Our recent paper on “the mesh” in kinetochore fibres (K-fibres) of the mitotic spindle was our first adventure in 3D electron microscopy. This post is about some of the new data analysis challenges that were thrown up by this study. I promised a more technical post about this paper and here it is, better late than never.
I recently finished reading The Art of Data Science by Roger Peng & Elizabeth Matsui. Roger, together with Jeff Leek, writes the Simply Statistics blog and he works at JHU with Elizabeth. The aim of the book is to give a guide to data analysis. It is not meant as a comprehensive data analysis “how to”, nor is it a manual for statistics or programming.
Previously, I wrote a post with tips for new PIs on lab organisation. Since that time, I’ve started using Trello to organise operations in my lab. Trello is basically a way to track the progress of projects. Collaborative working is built-in. A friend had begun using Trello as she got involved in building an app. It seems that Trello is popular among teams working to develop software.
For the past 3.5 yrs I’ve been using Unison to sync files between 3 macs. It works great. In fact, since I installed and set up my profiles for syncing, I’ve not needed to change a thing. Until yesterday. I upgraded to El Capitan on each of the 3 macs. I went to run Unison to sync the days work and – an error. -bash: unison: command not found Oh dear. I looked in the search path and couldn’t find Unison.
It’s been a while since I did some navel-gazing about who reads this blog and where they come from. This week, quantixed is close to 25K views and there was a burst of people viewing an old post, which made me look again at the visitor statistics. Where do the readers of quantixed come from? Well, geographically they come from all around the world.
This post follows on from a previous post on citation distributions and the wrongness of Impact Factor.
This is just a quick tip as it took me a little while to sort this out. In the lab we have two QNAP TS-869 Pro NAS devices. Each was set up with a single RAID6 storage pool and I ran them as a primary and replicant via rsync. We recently bought a bigger server and so the plan was to repurpose one of the NAS boxes to be a Time Machine for all the computers in the lab.
In the lab we have been doing quite a bit of analysis of cell migration in 2D. Typically RPE1 cells migrating on fibronectin-coated glass. There are quite a few tools out there to track cell movements and to analyse their migration. Naturally, none of these did quite what we wanted and none fitted nicely into our analysis workflow. This meant writing something from scratch in IgorPro. You can access the code from my GitHub pages.
I’ve previously written about analysing my iTunes library and about generating Smart Playlists in iTunes. This post takes things a bit further by generating a “perfect playlist” outside of iTunes… it is exclusively for nerds . How can you put together a perfect playlist? What are your favourite songs? How can you tell what they are?
I’m putting this up here in case it is useful for somebody. We capture Z-stacks on a Perkin Elmer Spinning Disk microscope system. I wanted to turn each stack into a single image so that we could quickly compare them. This simple macro does the job. We import the images straight from the *.mvd2 library using the wonderful BioFormats import tool. We open all files as composite hyperstacks.
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.
