Coming Soon: The Digital Cell

Long-time readers might remember the short-lived series on quantixed called The Digital Cell. There is a reason why I stopped these posts, which I can now reveal… The Digital Cell will soon be a book! Published by Cold Spring Harbor Laboratory Press, The Digital Cell is a handbook to help cell and developmental biologists get to […]

Blind To The Truth

Molecular Biology of The Cell, the official journal of the American Society for Cell Biology, recently joined a number of other periodicals in issuing guidelines for manuscripts, concerning statistics and reproducibility. I discussed these guidelines with the lab and we felt that there are two areas where we can improve: blind analysis power calculations A post about power […]

The Arcane Model

I’m currently writing two manuscripts that each have a substantial data modelling component. Some of our previous papers have included computer code, but it was straightforward enough to have the code as a supplementary file or in a GitHub repo and leave it at that. Now with more substantial computation in the manuscript, I was wondering how best to […]

The Digital Cell: Getting started with IgorPRO

This post follows on from “Getting Started“. In the lab we use IgorPRO for pretty much everything. We have many analysis routines that run in Igor, we have scripts for processing microscope metadata etc, and we use it for generating all figures for our papers. Even so, people in the lab engage with it to varying extents. The […]

The Digital Cell

If you are a cell biologist, you will have noticed the change in emphasis in our field. At one time, cell biology papers were – in the main – qualitative. Micrographs of “representative cells”, western blots of a “typical experiment”… This descriptive style gave way to more quantitative approaches, converting observations into numbers that could be objectively assessed. […]