Previously I wrote about our move to electronic lab notebooks (ELNs). This post contains the technical details to understand how it works for us. You can even replicate our setup if you want to take the plunge. Why go electronic? Many reasons: I wanted to be able to quickly find information in our lab books.

We finally took the plunge and adopted electronic lab notebook (ELNs) for the lab. This short post describes our choice of software. I will write another post about how it’s going, how I set it up and other technical details. tl;dr we are using WordPress as our ELN. First, so you can understand my wishlist of requirements for the perfect ELN. Easy-to-use. Allow adding pictures and notes easily.

I recently asked on Twitter for any recommendations for software to organise my PDFs. I got several replies, but nothing really fitted the bill. This is a brief summary. My situation I have quite a lot of books, textbooks, cheat sheets, manuals, protocols etc. in PDF format and I need a way to organise them.

BBC 6Music recently went back in time to 1994. This made me wonder what albums released that year were my favourites. As previously described on this blog, I have this information readily available. So I quickly crunched the numbers. I focused on full-length albums and, using play density (sum of all plays divided by number of album tracks) as a metric, I plotted out the Top 20.

Lab meetings: love them or loathe them, they’re an important part of lab-life. There’s many different formats and ways to do a lab meeting. Sometimes it feels like we’ve tried them all! I’m going to describe our current format and then discuss some other things to try. Our current lab meeting format is: Weekly. For one hour (Wednesdays at 9am) One person each week talks about their progress. It rotates around.

A large amount of time doing data analysis is the process of cleaning, importing, reorganising and generally not actually analysing data but getting it ready to analyse. I’ve been trying to get over the idea to non-coders in the group that strict naming conventions (for example) are important and very helpful to the poor person who has to deal with the data.

I was recently an external examiner for a PhD viva in Cambridge. As we were wrapping up, I asked “if you were to do it all again, what would you do differently?”. It’s one of my stock questions and normally the candidate says “oh I’d do it so much quicker!” or something similar. However, this time I got a surprise. “I would write my thesis in LaTeX!”, was the reply. As a recent convert to LaTeX I could see where she was coming from.

I use a Garmin 800 GPS device to log my cycling activity. including my commutes. Since I have now built up nearly 4 years of cycling the same route, I had a good dataset to look at how accurate the device is. I wrote some code to import all of the rides tagged with commute in rubiTrack 4 Pro (technical details are below). These tracks needed categorising so that they could be compared.

Outreach means trying to engage the public with what we are doing in our research group. For me, this mainly means talking to non-specialists about our work and showing them around the lab. These non-specialists are typically interested members of the public and mainly supporters of the charity that funds work in my lab (Cancer Research UK). The most recent batch of activities have prompted this post on doing outreach.

Towards the end of 2015, I started distance running. I thought it’d be fun to look at the frequency of my runs over the course of 2016. Most of my runs were recorded with a GPS watch. I log my cycling data using Rubitrack, so I just added my running data to this. This software is great but to do any serious number crunching, other software is needed.

We have some macros for ImageJ/FIJI for making figures and blind analysis which could be useful to others. I made an ImageJ Update Site so that the latest versions can be pushed out to the people in the lab, but this also gives the opportunity to share our code with the world. Feel free to add the quantixed ImageJ update site to your ImageJ or FIJI installation. Details of how to do that are here.