A couple of years ago, a colleague sent me this picture* to say “who put J Cell Biol on a diet?”. I joked that maybe they publish too many autophagy papers and didn’t think much more of it. Recently, Ron Vale put up this very interesting piece on bioRxiv discussing what it takes to publish a paper in the field of cell biology these days. In the main, he questions whether this is now out of reach of many trainees in our labs.

A while back I made this little Automator script to convert Microsoft Word doc and docx files to PDF. It’s useful for when you are sent a bunch of Word files for committee work. Opening PDFs in Preview is nice and hassle-free. Struggling with Word is not. It’s not my own work, I just put it together after googling around a bit. I’ll put it here for anyone to use. To get it working: Open Automator.

We have a new paper out! You can access it here. Title of the paper: The mesh is a network of microtubule connectors that stabilizes individual kinetochore fibers of the mitotic spindle What’s it about? When a cell divides, the two new cells need to get the right number of chromosomes. If this process goes wrong, it is a disaster which may lead to disease e.g. cancer.

I was searching for the excitation and emission spectra for mNeonGreen. I was able to find an image, but no values for the spectra. Here is an approximation of the spectra (xlsx format, still haven’t figured out csv for wordpress). I got these values using IgorThief.ipf a very handy tool that allows the extraction of XY coordinates from a bitmapped plot (below). mNeonGreen is available from Allele Biotechnologies.

I recently gave a talk at a retreat for new PIs working at QMUL. My talk was focussed on tips for getting started, i.e. the nitty gritty of running an efficient lab. It was a mix of things I’ve been told, worked out for myself or that I’d learned the hard way. PIs are expected to be able to do lots of things that can be full-time jobs in themselves.

I have just finished reading this excellent book, Statistics done wrong: a woefully complete guide by Alex Reinhart . I’d recommend it to anyone interested in quantitative biology and particularly to PhD students starting out in biomedical science. Statistics is a topic that many people find difficult to grasp. I think there are a couple of reasons for this that I’ll go into below.

I put a recent code snippet put up on the IgorExchange. It’s a simple procedure for averaging a set of 1D waves and putting the results in a new wave. The difference between this code and Average Waves.ipf (which ships with Igor) is that this function takes the average of all points in the wave and places this single value in a new wave. You can specify whether the mean or median is used for the average.

This is a long post about Journal Impact Factors. Thanks to Stephen Curry for encouraging me to post this.

I saw this great tweet (fairly) recently: I thought this was such a great explanation of when to submit your paper. It reminded me of a diagram that I sketched out when talking to a student in my lab about a paper we were writing. I was trying to explain why we don’t exaggerate our findings. And conversely why we don’t undersell our results either. I replotted it below:

We were asked to write a Preview piece for Developmental Cell. Two interesting papers which deal with the insertion of amphipathic helices in membranes to influence membrane curvature during endocytosis were scheduled for publication and the journal wanted some “front matter” to promote them. Our Preview is paywalled – sorry about that – but I can briefly tell you why these two papers are worth a read.

Our most recent manuscript was almost ready for submission. We were planning to send it to an open access journal. It was then that I had the thought: how many papers in the reference list are freely available? It somehow didn’t make much sense to point readers towards papers that they might not be able to access. So, I wondered if there was a quick way to determine how papers in my reference list were open access.