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.

I’ve returned from the American Society for Cell Biology 2016 meeting in San Francisco. Despite being a cell biologist and people from my lab attending this meeting numerous times, this was my first ASCB meeting. The conference was amazing, so much excellent science and so many opportunities to meet up with people.

This is part-tip, part-adventures in code. I found out recently that it is possible to comment out multiple lines of code in Igor and thought I’d put this tip up here.

I don’t often write about music at quantixed but I recently caught Survivor’s “Eye of The Tiger” on the radio and thought it deserved a quick post. Surely everyone knows this song: a kind of catchall motivational tune.

Molecular Biology of The Cell , the official journal of the American Society for Cell Biology, recently joined a number of other periodicals in issuing guidelines for manuscripts, concerning statistics and reproducibility.

This is a quick post about the punch card feature on GitHub. This is available from Graphs within each repo and is also directly accessible via the API. I was looking at the punch card for two of my projects: one is work related and the other, more of a kind of hobby. The punch cards were different (the work one had way more commits, 99, than the hobby, 22). There was an interesting pattern to them. Here they are overlaid.