As part of the series on development of early career researchers in the lab, we spent three sessions over three weeks learning the basics of R. In my book “The Digital Cell”, I advocate R as the main number-crunching software but the R literacy in my lab is actually quite mixed. In order to know […]
Category: the digital cell
Modern Cell Biology Is Computational
I wrote a short opinion piece for the December Newsletter for the American Society for Cell Biology (ASCB). The content is reproduced below, or you can read the newsletter version here on page 14 of the PDF. The theme of this year’s ASCB|EMBO Meeting is Cell Biology for the 21st Century. So what skills are essential […]
A Book Like This: The Digital Cell
It’s real! I recently received a physical copy of my book, The Digital Cell: Cell Biology as a Data Science. It is published by Cold Spring Harbor Laboratory Press and is available here. The official release date is 1st December 2019. As I’ve described before, “The Digital Cell” a handbook to doing cell, developmental and […]
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: Statistical tests
Statistical hypothesis testing, commonly referred to as “statistics”, is a topic of consternation among cell biologists. This is a short practical guide I put together for my lab. Hopefully it will be useful to others. Note that statistical hypothesis testing is a huge topic and one post cannot hope to cover everything that you need 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: Getting Started
More on the theme of “The Digital Cell“: using quantitative, computational approaches in cell biology. So you want to get started? Well, the short version of this post is: Find something that you need to automate and get going! Programming I make no claim to be a computer wizard. My first taste of programming was the […]
The Digital Cell: Workflow
The future of cell biology, even for small labs, is quantitative and computational. What does this mean and what should it look like? My group is not there yet, but in this post I’ll describe where we are heading. The graphic below shows my current view of the ideal workflow for my lab. The graphic is pretty self-explanatory, but […]