy** (cerebrum, cerebellum, pons, medulla, midbrain, diencephalon, hippocampus, the limbic system, the cortical lobes and Brodmann areas, the cranial and spinal nerves, the autonomic / sympathetic / parasympathetic divisions, the cortical homunculus) and of **named cell types** (sensory, motor, glial, and neural stem cells) was dropped as different-visualization material, along with **diseases** (stroke, epilepsy, ALS, the neurodegenerative and neurodevelopmental disorders), **organisations, journals, and books** (the [[Society]] for Neuroscience, the BRAIN Initiative, the Human Brain Project, *Principles of Neural Science*, *The Man Who Mistook His Wife for a Hat*), broad **cognitive nouns** with no specific in-pool model (consciousness, cognition, perception, memory, learning, emotion), generic **methodology** (mathematical modelling, computer simulation, statistics), and the usual `Category:*`, `Template_talk:*`, `List_/Outline_/Glossary_of_*`, and `*_(identifier)` cruft. Synonym and plural twins were collapsed to one slug each (Action_potentials → `Action_potential`; Synapses → `Synapse`; Biological_neuron_models → `Biological_neuron_model`; Neural_networks_(biology) → `Neural_network_(biology)`; Artificial_neural_networks → `Neural_network_(machine_learning)`). Positron-emission tomography is shared with the **R — Radiochemistry** room (built once, referenced from both). The result is a focused set of **40** — below the 50-item target, but the dynamic, quantitative core of this particular crawl genuinely tops out here, and a padded list would only dilute it. ### Top 10 — start here (10) · *the most canonical, visually striking neuroscience sims; build these first* - [x] Action potential *✅ https://wikitube-3d-microsims.netlify.app/Action_potential.html* - [ ] Hodgkin–Huxley model - [ ] Neurotransmission - [ ] Synapse - [ ] Neural network (biology) - [ ] Neuroplasticity - [ ] Reflex - [ ] Grid cell - [ ] Circadian rhythm - [x] Electroencephalography *✅ https://wikitube-3d-microsims.netlify.app/Electroencephalography.html* ### Excitable membranes & spiking-neuron models (5) · *dynamical-system / phase-plane sim; cross threshold, fire, and trace the gating variables around their loop* - [ ] Cell excitability - [ ] FitzHugh–Nagumo model - [ ] Morris–Lecar model - [ ] Biological neuron model - [ ] Models of neural computation ### The neuron & chemical signaling (4) · *structure-builder / process animation; assemble the cell, then release, diffuse, bind, and modulate* - [ ] Neuron - [ ] Neurotransmitter - [ ] Signal transduction - [ ] Neuromodulation ### Circuits, networks & computation (4) · *network / attractor sim; wire neurons into circuits and watch the population compute* - [ ] [[Neural_circuit]] - [ ] [[Neural_network_(machine_learning)]] - [ ] Large-scale brain network - [x] [[Connectomics]] *✅ https://wikitube-3d-microsims.netlify.app/Connectomics.html* ### Coding, decision & sensorimotor representation (6) · *decoding / accumulator / firing-field sim; turn spikes into percepts, decisions, and maps of space* - [ ] Neural decoding - [ ] [[Detection_theory]] - [x] [[Decision_theory]] *✅ https://wikitube-3d-microsims.netlify.app/Decision_theory.html* - [ ] Place cell - [ ] Multisensory integration - [ ] Motor control ### Neurodevelopment (7) · *spatial-patterning / lineage sim; pattern the neural tube, divide and specify fates, then migrate and wire* - [x] Development of the nervous system *✅ https://wikitube-3d-microsims.netlify.app/Development_of_the_nervous_system.html* - [ ] Regional specification - [ ] Neuronal migration - [ ] Neurogenesis - [ ] Gliogenesis - [ ] Synaptogenesis - [ ] Cellular differentiation ### Recording, imaging & stimulation (4) · *signal / detector-schematic sim; record the rhythms, map activation, and drive neurons with light* - [ ] Magnetoencephalography - [ ] Functional neuroimaging - [ ] Positron emission tomography - [ ] Optogenetics *Thickened via a live Chrome re-crawl of `Action_potential`: +33 process sims.