In this post I’ll describe a computational method for splitting two sides of a cell biological structure. It’s a simple method that relies on principal component analysis , otherwise known as PCA.

We have a new paper out! You can access it here. The work was mainly done by Cristina Gutiérrez Caballero, a post-doc in the lab. We had some help from Selena Burgess and Richard Bayliss at the University of Leicester, with whom we have an ongoing collaboration. The paper in a nutshell We found that TACC3 binds the plus-ends of microtubules via an interaction with ch-TOG. So TACC3 is a +TIP.

Having recently got my head around violin plots, I thought I would explain what they are and why you might want to use them. There are several options when it comes to plotting summary data. I list them here in order of granularity, before describing violin plots and how to plot them in some detail. Bar chart This is the mainstay of most papers in my field.

When I started this blog, my plan was to write about interesting papers or at least blog about the ones from my lab. This post is a bit of both. I was recently asked to write a “Journal Club” piece for Nature Reviews Molecular Cell Biology, which is now available online. It’s paywalled unfortunately. It’s also very short, due to the format. For these reasons, I thought I’d expand a bit on the papers I highlighted.

I have been doing paper of the day (#potd) again in 2014. See my previous post about this. My “rules” for paper of the day are: Read one paper each working day. If I am away, or reviewing a paper for a journal or colleague, then I get a pass. Read it sufficiently to be able to explain it to somebody else, i.e. don’t just scan the abstract and look at the figures.

Back of the envelope calculations for this post. An old press release for a paper on endocytosis by Tom Kirchhausen contained this fascinating factoid: If this is true it is absolutely staggering. Let’s check it out. A synaptic vesicle is ~40 nm in diameter.

I was talking to a speaker visiting our department recently. While discussing his postdoc work from years ago, he told me about the identification of the sperm factor that causes calcium oscillations in the egg at fertilisation. It was an interesting tale because the group who eventually identified the factor – now widely accepted as PLCzeta – had earlier misidentified the factor, naming it oscillin.

I realised recently that I’ve maintained a consistent iTunes library for ~10 years. For most of that time I’ve been listening exclusively to iTunes, rather than to music in other formats.

A bit of navel gazing for this post. Since moving the blog to wordpress.com in the summer, it recently accrued 5000 views. Time to analyse what people are reading… The most popular post on the blog (by a long way) is “Strange Things“, a post about the eLife impact factor (2824 views). The next most popular is a post about a Twitter H-index, with 498 views.

The transition for scientific journals from print to online has been slow and painful. And it is not yet complete. This week I got an RSS alert to a “new” paper in Oncogene.

An IgorPro tip this week. The default font for plots is Geneva. Most of our figures are assembled using Helvetica for labelling. The default font can be changed in Igor Graph Preferences, but Preferences need to be switched on in order to be implemented. Anyway, I always seem to end up with a mix of Geneva plots and Helevetica plots.