I have been rather quiet here, my personal blog for a variety of reasons, mainly because past collaborations encroaching into the spare after-hours I would otherwise dedicate to it (i.e. weekend early mornings). I have been involved in various projects, many of which I would like to write blog post about or people would like me to write about, so I am well behind on what I would like to post. However, as part of OPIG, I have written a few posts there (Blopig), some on requests (who would willingly write about fixing CUDA installations or exposing Jupyter notebooks in a compute node via reverse port forwarding?) and some out of personal choice.
The art of blowing up protein
A segfault and NaN driven series of disconnected ideas, analyses and just plain silly posts about computational biochemistry, synthetic biology and microbiology.
Sunday 10 March 2024
Monday 22 January 2024
Custom carbon colours in py3Dmol
Due to NGLView (the Python module) having a frozen older IPywidget version it breaks Colab and the major change for the latter library was a year ago (early 2023), so I am forced to revisit old code and switch to py3Dmol in my Colab demos. Today I figured out how to use custom carbon colours.
Sunday 31 December 2023
A possible BioB bipass route
Thursday 24 August 2023
Reading compressed molecular files on NFS
There are some tasks that make one feel like a failed door-to-door evangelist, one amongst these is proselyting about using compressed files on networked file systems. Namely, NFS are slower than local SSD drives, so most often it is actually quicker to read compressed files in memory rather than decompress them to disk. Here are two Python snippets for dealing with small molecule files.
Sunday 2 July 2023
A note on PLIP interactions
PLIP is a handy tool to enumerate the interactions of a given ligand. However, a few of tripping point I keep having is related to the fact the interactions are namedtuples. Here are some notes to circumvent the traps.
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!