* ### Membrane potential & spike dynamics (9) · *membrane-voltage / threshold sim* - [ ] Membrane potential - [ ] Resting potential - [ ] Depolarization - [ ] Repolarization - [ ] Hyperpolarization (biology) - [ ] Threshold potential - [ ] Refractory period (physiology) - [ ] All-or-none law - [ ] Graded potential ### Ion channels & pumps (7) · *gated-channel / ion-flux sim* - [ ] Ion channel - [ ] Voltage-gated ion channel - [ ] Ligand-gated ion channel - [ ] Sodium channel - [ ] Potassium channel - [ ] Calcium channel - [ ] Sodium–potassium pump ### Conduction & neuron models (7) · *cable / Hodgkin–Huxley sim* - [ ] Saltatory conduction - [ ] Conduction velocity - [ ] Cable theory - [ ] Myelin - [ ] Node of Ranvier - [ ] Nernst equation - [ ] Goldman equation ### Synaptic transmission & plasticity (10) · *synapse / summation sim* - [ ] Chemical synapse - [ ] Excitatory postsynaptic potential - [ ] Inhibitory postsynaptic potential - [ ] Spatial summation - [ ] Temporal summation - [ ] Long-term potentiation - [ ] Spike-timing-dependent plasticity - [ ] Neuromuscular junction - [ ] Neural oscillation - [ ] Central pattern generator ## O — Oncology Oncology is the study and treatment of cancer — how a normal cell accumulates the changes that free it from growth control, how the resulting tumour proliferates, rewires its metabolism, evades the immune system, and is screened for, imaged, and treated. Its microsimmable seam is narrow but real: the genuinely dynamic, quantitative pieces are the **processes and models** — multi-hit carcinogenesis and the two-hit loss of a tumour-suppressor, the Warburg metabolic switch, the log-kill kinetics of chemotherapy and the linear–quadratic survival curve of radiotherapy, effector-versus-tumour immune dynamics, the Bayesian arithmetic of screening (sensitivity, specificity, lead-time and length bias, predictive value), and the reconstruction maths behind the scans — every one of these a learner can drive from a p5.js canvas. **18 articles** selected from the 272 validated candidates, grouped by p5.js pattern and led by a build-first top-10. ⚠️ **Under-seeded (18 < 50; not padded).** The Oncology parent is a short clinical-overview page whose link graph is overwhelmingly *not* dynamic. The single largest block is the shared **medicine navbox** — dozens of clinical specialties and sub-specialties (cardiology, dermatology, gastroenterology, nephrology, pulmonology, urology … and the "-oncology" sub-fields: surgical, radiation, gynecologic, pediatric, geriatric, ocular, veterinary, psycho-, cardio-, molecular, mathematical, and comparative oncology) — each a discipline rather than a sim, dropped exactly as the "-genetics" sub-disciplines were in the **G** room. Per the life-science rule, the large catalog of **named cancers and tumours** (breast, prostate, bone, skin, oral, laryngeal, head-and-neck, gastrointestinal, mesothelioma, the leukemias, sarcoma, carcinoma, adenoma, blastoma, hamartoma, papilloma, and the organ-system neoplasms) and of **disease states, symptoms, and pathology grades** (dysplasia, hyperplasia, carcinoma in situ, anaemia, weight-loss, nausea, pain, the paraneoplastic syndromes) was dropped as different-visualization material, along with the **staging and grading classifications** (TNM, Ann Arbor, Dukes, Gleason, tumour grading — classification catalog, not dynamic), the **procedures** (biopsy, endoscopy, the surgeries and resections, transplantation), the **named drugs and companies** (rituximab, trastuzumab; AstraZeneca, Bristol-Myers Squibb, Merck, Novartis, Pfizer, Roche), and the **organisations, journals, degrees, people, and books** (the cancer societies, NCI / NCCN / NICE, the medical degrees and training programs, Siddhartha Mukherjee, *The Emperor of All Maladies*), plus the usual `Category:*`, `Template_talk:*`, `Index_/Outline_/History_of_*`, and `*_(identifier)` cruft. Synonym twins were collapsed to one slug each (Computed_axial_tomography / CT_scan → `X-ray_computed_tomography`; Radiotherapy → `Radiation_therapy`; Immunotherapy → `Cancer_immunotherapy`). ⚠️ **Note on the pool:** the cell-cycle, checkpoint, angiogenesis, clonal-[[Evolution|evolution]], and tumour-growth-curve articles the theme calls for are **not in this crawl** — they live on other parent pages — so a re-crawl from `Cancer`, `Carcinogenesis`, or `Tumor` would lift this branch past 50. Imaging-reconstruction sims (CT, MRI, SPECT, PET-CT, scintigraphy, ultrasound) are shared with the **R — Radiochemistry** / PHYSICS rooms and built once. ### Top 10 — start here (10) · *the most canonical, visually striking oncology sims; build these first* - [ ] Cancer cell - [ ] Carcinogenesis - [ ] Chemotherapy - [ ] Radiation therapy - [ ] Cancer immunotherapy - [ ] Tumor suppressor gene - [ ] Warburg effect (oncology) - [ ] Screening (medicine) - [ ] X-ray computed tomography - [ ] PET-CT ### Tumour dynamics, metabolism & targeted therapy (4) · *agent / flux / parameter sims; spread a transmissible lineage, reroute cancer metabolism, and block a molecular or hormonal driver* - [ ] Clonally transmissible cancer - [ ] Oncometabolism - [ ] Targeted therapy - [ ] Hormonal therapy (oncology) ### Imaging, reconstruction & detection (4) · *reconstruction / wave / detector-schematic sims; fill k-space, back-project a slice, sweep a gamma camera, and read the echoes* - [ ] [[Magnetic_resonance_imaging]] - [ ] Single Photon Emission Computed Tomography - [ ] Scintigraphy - [ ] Ultrasound *Thickened via a live Chrome re-crawl of `Cancer`: +31 process sims.