category: blog

Open Reviewing

I normally sign my reviews, see the websites of Bertrand Meyer and Carl Boettiger for some reasoning on this which I agree with. Anonymity in reviewing is a good idea but on balance I think it’s best to be open. Furthermore, some journals have come to a similar conclusion, notably Faculty of 1000.So if …

I added my first segment on Strava

I am aware that my own attempts are not very impressive but I think it’s a nice route that others will enjoy. Starts in the field near Whitehough Head Lane and ends at the top of Eccles Pike somewhere near the topograph, hard to tell exactly. To be sure go …

Fake plastic fees

Am I the only one who uses carrier bags to line the kitchen bin and bag other waste before putting it out?Governments all over the world are falling over themselves to introduce disincentives for using plastic bags to take your shopping home, supposedly for environmental reasons. I am highly skeptical …

GPS mapping and fitness tracking

GPS mapping makes exploring new routes really easy and has certainly helped me get out more due to ease of finding routes. I also recently started using Strava to track my performance when running and cycling, providing additional motivation to get out. This post is about how I use Viewranger for mapping …

3D printing for research

We have just received funding from MMU to allow us to buy a 3D printer for research. I am exploring the use of this disruptive technology in my own environmental microbiology research, and am collaborating with other researchers who are interested in applying it in other projects including bryophyte photosynthesis …

Networks of Power and Influence

This week I am attending the 33rd New Phytologist symposium (Networks of Power and Influence) with Robin Sen and Francis Brearley from MMU. I will present a poster of work supported by MMU and Moors for the Future.The poster shows a preliminary network analysis of bacterial and fungal microbial communities …

Reproducible research

The statistical analyses for our recent paper on the bacterial communities of biological soil crusts in the Kalahari can be fully examined and reproduced via code and data I have deposited on GitHub.The analysis relies heavily on the phyloseq package for R. The phyloseq paper and associated documentation were really an inspiration, and provided …

Override autocorrect in Excel cells

As a microbial ecologist I often work with spreadsheets where I want to use the header “OTU” which means operational taxonomic unit. We use this acronym instead of saying species because the species concept for microbes is not very clear. Anyway, in Excel you can’t write “OTU” in a cell …

Transparency in PDF output from MS publisher

When using Microsoft Publisher you will likely want to export to PDF for circulation or printing. At this stage I found that all my transparent layers got spoilt and I found some tricky ways to work around it like printing to a PDF printer, but this is not very satisfactory.The …

3D design software

I know nothing about design but I often design make my own research equipment. I have been preparing to expand my experimental possibilities by using 3D printing: Make my experiments more reliable (quality of construction) Increase experimental throughput (replication) Share designs for my equipment so others can use and improve (open …