Today’s group meeting was the GOAT (Greatest Of ALL Time) as we were honoured with the presence of Daisy (professional internet goat) from Cronkshaw Farm.
Goatcrashing OPIG
Author Archives: Eoin Malins
Solving WORDLE with grep
People seem to have become obsessed with wordle, just like they became obsessed with sudoku. After my initial burst of “oh a new game!” had waned, I was left thinking “my time is precious and this is exactly what we have computers for”. With this in mind, below is my quick and dirty way of solving these. I’m sure the regexp gurus amongst you will have a more elegant solution.
Step 1: Make sure you’ve got /usr/share/dict/words installed. This is just a huge list of words in a specific language and for me, this required installing the British words list.
sudo apt-get install wbritish
Step 2: Go to wordle
Step 3: Pick a random 5-letter word as your starting point. This is where grep and /usr/share/dict/words comes in:
Continue readingA handful of lesser known python libraries
There are more python libraries than you can shake a stick at, but here are a handful that don’t get much love and may save you some brain power, compute time or both.
Fire is a library which turns your normal python functions into command-line utilities without requiring more than a couple of additional lines of copy-and-paste code. Being able to immediately access your functions from the command line is amazingly helpful when you’re making quick and dirty utilities and saves needing to reach for the nuclear approach of using getopt.
Continue readingEnhance your presentation by using virtual webcams and scene transitions
If you haven’t checked out Matt’s post on using OBS for recording video, I highly recommend doing so. OBS is a terrific way to present your work online. It can provide (amongst many, many other things) the ability to create live picture-in-picture scenes, so you can move through your powerpoint deck whilst overlaying video of your tiny talking head in the corner.
Continuing on from Matt’s post, I’d like to promote the OBS virtual camera plugin and Touch Portal.
Every company, department or course has its own favourite video conferencing application and whilst they all have their strengths, consistency is not one of them. If you want to consistently display your presentation and your live video regardless of the platform in use, this quickly gets into the “messy” territory. This is where the virtual camera comes in.
The right tool for the job – The Joy of Excel
Excel’s pervasiveness has resulted in it being used (correctly or incorrectly) in just about every area of science.
Unfortunately, Excel has some traps for the new player and unless you’ve fallen for them before, they are not entirely obvious. They stem from the fact that Excel will try to help the user by reformatting data into what it thinks you mean.
Continue readingHERO proteins are here to save you (assuming you’re another protein or a fruit fly)
For one of OPIG’s short talks, I recently introduced the work done by Kotaro Tsuboyama et al. found in the paper A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation. As the name implies, HERO proteins have been found to retain function even after being boiled at 95C and have been found both in Drosophila and human HEK293T cell lines. Whilst it’s not impossible to find proteins which can “survive” 90+ Celsius, these are expected to be the reserve of extremophiles, not found in humans or fruit flies.
Continue readingConsidering Containers? – Go for Singularity
Docker is an excellent containerisation system ideally suited to production servers. It allows you to do one small thing but do it well. For example, breaking a large blog up into individually maintained containers for a web-server, a database and (say) a wordpress instance. However due to inherent security woes, Docker doesn’t play nicely with multi-tenanted machines, the kind which are the bread and butter for researchers and HPC users. That’s where Singularity steps in.
Continue readingA collection of prion factoids
It’s been several years since I last presented a talk on prions to OPIG, so I thought a neat way of getting up to date would be to read “The prion 2018 round tables“. What’s the current understanding and are we any closer to determining a structure of PrPSc?
Continue readingMaking the most of your CPUs when using python
Over the last decade, single-threaded CPU performance has begun to plateau, whilst the number of logical cores has been increasing exponentially.
Like it or loathe it, for the last few years, python has featured as one of the top ten most popular languages [tiobe / PYPL]. That being said however, python has an issue which makes life harder for the user wanting to take advantage of this parallelism windfall. That issue is called the GIL (Global Interpreter Lock). The GIL can be thought of as the conch shell from Lord of the Flies. You have to hold the conch (GIL) for your thread to be computed. With only one conch, no matter how beautifully written and multithreaded your code, there will still only be one thread will be executed at any point in time.
Le Tour de Farce v6.0
Tuesday the 12th of June brought sun, cycling and beer to the land of OPIG. It was once again time for the annual Tour de Farce.
Le tour, now in its highly refined 6.0 version, covered a route which took us from the statistics department at Oxford (home to many OPIGlets) to our first port of call, The Head of the River pub. We then followed the river Isis (or Thames if you prefer) from the head of the river towards Osney mead.
Passing though Osney we soon arrived at our second waypoint. The Punter. One of the OPIGlets lived locally and so we were met by their trusty companion, who was better behaved than many of the others on Le Tour.
Departing the punter on two wheels (or in one case, on one) we followed the river upstream to The Perch.
Our arrival at The Perch was slightly hampered by a certain OPIGlet taking out anything in her path in her excitement. Mr Sulu.. Ramming speed.
Those that survived soon left the perch, as we were once again headed upstream, this time to The Trout.
Having braved about half the journey it was now time for another restorative beverage and to take on supplies. Sustenance was provided by Jacob’s Inn. Jacob’s Inn has the advantage of goats, chickens and pigs in the back garden. Having spent most of the afternoon in each other’s company, the company of pigs was preferable for some.
As we finished dinner, the sun was beginning to set and so we abandoned the original plan of finishing off at The Fishes. Instead we returned southwards where we closed off the evening with a drink at The Royal Oak, mere yards from where we started the day.
The route of the 2018 v6.0 Tour de Farce.