* ### Tumour growth & the cell cycle (8) · *growth-curve / cell-cycle sim* - [ ] Cell growth - [ ] Apoptosis - [ ] Mitotic catastrophe - [ ] Hyperplasia - [ ] Dysplasia - [ ] Neoplasm - [ ] Malignant transformation - [ ] Biological immortality ### Invasion, metastasis & angiogenesis (7) · *spread / vessel-growth agent sim* - [ ] Metastasis - [ ] Angiogenesis - [ ] Angiogenesis inhibitor - [ ] Invasion (cancer) - [ ] Intravasation - [ ] Extravasation - [ ] Cancer stem cell ### Genetic & epigenetic drivers (9) · *mutation-accumulation / repair sim* - [ ] Oncogene - [ ] Carcinogen - [ ] Genome instability - [ ] DNA mismatch repair - [ ] Homologous recombination - [ ] DNA methylation - [ ] Histone modification - [ ] MicroRNA - [ ] Cancer epigenetics ### Metabolism, hypoxia & immunotherapy (7) · *metabolic-flux / checkpoint sim* - [ ] Glycolysis - [ ] Oxidative phosphorylation - [ ] Metabolic theory of cancer - [ ] Hypoxia (medical) - [ ] Immune checkpoint - [ ] Grading (tumors) - [ ] Cancer staging ### Carcinogens, oncoviruses & biomarkers (3) · *infection→transformation / detection sim* - [ ] Oncovirus - [ ] Genotoxin - [ ] Cancer biomarker ## M — Microbiology Microbiology studies microorganisms — bacteria, archaea, fungi, protists, algae, and viruses — the life too small to see without a microscope. Its microsimmable seam is narrow but lively: the genuinely dynamic, quantitative pieces are the **behaviors of microbial cells and populations**. A flagellated cell runs and tumbles up a chemical gradient, a biofilm thickens until a quorum-sensing circuit flips once cell [[Density|density]] crosses a threshold, a culture's growth curve bends through lag, log, and stationary phases, an antibiotic clears the susceptible cells and selects the resistant survivors, a fermenter turns sugar into ethanol, and a marine viral shunt loops carbon back to the dissolved pool — every one of these a learner can drive from a p5.js canvas. **57 articles** — the original 39 plus a live Chrome re-crawl of `Microbiology` (growth, motility, cell [[Structure|structure]], gene transfer) — grouped by p5.js pattern and led by a build-first top-10. ✅ **Re-crawled past 50.** Despite being one of the larger crawls in the sheet, the Microbiology parent's link graph is overwhelmingly *catalog* rather than dynamic, and most of it dropped. The single largest blocks were the **protist & algal structure catalog** (flagella, cilia, kinetoplasts, frustules, coccoliths, contractile vacuoles, pyrenoids, trichocysts, loricas …), the **fungal spore-and-hypha catalog** (ascospore, basidiospore, conidium, sporangium, mycelium, haustorium, ascus, basidium …), and the **bacterial cell-envelope catalog** (peptidoglycan, teichoic acid, lipopolysaccharide, the capsule, S-layer, pilus, fimbria …) — all anatomy / structure, dropped as different-visualization material. Then came the roster of **named organisms and taxa** (*Bacillus*, *Streptomyces*, *Mycobacterium tuberculosis*, *Clostridium*, *Myxococcus*, the diatoms, dinoflagellates, ciliates, and amoebae, plus the taxonomy scaffolding Monera / Prokaryota / Gracilicutes / Bacillota / Mollicutes and the cell-shape terms coccus / bacillus / spirillum), the **nutritional-mode terminology** (auto-/hetero-/photo-/chemo-/phago-/osmo-/sapro-/mixotrophy) and **oxygen-tolerance classes** (obligate and facultative aerobe/anaerobe, microaerophile, aerotolerant, nanaerobe), and the long list of **named microbiomes** (gut, oral, skin, vaginal, lung, placental, plant, root, soil, coral, marine …) — composition catalogs, not sims. Per the life-science rule, named **genes/proteins** (Taq polymerase, reporter genes, two-hybrid screening), **compounds and polymers** (ethanol, vinegar, phenol, xanthan, alginate, cellulose, hyaluronic acid, cyanophycin), and **diseases** (tuberculosis, anthrax, smallpox, rabies, scabies, mycosis) were dropped too, along with the field's **people** (Pasteur, Koch, Hooke, Kircher, Beijerinck, Cohn, Winogradsky, d'Hérelle, Lister, Fracastoro), **places** (Delft, Ancient Rome), **journals, societies, and books** (ASM, FEMS, *Journal of Bacteriology*, *Nature Reviews Microbiology*, *Microbes and Man*), and the usual `Category:*`, `Template_talk:*`, `List_/Outline_/Glossary_/History_of_*`, `*_(identifier)`, and `(disambiguation)` cruft. Cross-page items were routed to their canonical room rather than rebuilt here: the **microbial loop** and **nitrogen fixation** live in **E — Ecology**, **bacterial conjugation / horizontal gene transfer / plasmids** in **G — Genetics**, **16S ribosomal RNA** in **S — Systematics**, and the **epidemic (SIR) model** is reserved for **I — Immunology** — cross-page sharing is allowed and the registry routes each to one article. Synonym twins were collapsed to one slug each (Antibiotics → `Antibiotic`; Mold / Mold_(fungus) dropped as structure). ⚠️ **Note on the pool:** there is no standalone *Bacterial growth* article in this crawl, so the growth-curve dynamics are carried by `Microbiological_culture`, `Microbial_population_biology`, and `Impedance_microbiology`; a re-crawl from `Bacterial_growth` or `Microbial_ecology` would lift this branch past 50. ### Top 10 — start here (10) · *the most canonical, visually striking microbiology sims; build these first* - [x] Biofilm *✅ https://wikitube-3d-microsims.netlify.app/Biofilm.html* - [ ] [[Quorum_sensing]] - [x] Antimicrobial resistance *✅ https://wikitube-3d-microsims.netlify.app/Antimicrobial_resistance.html* - [ ] Run-and-tumble motion - [x] Bacterial motility *✅ https://wikitube-3d-microsims.netlify.app/Bacterial_motility.html* - [ ] Microbiological culture - [x] Agar plate *✅ https://wikitube-3d-microsims.netlify.app/Agar_plate.html* - [ ] Industrial fermentation - [ ] Microswimmer - [ ] Lysogenic cycle ### Motility, taxis & microswimmers (6) · *agent-based sim; run, tumble, twitch, glide, and swim up a gradient at low Reynolds number* - [ ] Twitching motility - [ ] Gliding motility - [ ] Protist locomotion - [x] Amoeboid movement *✅ https://wikitube-3d-microsims.netlify.app/Amoeboid_movement.html* - [x] Bacteria collective motion *✅ https://wikitube-3d-microsims.netlify.app/Bacteria_collective_motion.html* - [ ] Biohybrid microswimmer ### Biofilms, quorum sensing & microbial consortia (5) · *threshold / agent sim; couple species into a community and watch cooperation, synergy, and imbalance emerge* - [ ] Microbial consortium - [ ] Synthetic microbial consortia - [ ] Microbial synergy - [ ] Holobiont - [ ] Dysbiosis ### Growth, survival, culture & detection (7) · *process / curve / schematic sim; inoculate, incubate, count colonies, and read the growth curve under changing conditions* - [ ] Pure culture - [x] Enrichment culture *✅ https://wikitube-3d-microsims.netlify.app/Enrichment_culture.html* - [ ] Microscopy - [ ] Dark-field microscopy - [ ] Impedance microbiology - [ ] Physical factors affecting microbial life - [x] Endospore *✅ https://wikitube-3d-microsims.netlify.app/Endospore.html* ### Microbial ecology, populations & biogeochemical flux (5) · *dynamical-system / flow sim; push microbial populations and loop carbon and sulfur through the pools* - [ ] Microbial population biology - [ ] Kill the Winner hypothesis - [ ] Viral shunt - [ ] Biological pump - [ ] Microbial oxidation of sulfur ### Fermentation, applied & industrial microbiology (6) · *process / parameter sim; ferment, preserve, degrade, and inhibit* - [ ] Brewing - [ ] Pasteurization - [ ] Food preservation - [x] Bioremediation *✅ https://wikitube-3d-microsims.netlify.app/Bioremediation.html* - [ ] Microbial biodegradation - [x] Antibiotic *✅ https://wikitube-3d-microsims.netlify.app/Antibiotic.html* ### More — live Chrome re-crawl of `Microbiology` (18) · *growth, motility, structure & gene transfer* - [x] Bacterial growth *✅ https://wikitube-3d-microsims.netlify.app/Bacterial_growth.html* - [x] Binary fission *✅ https://wikitube-3d-microsims.netlify.app/Binary_fission.html* - [x] Bacterial flagellum *✅ https://wikitube-3d-microsims.netlify.app/Bacterial_flagellum.html* - [x] Chemotaxis *✅ https://wikitube-3d-microsims.netlify.app/Chemotaxis.html* - [ ] Gram stain - [x] Bacteriophage *✅ https://wikitube-3d-microsims.netlify.app/Bacteriophage.html* - [x] Coccobacillus *✅ https://wikitube-3d-microsims.netlify.app/Coccobacillus.html* - [x] Chemostat *✅ https://wikitube-3d-microsims.netlify.app/Chemostat.html* - [x] Bacterial cell wall *✅ https://wikitube-3d-microsims.netlify.app/Bacterial_cell_wall.html* - [x] Bacterial capsule *✅ https://wikitube-3d-microsims.netlify.app/Bacterial_capsule.html* - [x] Bacterial outer membrane *✅ https://wikitube-3d-microsims.netlify.app/Bacterial_outer_membrane.html* - [x] Bacterial cellular morphologies *✅ https://wikitube-3d-microsims.netlify.app/Bacterial_cellular_morphologies.html* - [x] Coccus *✅ https://wikitube-3d-microsims.netlify.app/Coccus.html* - [x] Bacillus (shape) *✅ https://wikitube-3d-microsims.netlify.app/Bacillus_%28shape%29.html* - [x] Bacterial cell structure *✅ https://wikitube-3d-microsims.netlify.app/Bacterial_cell_structure.html* - [x] Flagellin *✅ https://wikitube-3d-microsims.netlify.app/Flagellin.html* - [x] Bacterial morphological plasticity *✅ https://wikitube-3d-microsims.netlify.app/Bacterial_morphological_plasticity.html* - [x] Gene transfer agent *✅ https://wikitube-3d-microsims.netlify.app/Gene_transfer_agent.html* ## I — Immunology Immunology studies the immune system — how the body distinguishes self from non-self, recognizes a pathogen, mounts and remembers a response, and holds that response in check so it does not turn on its host. Its microsimmable seam is the set of **dynamic, quantitative processes** at the heart of that response: an antibody docks onto an epitope by shape complementarity, a single antigen selects and clonally expands the one lymphocyte that fits it, V(D)J recombination shuffles gene segments into millions of distinct receptors, somatic hypermutation and affinity maturation evolve a tighter-binding antibody inside a germinal center, the complement cascade amplifies down a chain of cleavages, a phagocyte engulfs its target, leukocytes roll, arrest, and extravasate out of a vessel into inflamed tissue, and a haematopoietic stem cell branches down the erythroid, myeloid, and lymphoid lineages under cytokine control — every one of these a learner can drive from a p5.js canvas. **55 articles** selected from the 276 validated candidates by the quality bar *"can this be shown as an effective interactive MicroSim?"*, grouped by p5.js pattern and led by a build-first top-10. The pool was heavily diluted and most of it — **221 links** — dropped. The single largest block was the enormous **blood-cell catalog**: the haematopoietic lineage rendered as named cell types and progenitors (the CFU-GEMM / CFU-GM / CFU-Meg colony-forming units, the myeloblast → promyelocyte → metamyelocyte → band-cell maturation stages, the proerythroblast / normoblast / reticulocyte series, and the full roster of B-, T-, NK-, dendritic, mast, giant, and memory cells) — kept here only as a *process* through the `-poiesis` articles and dropped wherever it was a static cell card. Per the life-science rule, the large catalog of **named lymphoid and myeloid organs** (thymus, spleen, bone marrow, lymph node, tonsil, adenoid, the lymphatic system), **diseases and syndromes** (AIDS, lupus, rheumatoid arthritis, the Hashimoto and Crohn diseases, asthma, myasthenia gravis), **named molecules and hormones** (the selectins and integrins, the cytokines and glycoproteins, the autoantibodies, estrogen, testosterone, DHEA), and **named pathogens and organisms** (HIV, MRSA, *Staphylococcus*, *Pseudomonas*, plus the monarch butterfly and milkweed of the behavioral-immune-system tail) was dropped as different-visualization material. So were the field's **people** (Metchnikoff, Ehrlich, Burnet, Jerne, von Behring, Matzinger, Thucydides), its **journals, prizes, and bodies** (the *Immunobiology* and *International Reviews of Immunology* journals, the Nobel Prize, NIAID), the `-immunology` **sub-discipline** names (cancer, clinical, eco-, osteo-, reproductive immunology, immunomics — each a discipline rather than a sim, dropped exactly as the `-genetics` sub-disciplines were in the **G** room), the off-theme **reproductive / behavioral tail** (gestation, fetus, neonate, puberty, disgust, pathogen avoidance, the behavioral immune system), the `In_vitro` / `In_vivo` / `In_situ` Latin method tags, and the usual `Category:*`, `Template_talk:*`, `List_/Index_/Outline_/Timeline_/History_of_*`, and `*_(identifier)` cruft. Synonym and near-twin pairs were collapsed to one slug each (Adaptive_immunity → `Adaptive_immune_system`; Clonal_selection_theory → `Clonal_selection`; Complement_cascade → `Complement_system`; Human_leukocyte_antigen → `Major_histocompatibility_complex`; the Macrophage/Macrophages and Dendritic_cell/Dendritic_cells plurals dropped as cell catalog). ⚠️ **Note on the pool:** the epidemic **SIR / herd-immunity / vaccination** sims the theme calls for are **not in this crawl** — no `Herd_immunity`, `Vaccine`, or compartmental-model article appears among the 276 (only a `Vaccination_schedule` table, dropped as catalog) — so a re-crawl from `Vaccination` or `Epidemiology` would extend this branch further. Cross-page items route to their canonical