I am having some fun running AlphaPulldown on a computing cluster. A requirement is to have input sequences in FASTA format. I found that I needed to get ~600 sequences. I had a list of the relevant Uniprot IDs. Surely getting the sequences for these proteins should be straightforward? Solution The Uniprot IDs can be converted – using the ID Mapping Tool on the Uniprot website – into any number of other IDs.

I like to set up a standardised directory structure for RStudio projects. The idea came from here. In brief, the structure is: Data/ Output/Data/ Output/Plots/ Script/ My typical workflow is therefore to: select File > New Project in RStudio make a new directory and RProj file then use this R script or these shell commands to setup the directories. So far, so good. However, this process is a bit tedious.

Generating movie files for publication can be a bit tricky. We have a protocol for making them for microscopy data, which simplifies things. However, we recently got this question from a journal: How can we do this? What information is needed for movie files?

If I struggle to find the answer to something, it must be worth a post to help out others. So, here’s where to find the php.ini file on a standard WordPress install on Raspberry Pi. I installed a LAMP stack and WordPress on a Raspberry Pi following these excellent instructions. The aim was to import our lab’s ELN onto a fresh WordPress install.

I was working on a figure in Adobe Illustrator today. The ai file had 32 embedded TIFF files (we tend to embed images rather than linking them for portability reasons). I wanted to change all of the images, but to do this I needed to know where the originals were.

I searched several times in vain to solve this problem. After finding a solution, I thought i’d put it up here. The problem Formatting of units using siunitx in LaTeX does not match the typeface of the body text. We like to use the helvet package to get a close approximation to Helvetica in LaTeX.

This is a quick set of tips to improve your Twitter experience. YMMV on these tips. Plus I can see Twitter changing things so that they no longer work, but this advice is correct as of today.

A long time ago I posted a little Automator routine to convert Word doc/docx files to PDF. Not long after that, this routine ceased to work due to changes in Microsoft Word (I think). It’s still very useful to convert a whole folder of docx files to PDF in order to avoid Word and just use Preview on the Mac. For committee work or for marking students’ work, I often have a whole folder of docx files and would prefer it if they were in PDF format.

Here’s a quick tech tip. We’ve been writing papers in TeX recently, using Overleaf as a way to write collaboratively. This works great but sometimes, a Word file is required by the publisher. So how do you convert from one to the other quickly and with the least hassle? If you Google this question (as I did), you will find a number of suggestions which vary in the amount of effort required. Methods include latex2rtf or pandoc.

University of Warwick is a popular conference destination, with thousands of visitors per year. Next time you visit and stay on campus, why not bring your running shoes and try out these routes?