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Articles / notes from every floor

Notes from building the operating system for the cell culture lab

How labs actually track experiments, samples, instruments and money, what breaks when that lives in spreadsheets, and what we are building instead. Each one is filed under the floor it is written for.

14 articlesCambridge, UKRSS

Latest / ELN and protocols

What should a batch record contain before you sign it?

What goes in a batch record, what the signer should check first, and why a signed record can't change, shown on one mycoplasma test with an invalid well.Masum Ahmed05 NOV 20266 min

Stories / one example, every floor

Read top to bottom

Some articles follow one piece of work through a whole lab, the way the home page follows one cell bank. Each part stands on its own and is written for the people on that floor.

A story in 4 parts

One cell bank, from the budget to the bench and back

One example project, followed through a lab: a working bank of HEK293 cells. The lead funds it, operations orders and stocks what it needs, the bench runs it and banks 40 vials, and the cost comes back up to the project the lead funded. Each part is written for the people on that floor.

Start with the overview

A story in 5 parts

One mycoplasma test, from the SOP to the signed record

One routine test, followed through a lab: the monthly mycoplasma PCR that clears the example lab's new HEK293 cell bank. Operations releases a new SOP and builds it into a workflow, the bench plans the week and runs the plate, QA signs the record, and what the run taught goes back into the SOP. Each part is written for the people on that floor.

Start with the overview

Every article / newest first

From every floor

ELN and protocols

Which calculations does a cell culture bench do every day?

Four everyday bench calculations worked through with real numbers: a PCR mastermix, a cell count, a seeding plan and a doubling time.Dr Salavat Magazov03 NOV 20265 min ELN and protocols

How should a lab team plan its week at the bench?

A real week on a lab task board: what goes on it, what doesn't, why waiting needs its own state, and how far ahead is worth planning.Dr Salavat Magazov01 NOV 20265 min ELN and protocols

How do you turn a written protocol into a workflow the bench can run?

An SOP becomes a runnable workflow: steps, materials, a wait the software enforces, a QC checkpoint, and a released version every run names.Masum Ahmed30 OCT 20266 min Operations

How should a lab control its SOP versions?

One SOP change followed through release: what goes in the release note, how to check the change, and how the bench knows which version it's running.Dr Salavat Magazov28 OCT 20266 min ELN and protocols

How do you calculate relative gene expression with the ΔΔCt method?

A worked ΔΔCt example with the numbers at every step, the Pfaffl ratio for real primer efficiencies, and the per-sample method MIQE 2.0 now recommends.Dr Salavat Magazov26 OCT 20267 min Samples and cell lines

How do you track a lab sample from the vial to the result?

What a sample record needs, from labels and storage to custody, corrections and lineage, following 40 vials of a HEK293 working cell bank.Dr Salavat Magazov27 SEPT 20266 min Operations

What should a purchase order process look like in a research lab?

What a lab purchase order needs, the stages it moves through, and how to handle a partial delivery, following one £688.10 order for a cell bank.Dr Salavat Magazov27 SEPT 20267 min Operations

How should a lab manage its reagent and consumable inventory?

Why 50 vials on the shelf can be low stock: track by lot, keep on hand, reserved and available apart, use the first to expire, and reorder on available.Dr Salavat Magazov27 SEPT 20267 min Lab finance

How do you track a lab budget across several grants and projects?

The four numbers a lab budget needs, how to work out runway, and when an order counts as spent, following one £2,500 cell bank project.Dr Salavat Magazov27 SEPT 20267 min Getting started

What is all-in-one lab management software, and what should it cover?

What all-in-one lab software should cover, how it compares with an ELN, a LIMS and spreadsheets, and how to test it before you buy.Masum Ahmed27 SEPT 202610 min Hardware

Fluorescence modelling: choosing filters for a multichannel microscope

Picking excitation filters, dichroic mirrors and emission filters means working out how much light survives each element. Here is the spectral maths, the open source app we built to do it, and the filter cube we designed around the answer.Dr Salavat Magazov27 AUG 20265 min ELN and protocols

ELN vs LIMS: which one does a cell culture lab actually need?

An ELN records what you did and a LIMS tracks what you have. A cell culture lab needs both, and they need to be connected. Here is how they differ and what to look for.CCA Bio27 JUL 20264 min Samples and cell lines

Why the freezer spreadsheet always drifts

Every lab starts with a freezer spreadsheet, and it works until the freezer gets busy. Here is why it drifts out of step with what is actually in the box, and what to do about it.CCA Bio20 JUL 20263 min

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