Tasks
Most people arrive knowing what they need to do, not what the tool is called. These pages start from the job — what decides the choice, what tends to go wrong, and which two or three tools are worth your time.
Laboratory calculators
How much powder do I weigh out for a solution at this concentration?
Make up a solutionGetting from a target molarity and volume to a mass on the balance.
How much stock and how much diluent do I need?
Dilute a stockSingle and serial dilutions, and when to do one rather than the other.
How do I make a buffer at the pH I need?
Prepare a bufferChoosing a buffer for a target pH, and the temperature trap that catches everyone.
My protocol says × g but my centrifuge is set in rpm — what speed do I use?
Spin down a sampleConverting between relative centrifugal field and rotor speed, and which radius to use.
Molecular biology
Will this primer work, and what annealing temperature do I use?
Design or check a PCR primerWhat makes a primer work, and why two calculators give it different melting points.
How do I reverse complement, translate, or check the composition of a sequence?
Work with a DNA sequenceThe everyday sequence operations, and the conventions that silently differ.
Which enzymes cut my insert and vector where I need them to?
Plan a restriction digestChoosing enzyme pairs for a clone, and the compatibility questions that decide it.
Protein tools
What is the mass, pI and extinction coefficient of my protein?
Work out a protein’s propertiesPhysicochemical parameters from a sequence, and how much to trust each one.
Which structure prediction tool should I use for my sequence?
Predict a protein structureChoosing between AlphaFold Server, ColabFold and the older threading servers.
How similar are these two structures, and where do they differ?
Compare two protein structuresSuperposition, TM-score against RMSD, and reading the difference honestly.
Cell biology
How many cells do I have, and how much do I put in each well?
Count cells and seed a plateCounting on a haemocytometer, and turning that count into a seeding plan.
What does my OD600 reading actually mean in cells per millilitre?
Measure how dense a culture isReading optical density honestly, and converting it to cell density if you must.
Statistics and plotting
Is my treatment different from my control?
Compare two groupsChoosing and running a two-group comparison, and reporting it usefully.
Which of my conditions differ from each other?
Compare three or more groupsANOVA, its non-parametric equivalents, and what to do about post-hoc tests.
Does one measurement predict the other?
Test whether two variables are relatedCorrelation, linear regression, and the difference between them.
Do these categories occur at different rates?
Compare counts or proportionsChi-square, Fisher’s exact test, and when each applies.
What n do I need for this experiment?
Work out how many samples you needPower analysis, done before the experiment rather than after.
I ran thousands of tests — which results are real?
Correct for multiple testingBonferroni, Benjamini–Hochberg, and choosing between them.
How should I show this data instead of a bar chart?
Plot your data so the reader can see itShowing distributions and replicate structure rather than hiding them.
How do I plot fold change against significance?
Make a volcano plotTurning a differential expression table into a labelled figure.
How do I visualise an expression matrix?
Make a heatmapClustered heatmaps, and the scaling decision that changes what they show.
How do I make a diagram of my model?
Draw a schematic or graphical abstractDiagrams and figure assembly, as distinct from plotting data.