This is the story behind “Comparing process-based and constraint-based approaches for modeling macroecological patterns” by my former PhD student Xiao Xiao, James O’Dwyer, and myself. Background I was on sabbatical in the fall of 2013 and was doing a lot of reading, and I reread “An integrative framework for stochastic, size-structured community assembly” by James O’Dwyer, Jessica Green, and colleagues.

Data Science is all the rage these days. But this current craze focuses on a particular kind of data analysis. I conducted an informal poll as an icebreaker at a recent data science party, and most of the people I talked to said that it wasn’t data science if it didn’t include machine learning. Companies in all industries have been hiring “quants” to do statistical modeling. Even in the humanities, “distant reading” is a growing trend.

It is with great glee that I can announce the latest release of the Portal Project Database. For those of you who just want to go play with the data – here’s the link to the Data Paper we just published in Ecology. But I would encourage you to read on, as there is more data-related news below. But first, a story. As some of you know, I manage a long-term ecological study: the Portal Project.

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 http://www.instruction-manuals.co.uk/imageIM/four/seven/bbc.gif I make no claim to be a computer wizard.

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 to walk you through: A lab member sets up a microscopy experiment.

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.

Today I saw a tweet from Manuel Théry (an Associate Ed at Mol Biol Cell ). Which said that he heard that the Editor-in-Chief of MBoC, David Drubin shops for interesting preprints on bioRxiv to encourage the authors to submit to MBoC.

I have written previously about Journal Impact Factors (here and here). The response to these articles has been great and earlier this year I was asked to write something about JIFs and citation distributions for one of my favourite journals. I agreed and set to work. Things started off so well. A title came straight to mind.

In her recent editorial on Sci-Hub (an initiative I support), editor-in-chief of Science Magazine Marcia McNutt wrote: The editorial is essentially trying to make the somewhat tenuous but not implausible case that using sci-hub may lead to subscription cancellations which, in turn, may lead to scholarly societies (like those of Dr. McNutts employer, AAAS) to miss revenue they need in order to pay for important services (such as paying

Yesterday I tried a gedankenexperiment via Twitter, and asked: If you could visualise a protein relative to an intracellular structure/organelle at ~5 nm resolution, which one would you pick and why? https://twitter.com/clathrin/status/707949738323218432 I got some interesting replies: Myosin Va and cargo on actin filaments in melanocytes – Cleidson Alves @cleidson_alves COPII components relative to ER and Golgi for export of