room: **somatic mutation** and **DNA repair** live in **G — Genetics**, **apoptosis** and the **immune checkpoint** in **O — Oncology**, and the registry enforces one article per topic vault-wide. ### Top 10 — start here (10) · *the most canonical, visually striking immunology sims; build these first* - [x] Clonal selection *✅ https://wikitube-3d-microsims.netlify.app/Clonal_selection.html* - [ ] Phagocytosis - [x] Complement system *✅ https://wikitube-3d-microsims.netlify.app/Complement_system.html* - [x] Antigen presentation *✅ https://wikitube-3d-microsims.netlify.app/Antigen_presentation.html* - [x] Affinity maturation *✅ https://wikitube-3d-microsims.netlify.app/Affinity_maturation.html* - [ ] V(D)J recombination - [ ] Inflammation - [ ] Leukocyte extravasation - [ ] Haematopoiesis - [ ] Major histocompatibility complex ### Antigen recognition & epitope binding (8) · *binding / lock-and-key sim; dock a paratope onto its epitope and probe specificity, cross-reactivity, and the carrier effect* - [x] Antigen *✅ https://wikitube-3d-microsims.netlify.app/Antigen.html* - [x] Epitope *✅ https://wikitube-3d-microsims.netlify.app/Epitope.html* - [ ] Linear epitope - [x] Conformational epitope *✅ https://wikitube-3d-microsims.netlify.app/Conformational_epitope.html* - [ ] Paratope - [ ] Hapten - [ ] Mimotope - [x] Cross-reactivity *✅ https://wikitube-3d-microsims.netlify.app/Cross-reactivity.html* ### Antibodies, immune complexes & abnormal activation (5) · *structure-builder / lattice sim; assemble the Y-shaped immunoglobulin, lattice antigen into complexes and agglutinated clumps, then watch a superantigen short-circuit activation* - [ ] Immunoglobulin - [ ] Immune complex - [x] Agglutination (biology) *✅ https://wikitube-3d-microsims.netlify.app/Agglutination_%28biology%29.html* - [ ] Idiotype - [ ] Superantigen ### Receptor diversity & antibody maturation (4) · *combinatorial / mutation–selection sim; recombine gene segments, add junctional noise, switch class, and broaden a polyclonal response* - [ ] Somatic hypermutation - [ ] Immunoglobulin class switching - [ ] Junctional diversity - [ ] Polyclonal B cell response ### Clonal activation, tolerance & autoimmunity (8) · *selection / agent sim; require a second signal to activate, then delete or anergize the self-reactive clones — and watch tolerance fail* - [x] Co-stimulation *✅ https://wikitube-3d-microsims.netlify.app/Co-stimulation.html* - [x] Clonal anergy *✅ https://wikitube-3d-microsims.netlify.app/Clonal_anergy.html* - [x] Clonal deletion *✅ https://wikitube-3d-microsims.netlify.app/Clonal_deletion.html* - [x] Central tolerance *✅ https://wikitube-3d-microsims.netlify.app/Central_tolerance.html* - [ ] Peripheral tolerance - [ ] Immune tolerance - [x] Autoimmunity *✅ https://wikitube-3d-microsims.netlify.app/Autoimmunity.html* - [ ] Danger model ### Transplantation & alloimmunity (3) · *matching / rejection-kinetics sim; match donor to recipient, then watch an unmatched graft get rejected and immunosuppression hold it back* - [x] Alloimmunity *✅ https://wikitube-3d-microsims.netlify.app/Alloimmunity.html* - [ ] Transplant rejection - [ ] Immunosuppression ### Immunity types & response modes (6) · *compartment / response-curve sim; compare innate vs adaptive and humoral vs cell-mediated, and watch a passively transferred titer decay* - [ ] Innate immunity - [ ] Intrinsic immunity - [ ] Adaptive immune system - [ ] Humoral immunity - [x] Cell-mediated immunity *✅ https://wikitube-3d-microsims.netlify.app/Cell-mediated_immunity.html* - [ ] Passive immunity ### Hematopoiesis & blood-cell differentiation (6) · *lineage-tree / maturation sim; drive a stem cell down the erythroid, myeloid, and lymphoid branches under cytokine control* - [x] Erythropoiesis *✅ https://wikitube-3d-microsims.netlify.app/Erythropoiesis.html* - [ ] Granulopoiesis - [ ] Lymphopoiesis - [ ] Myelopoiesis - [ ] Monocytopoiesis - [ ] Thrombopoiesis ### Immune dynamics, escape & assays (5) · *time-series / curve / detection sim; track hypersensitivity reactions, antigenic escape, and thymic decline, then read the binding curves behind the assays* - [ ] Hypersensitivity - [x] Antigenic variation *✅ https://wikitube-3d-microsims.netlify.app/Antigenic_variation.html* - [ ] Thymic involution - [ ] Immunoassay - [ ] Immunoprecipitation ## C — Cytology Cytology — cell biology — studies the structure, function, and life cycle of the cell: how its contents are imaged, isolated, and counted, how signals propagate through it, and how it recycles its own material. Its microsimmable seam is narrow but