Molecular Model Simulator vs BenchBuddy

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BenchBuddy bundles the calculations you reach for every day at the molecular-biology and biochemistry bench — from reagent weighing to PCR, gels, and pipetting steps — fast, in one place. Tools included • Reagent mass — how much to weigh from concentration × volume × molecular weight, with optional solvent correction from the actual mass weighed. • Dilution — the volumes you need from stock concentration, target concentration, and final volume. Supports multi-component mixes. • Serial dilution — build a serial dilution series from a stock; see per-tube transfer and diluent volumes, with a warning when transfers get too small to pipette accurately. • PCR master mix — build a master mix from reaction volume, reaction count, and overage, including per-tube additions. • Tm (melting temperature) — compute Tm and a suggested annealing temperature from a primer sequence, via the basic rule or the nearest-neighbor (NN, SantaLucia) method, with Na⁺ and oligo concentration. • OD260 → nucleic-acid concentration — concentration from A260 and nucleic-acid type (dsDNA/ssDNA/ssRNA), with A260/A280 purity. • Mass ↔ moles — convert amount (pmol) ↔ mass (µg) and copy number from length (bp/nt) or molecular weight. • Ligation ratio — insert amount (ng) needed for a target molar ratio (1:1–5:1) from vector/insert lengths and vector mass. • Hemocytometer — from your cell counts, compute cell concentration, viability (trypan blue), and seeding volume. Pick the chamber type (Neubauer improved / Bürker-Türk / Fuchs-Rosenthal / Thoma / custom) to auto-set the chamber factor. • OD600 → cell density — estimate density from OD600 with an organism preset (E. coli / yeast / custom) and dilution; editable factor; reverse to the OD600 for a target density. • Doubling time — doubling time, population doublings, and specific growth rate from initial/final counts and elapsed time (hours or days). • Confluency → cell number — estimate cell number from confluency (%) and vessel area (T25–T175, 6–96-well). • Passage planner — toggle seeding-density / split-ratio; computes suspension volume, medium to add, and the number of new vessels. • Gel predictor — preview how bands migrate from your ladder, agarose percentage, and sample band sizes. • Plate layouts — design 6–384-well (6/12/24/48/96/384) plate maps: group samples/conditions, set per-well concentrations and serial-dilution gradients down columns, and export as an image, CSV, or Markdown. • Bench steps — create pipetting steps over well ranges (e.g. A1:A12) and track progress in row- or column-major order. • Recipe saving & sharing — save the calculations you use often and recall them with one tap; export/import recipes as .benchbuddy.json files to share with labmates. • Result sharing — copy or share any calculation result as text, ready to paste into Notion, Slack, or your ELN. All calculations run on your device. The app is free and supported by ads.