dubiumlabsBiology

Biology

Simulators that model living systems: from population dynamics to cellular processes, with visualizations that show how they evolve over time.

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Cell Doubling TimeGrowth and population dynamicsCalculate doubling time and growth rate from cell population dataLogistic Population Growth (r, K)Growth and population dynamicsSimulate the logistic growth of a population: sigmoid curve, carrying capacity K, inflection point, maximum rate (MSY), and comparison with exponential growthEnzyme Kinetics (Michaelis-Menten)Biochemistry and molecular biologySimulate Michaelis-Menten enzyme kinetics and reversible inhibition models: reaction velocity, kcat, catalytic efficiency, and Lineweaver-Burk plotsFick Membrane DiffusionCell biologySimulate passive membrane diffusion with Fick's law: initial flux, permeability, membrane resistance, and time to equilibriumCell Osmotic Equilibrium: Osmolarity and TonicityCell biologyComputes the total, effective and impermeant osmolarity on both sides of the membrane, the van't Hoff osmotic pressure, the initial water direction and the equilibrium cell volume from the solutes of each compartment, their i factor and their reflection coefficient σLotka-Volterra Population DynamicsGrowth and population dynamicsSimulate Lotka-Volterra predator-prey dynamics: time evolution, phase space and equilibrium pointsMendelian crossesGeneticsCalculate genotype and phenotype probabilities for crosses involving 1 to 4 independent biallelic genes under complete dominance, with a Punnett square for 1 or 2 genesSIR ModelEpidemiology and healthEducational SIR simulator: S–I–R curves and incidence, R₀ and Re, maxima and the herd immunity thresholdSEIR ModelEpidemiology and healthEducational SEIR simulator: latent period, S–E–I–R curves, growth and doubling, maxima and comparison with SIRHardy-Weinberg EquilibriumGeneticsComputes allele (p, q) and genotype (p², 2pq, q²) frequencies from a single input, with an optional χ² goodness-of-fit test to validate equilibrium in observed populationsGenetic drift · Wright–FisherGeneticsFollow five populations from the same starting point and compute how much of the initial diversity is retained, with constant size or a bottleneckMembrane Potential (Goldman-Hodgkin-Katz)Cell biologyCalculate the resting membrane potential and Nernst potential using the Goldman-Hodgkin-Katz equation for Na⁺, K⁺, Cl⁻ and Ca²⁺ with configurable permeabilitiesDiagnostic Validity (Bayes' Theorem)Epidemiology and healthApply Bayes' Theorem to a diagnostic test: compute PPV, NPV, accuracy, likelihood ratios (LR+, LR−), Youden's index and DOR. Visualise the prevalence paradox with a natural-frequency tree, 2×2 table and PPV vs prevalence curveLipid Profile & LDL CholesterolEpidemiology and healthEstimates LDL cholesterol via Friedewald, Sampson-NIH (2020) and Martin-Hopkins, with non-HDL, VLDL and the Castelli I/II and TG/HDL atherogenic indices. Bidirectional input, mg/dL ↔ mmol/L conversion and clinical alertsPrimer Melting Temperature (Tm)Biochemistry and molecular biologyComputes PCR primer Tm with the Nearest-Neighbor model (SantaLucia 1998) and Owczarzy salt correction (Na⁺/Mg²⁺/dNTP). Reports ΔG, ΔH, ΔS, %GC, annealing temperature, melting curve and primer quality checks