Ben's spreadsheet, and a promise I made to myself
Before every cloning reaction there's a small ritual I never really chose. Open the Gibson spreadsheet. Type in the vector's length and concentration. Type in each insert. Squint at the molar-ratio column, confirm the fold excesses are the ones I meant, and copy the microlitres onto a scrap of paper by the pipette. Dull, quick, and exactly the kind of task where a tired brain makes a quiet mistake.
For years the spreadsheet I opened was Ben's Gibson Assembly calculator from the Barrick Lab's cloning protocol, and I want to be clear: it's excellent. The method it encodes is sound — genuinely the reason my reactions work at all. Ben and that spreadsheet have quietly helped an enormous number of grad students and postdocs get their cloning right, mine included. This whole page is, more than anything, a thank-you note.
The math is not hard. That's exactly why it's dangerous — beneath your attention, but able to quietly ruin an experiment.
The problem was never the math
The problem was, honestly, me and Excel. I have a small, stubborn wish to never open a spreadsheet again if I can possibly avoid it. A `.xlsx` is a wonderful place to author a formula and a slightly awkward place to use one at the bench — three tabs deep, cursor in the wrong cell — when all you want is one instant answer to "how much of each do I pipette?"
The formula itself is compact: the volume of the n-th fragment is v_n = (f_n · l_n / c_n) · (m_1 / l_1), with the vector mass m_1 the minimum of three limits — a volume limit, a molarity limit from p_max, and a hard 100 ng cap. Every piece is knowable, and every piece is a place to fat-finger a decimal at six in the evening. The real cost was never the minutes; it was not quite trusting the number — re-checking it, doubting it — instead of it being a solved problem.
A faithful port, not a reinvention
So I did what I've started doing whenever a small, repeated task keeps costing more than it should: I took the spreadsheet's math and rebuilt it as a browser tool. Underneath, it's a faithful port of the Barrick Lab spreadsheet — the same formula, the same three limits, the same conversion constant. I didn't want to improve the method; I wanted to reproduce it exactly and wrap it in something quicker to use. All credit for the method stays with Ben and the Barrick Lab.
On top of that faithful core I added what I kept wishing the spreadsheet had: a custom molar ratio for protocols that deviate from the NEB defaults, a master-mix multiplier so a plate of N reactions is one number instead of N, a printable protocol you can save as a PDF, CSV export, and named presets for constructs I build over and over. None of it is clever — that's the point. The value is in the sum being instant, correct, and reproducible.
A note on how it was built
I'm a scientist who's gotten good at building small tools, not a career software engineer — and I build these with AI assistance, which is the honest reason a bench frustration can turn into a working calculator in an afternoon. The idea, and the decision to port Ben's math faithfully rather than reinvent it, are mine; the AI was the implementation partner. It runs, it's already saved me more time than it took to build, and it turned a recurring source of quiet error into a solved problem.
All credit for the underlying method goes to Ben and the Barrick Lab. Read the original cloning protocol at barricklab.org. This tool is a homage — the math is theirs; only the spreadsheet is gone.