real, and the genuinely dynamic, quantitative pieces are the **instruments and processes** a learner can drive from a canvas: a microscope's illumination path resolves a cell by switching between bright-field, phase-contrast, fluorescence, confocal, and [[Electron|electron]] modes; a spinning rotor sediments organelles into a density gradient; a flow cytometer streams cells single-file past a laser and gates them by scatter and stain; a clonogenic assay reads a cell-survival curve off the colonies that grow back after a dose; a signaling cascade relays a message from receptor to nucleus; and autophagy engulfs and digests the cell's own worn-out parts. **55 articles** selected — the original microscopy/assay set plus a live Chrome re-crawl of `Cell_biology`, `Organelle`, `Cell_membrane`, and `Cell_cycle` — by the quality bar *"can this be shown as an effective interactive MicroSim?"*, grouped by p5.js pattern and led by a build-first start-here set. ✅ **Re-crawled past 50.** The Cytology parent is a short overview page whose link graph is overwhelmingly *biographical*: the single largest block — **29 of the 67 links** — is the roster of **cell biologists and microscopists** (van Leeuwenhoek, Hooke via *Micrographia*, Schleiden, Schwann, Virchow, Brown, Dutrochet, Carnoy, Purkyně, and the modern Nobel lineage — Ohsumi, Agre, Blobel, de Duve, Horvitz, Mitchell, Nurse, Palade, Porter, Tsien, Wilson …). Per the life-science rule, the catalog of **named organelles and anatomy** (the cell nucleus, human anatomy), **named molecules** (green fluorescent protein), **organisms** (viruses), and **diseases and procedures** (ribosomopathy, cervical cancer and intraepithelial neoplasia, the Pap smear) was dropped as different-visualization material, along with the **cell-X sub-discipline** names (cytochemistry, cell physiology, cell biophysics, histopathology — each a discipline rather than a sim, dropped exactly as the "-genetics" sub-disciplines were in the **G** room), the off-theme etymology-and-material tail (the monastic cell, cork, "bio-medical"), the **organisations and references** (the American Society for Cell Biology, NCBI, the *Encyclopædia Britannica* Eleventh Edition, the federal-copyright page), and the usual `Category:*`, `Template_talk:*`, `Outline_/History_of_*`, and `*_(identifier)` cruft. ⚠️ **Note on the pool:** the canonical cytology sims the theme calls for — **mitosis and meiosis, the cell cycle, membrane transport, osmosis, diffusion, the sodium–potassium pump**, and **organelle function** — are **not in this 67-link crawl**: mitosis and meiosis are already claimed by **G — Genetics** in this hub (deduped out here), and the transport/osmosis articles live on other parent pages, so a re-crawl from `Cell_(biology)`, `Cell_biology`, or `Cell_membrane` would lift this branch past 50. Cross-page shares route to their single canonical article: **phase-contrast microscopy** is shared with **PHYSICS / Interferometry** and **transmission electron microscopy** with **REACTION / Crystallography**, each built once and referenced from both. ### Top 10 — start here (9) · *the most canonical, visually striking cytology sims; build these first* - [ ] Optical microscope - [ ] Fluorescence microscope - [ ] Mitochondrion - [ ] Ribosome - [ ] Cell cycle - [ ] Endocytosis - [ ] Active transport - [x] Cytoskeleton *✅ https://wikitube-3d-microsims.netlify.app/Cytoskeleton.html* - [ ] Osmosis ### Microscopy, separation & quantitation (7) · *instrument / density-gradient / counting sim* - [ ] Phase-contrast microscopy - [ ] Confocal microscopy - [ ] Transmission electron microscopy - [ ] Cell fractionation - [ ] Cell disruption - [ ] Centrifugation - [ ] Cytometry ### Organelles (12) · *labelled-structure / function sim; tour the compartment and run its job* - [ ] Cell nucleus - [ ] Nucleolus - [ ] Nuclear envelope - [ ] Endoplasmic reticulum - [ ] Golgi apparatus - [ ] Lysosome - [ ] Peroxisome - [ ] Vacuole - [ ] Chloroplast - [ ] Centriole - [ ] Centrosome - [ ] Endosome ### Membrane & transport (10) · *bilayer / gradient / pump sim; move cargo across the membrane* - [ ] Plasma membrane - [ ] Lipid bilayer - [ ] Fluid mosaic model - [ ] Endomembrane system - [ ] Exocytosis - [ ] Pinocytosis - [ ] Receptor-mediated endocytosis - [ ] Facilitated diffusion - [ ] Proton pump - [ ] Vesicle (biology and chemistry) ### Cytoskeleton & motor proteins (9) · *filament / walking-motor sim; assemble the track and haul cargo* - [ ] Actin - [ ] Actin filaments - [ ] Microfilament - [ ] Microtubule - [ ] Intermediate filament - [ ] Dynein - [ ] Dynactin - [ ] Actomyosin - [ ] Cytoplasmic streaming ### Cell cycle & signaling (8) · *checkpoint / spindle / cascade sim* - [ ] Cytokinesis - [ ] Mitotic spindle - [ ] Cell cycle checkpoint - [ ] Kinesin - [ ] Cell signaling - [ ] Signaling pathway - [ ] Autophagy - [ ] Cell ablation ## S — Systematics Systematics is the science of classifying living things and reconstructing their evolutionary relationships — the tree of life and the methods that build it. It is the most microsimmable corner of taxonomy because its core objects are **trees and the algorithms that grow them**: a cladogram is a branching diagram inferred from a character matrix, speciation is a lineage splitting under geographic or ecological isolation, a molecular clock turns sequence distance into divergence time, and a fitness landscape drives the selection that separates the branches. (Added via a live Chrome crawl of the `Systematics` page, since this branch had no row in the sheet.) **50 articles** selected, grouped by MicroSim pattern and led by a build-first top-10. Named taxa, organisms, people (Linnaeus, Darwin), books, journals, and the roster of biology sub-disciplines were dropped as catalog / different-visualization material; items already claimed by **G — Genetics** or **E — Ecology** were deduped out (the registry shares one article per topic across branches). ### Top 10 — start here (7) · *tree-building / branching sim; the most canonical systematics sims* - [ ] Phylogenetic tree - [ ] Cladistics - [ ] Phylogenetics - [ ] Taxonomy (biology) - [ ] Homology (biology) - [ ] Phenetics - [ ] Adaptive radiation ### Trees, cladistics & classification (12) · *cladogram / character-matrix sim* - [ ] Phylogeny - [ ] Phylogenetic comparative methods - [ ] Evolutionary taxonomy - [ ] Evolutionary systematics - [ ] Taxonomic rank - [ ] Taxon - [ ] Alpha taxonomy - [ ] Cladogenesis - [ ] Apomorph - [ ] Plesiomorph - [ ] Extant taxon - [ ] Last universal common ancestor ### Speciation modes (10) · *geographic-isolation / branching sim* - [ ] Allopatric speciation - [ ] Sympatric speciation - [ ] Parapatric speciation - [ ] Peripatric speciation - [ ] Hybrid speciation - [ ] Ecological speciation - [ ] Reinforcement (speciation) - [ ] Anagenesis - [ ] Nonadaptive radiation - [ ] Species complex ### Evolutionary tempo & mode (8) · *rate / divergence sim* - [ ] Punctuated equilibrium - [ ] Phyletic gradualism - [ ] Convergent evolution - [ ] Divergent evolution - [ ] Parallel evolution - [ ] Mosaic evolution - [ ] Evolutionary arms race - [ ] Red Queen hypothesis ### Molecular phylogenetics (5) · *sequence-distance / molecular-clock sim* - [ ] Molecular evolution - [ ] Models of DNA evolution - [ ] 16S ribosomal RNA - [ ] Transitional fossil - [ ] Evidence of common descent ### Selection & evolutionary game theory (8) · *payoff / fitness-landscape sim* - [ ] Sexual selection - [ ] Inclusive fitness - [x] [[Evolutionarily_stable_strategy]] *✅ https://wikitube-3d-microsims.netlify.app/Evolutionarily_stable_strategy.html* - [ ] Fisher's principle - [ ] Reciprocal altruism - [ ] Evolutionary invasion analysis - [ ] Handicap principle - [ ] Signalling theory --- ## How to use this worklist 1. **Lease the branch.** `python3 ../MicroSim-Registry/microsim_registry.py branch-acquire --page Genomics --branch "<Letter> — <Name>"`. 2. **Populate it** per `../MicroSim-Registry/BRANCH-BUILD-METHOD.md` — but note this sheet's **flipped columns** (parent = col A, link = col B). Drop people, species, genes, proteins, diseases, and anatomy by name; keep dynamic/quantitative processes that make effective interactive MicroSims. Group by pattern with a build-first top-10. 3. **Build, register & release.** Build each sketch to the Betterfire standard (P5 JS EDITOR); `scan --write`, then `branch-release --built`. `check` is the collision gate. ```dataview TABLE status, editor_url FROM "Articles" WHERE contains(file.folder, "Genomics") SORT status ``` --- _Seed: the **G.E.N.O.M.I.C.S.** sheet (2,816 validated links) · 7 of 8 branches queued for scheduled population (S awaiting input) · one article per topic enforced vault-wide by MicroSim-Registry._ <!-- CRAFT-LINK:START g12 --> *Built to the [[WT!Three_js_Microsim_Master_Class|three.js Master Class]].* <!-- CRAFT-LINK:END --> ## Wikipedia : Wikitube **Strict pair:** [Wikipedia](https://en.wikipedia.org/wiki/Genomics) : [Wikitube](https://en.wikitube.io/wiki/Genomics) ## Previous hub tags Tree parent: [[Graph_theory]]. Legacy hubs: `GENOMICS`. --- *Sources: 2 legacy notes. Minted wave 1, 2026-07-30 (v1.6 order).*