Everything you almost remember from the bench.
A full plasmid editor, stats that pick their own test, standard curves and IC50s, Sanger traces, gRNAs, Gel Bench, Clone Bench, MS peaks, growth curves, and buffers that re-weigh themselves.
Feel free to use these tools I created.
If you have any suggestions for improvement, let me know! Tell me what broke, what's missing, or which tool you'd like to see next.
Every calculation runs in your browser — nothing you paste or upload leaves this page, except a question you ask the stats chat, which carries your data summary. Numbers are planning aids, not a substitute for your own controls.
Protein Desk
Paste a protein sequence for MW, pI, extinction coefficient, hydrophobicity and composition — and the gel percentage to run it on.
PCR & Primers
Check the pair, build the master mix, and get a cycling program that fits the amplicon — before you touch the thermocycler.
Reaction setup
Cycling
Gel Bench
Browser-only SDS-PAGE and Western blot quantification: mark the gel area, detect lanes and band rows, subtract local background, normalize to loading controls or total lane protein, and export the table, chart, and boxed image. Nothing is uploaded.
Clone Bench
From plasmid map to verified clone: open a construct and check its annotations, plan diagnostic digests on a virtual gel, design and check primers under your buffer, and verify Sanger reads against the reference. Biopython runs in this tab; your analyses are saved in this browser and can be downloaded as a file. Nothing is uploaded.
Buffer Book
42 recipes for the buffers every lab keeps on the shelf. Change the final volume or the strength and every component re-weighs itself — with the pH step, storage life, and the mistake everyone makes once.
Dilution Desk
The six solvers that cover most of what goes wrong before an experiment starts. Every answer shows the working, so you can check it against the label on the bottle.
Stock and target
Weigh out a solid
Percent ↔ molar
Plan the series
Change tips between every step — carry-over on the outside of a tip is the biggest source of drift down a series. Mix each tube before drawing the next transfer, and keep the transfer ≥ 10 µL so pipetting error stays under 2%.
RCF ↔ RPM
Unit converter
Cell Culture
Five things you do at the hood, worked out before you get there. Vessel areas and media volumes follow the standard Corning/Falcon formats.
Four corner squares
Improved Neubauer: each large square is 1 × 1 × 0.1 mm = 0.1 µL. A 1:1 trypan blue mix is a dilution factor of 2.
What you're plating
Two counts, some hours apart
Banking
Bacterial culture
qPCR Bench
Paste Ct values straight from the plate export. Livak 2^-ΔΔCt with replicate spread carried into the error bars, versus your chosen reference gene and calibrator — and primer efficiency from a standard curve before you trust a fold change under 2×.
Standard curve
Paste two columns from the plate export: dilution (or copy number) and its Ct. Tabs, commas or spaces all work.
Colony & Cell Counter
Photograph the plate on a plain background (lid off), or drop a DAPI field. Auto-threshold finds the dish then the colonies; size filters throw out dust; merged colonies get flagged; the count becomes CFU/mL.
Image
Detection
Back-calculate CFU
Image Lab
The ImageJ moves you actually use, without the menus. Calibrate a scale, then draw to measure length, area, perimeter, diameter and intensity; count with points; threshold for area fraction; trace an intensity profile; and check colocalization with Pearson and Manders coefficients.
Image
Tool
Drag on the image to measure a length.
Scale
1 px = 1 px. Use "Set scale" on a scale bar, or type the calibration (e.g. 1000 px = 100 µm).
Display
Display adjustments are for your eyes only — measurements always read the raw pixels.
Measurements
Colocalization
MS Peak Finder
Paste raw m/z–intensity data or drop a picture of a spectrum. Peaks are picked with signal-to-noise and resolution; click your target and every neighbour that is a common adduct, loss, isotope, dimer or charge state gets named. Then quantify, search a formula, or deconvolve a charge envelope.
Spectrum in
Then drag a box over the plot area (from the left axis at the top-left to the right end of the baseline), and enter the m/z at its left and right edges.
Peak picking
Noise = 1.4826 × median absolute deviation of the signal; S/N is peak height over that. Resolution = m/z ÷ FWHM from the profile (centroid data reports —).
Quantify
Spectrum
drag to zoom · double-click to reset · click a peak to target itTarget & related ions
Peak list
More analysis
Finds the neutral mass that explains a series of multiply-charged peaks (proteins, oligos). Uses the picked peaks above the intensity cutoff.
Every peak's distance from the target, matched against a library of 40 common mass differences (adduct swaps, neutral losses, homologue steps, modifications).
Residue-mass difference for a point substitution (monoisotopic, unmodified residues). Also handy for reading MS/MS ladders and spotting a missed modification.
Isotope peaks at +1.003 and +2.007 relative to the target; the M+1 ratio estimates carbon count (≈1.1% per carbon), spacing gives the charge.
