Sunday, 5 March 2023

7 colour electronic paper

For Christmas I recieved a 5.65" seven-colour e-paper display, which is awesome. The catch as everything with a Raspberry Pi or Arduino is that beyond the gloss of the advert is something that is far from a flexible plug and play system. I enjoyed my voyage, but it was rather odd even if typical of a Raspberry Pi project.

Saturday, 18 February 2023

Swapped university logo colour generator

Like many in academia I have moved across a few universities, each with their own colours, blue, gold, grey (I think) and even pine green (yes, like John Deer merch). Universities are quite possessive of their logos and have guidelines on their 'brand identity', which feels alien to academia as we are used to logos for tools being made in PowerPoint if they even have one. One thing that is frowned upon is changing the colours. But the fondness for ones former and present affiliations should not stand in the way. Luckily I have written a JS tool to help you swap the colours!

Sunday, 5 February 2023

Reading a mmCIF from PyMOL in PyRosetta

The mmCIF (PDBx as in extended PDB) format is meant to replace PDB format. Soon the RCSB PDB will have to adopt 4-letter codes for novel chemical components, which will break the PDB format. PDBx format is space separate as opposed to the really annoying column position in the PDB format and in the PDBx format the metadata can be stored in a nearly sensible manner. However, PDBx is solely a deposition format, but it is not really used as analysis format regardless of what the PDB claims. I personally had to add support for it because a reviewer asked me to. This lack of adoption is often attributed to the "if it ain't broken don't fix it" principle. Although I personally would argue that it may due to how it's implemented: opening a PDBx from one program ought to work in another, but this is not often the case. An example of this is PyMOL files read in PyRosetta.

Sunday, 22 January 2023

Typing emoji with a Pico keypad

Typing emoji with a Pico keypad

I got myself a Pimoroni RGB keypad, a keypad with 16 coloured buttons controlled by a Raspberry Pico. So the first thing I wanted to do was code it to output emoji, because I am very professional person. However, this was not a simple task as I had hoped.

Sunday, 20 November 2022

glibc 2.36 vs. CentOS 7: a tale of failure

My favourite part of coding is planning and implementing some cool idea for doing something, especially if it involves some fun maths I read up on Wikipedia a minute beforehand. In reality polishing dirty data, refactoring someone-else's bad code, reverse engineering the use of a module and trying to get stuff to work is what take up most of my time.

Having got cocky I thought I could get the latest GNU library for C (glibc) working on CentOS 7. I failed miserably, here is my sorry tale down the rabbit hole.

Friday, 4 November 2022

In ML a module is not a namespace but a base class, because... ?

Deep learning is changing the world and fast. The list of achievements is impressive, however, why focus on the positive, when we can moan about the negative? In this blog post I will discuss three minor details that I find annoying about deep learning, namely the key word Module, the limited use of Google/Coral Edge TPUs and the coding quality of the field.

Saturday, 8 October 2022

Star imports trick

Star-imports (from typing import *) in Python are a handy, but dangerous. They are meant for quick coding, i.e. like on a jupyterlab notebook. However they are bad as they can mask other variables and cause issues down the line. They are ubiquitous online as are guides explaining why they are bad, here I just want to share a handy snippet to iron out star-imports.