Stats & Plotting Desk
Paste your groups, get a publication-style plot, and let the desk work out which test the data actually call for. It checks normality, variance and sample size, explains the choice in plain words, runs the test with post-hoc comparisons and effect sizes, and draws the significance brackets. Ask the chat below anything about the result.
Data in
About the design
Normality: Shapiro–Wilk on each group (or on paired differences). Equal variance: Brown–Forsythe (median-centered Levene). Groups under n = 8 can't really fail a normality test, so the desk also looks at skew and says when it's guessing.
Plot
Export
SVG opens in Illustrator, Inkscape and PowerPoint; the CSV has descriptives, the test and every comparison.
Power & sample size
Two-sided t test; d is the difference in means over the SD (paired: over the SD of the differences). d fills in from the last result. Plan on the effect you'd care about, not the one you happened to see.
Plot
Suggested test
Result
Descriptives
Ask about this analysis
Plate Reader Desk
Standard curves and dose–response in one place. Paste standards and unknowns straight from the reader export; fit linear or 4-parameter logistic, get concentrations with replicate CVs and out-of-range flags. Or paste doses and responses for an IC50 / EC50 with Hill slope and standard errors.
Standards
Unknowns
Curve
Results
Doses & responses
How it fits
y = Bottom + (Top − Bottom) / (1 + 10^((logEC50 − x)·Hill)), fitted by Levenberg–Marquardt on log10(dose). Standard errors come from the Jacobian at the solution; the 95% CI on EC50 is asymmetric because it lives in log space. A Hill slope far from ±1 or a bottom that isn't reached means the curve is under-determined — add doses at the ends.
Fit
Parameters
Michaelis–Menten
Assay QC (Z′-factor)
Fit
Parameters
Growth Curve Analyzer
Paste a plate-reader time course — time in the first column, one well per column — and get the maximum specific growth rate, doubling time, lag time, max OD and area under the curve for every well, with the exponential window it used drawn on the log plot.
Time course
µ_max is the steepest slope of ln(OD) over a sliding window of the chosen size (R² ≥ 0.97 required); doubling time = ln 2 / µ_max. Lag = where the tangent at µ_max meets the starting OD. Only points above 2× the minimum OD are considered exponential.
Curves
ln ODlinearPer well
CRISPR & Codon Desk
Find every guide RNA in a target sequence for SpCas9, SaCas9 or Cas12a, ranked by simple design rules, with ready-to-order cloning oligos. Or paste a protein and get it back-translated with the codon usage of E. coli, human/CHO, yeast or Pichia, with a CAI score and unwanted restriction sites avoided.
Target
Ranking uses design rules, not an off-target search: GC 40–70%, no TTTT (Pol III terminator), G at the PAM-proximal end, no extreme homopolymers. Always check candidates against the genome (CRISPOR, CCTop) before ordering.
Guides
Sequence
Optimized DNA
Codon usage table (fraction per amino acid)
Gel Band Sizer
Drop a gel photo, click the ladder lane, pick which ladder it is, and every band you click after that gets a size in bp or kDa — interpolated in log space between the nearest ladder bands, the way you'd do it with a ruler and semi-log paper, minus the ruler.
Gel
1 · Ladder
No ladder yet.
2 · Bands
Bands outside the ladder range are extrapolated and flagged. Smiling gels: pick the ladder closest to the lane of interest.
Image
load a gelStandard curve
Sizes
Plate Layout Designer
Paint conditions onto a 6- to 384-well plate, drag to fill blocks, randomize replicates so plate position isn't your treatment, and export the map as CSV for the reader software or as a picture for the notebook. Edge wells are flagged because they evaporate.
Plate
Click a well to paint it, or click and hold while dragging to fill a block. Hovering alone does nothing. Right-click (or the Erase brush) clears. Click a row or column label to paint the whole row or column.
Conditions
Export
The layout is remembered in this browser.
96-well
Summary
Protocol Timer
Every incubation, wash and spin of a protocol as a timer you can run one after another or all at once — with a beep, a flashing tab title and an optional desktop notification when each one ends. Presets for the protocols everyone runs; edit steps or add your own.
Protocol
Timers keep running while you use the other tools; the tab title shows the next one to finish. Steps are remembered in this browser.
Quick timers
Adds a running timer straight away.
Steps
Sanger Trace Viewer
Drop the .ab1 file straight from the sequencing core. See the chromatogram with base calls and quality, trim the messy ends, spot mixed peaks (heterozygous sites or a dirty template), search for a motif, and align the read to your expected sequence to list every mismatch.
Trace
View
Mixed peaks: a second colour reaching ≥ 30% of the called peak at the same position. A few near the primer are normal; many throughout means a mixed template or heterozygous sample.